Data sharing is a fundamental part of DDD to aid diagnoses and discoveries in the future. We aim to publish as much of our research as possible in peer-reviewed publications to increase the understanding of developmental disorders. Below is the list of DDD manuscripts published so far. They include papers describing our methods and key findings, as well as manuscripts specialising in individual genes or specific developmental disorders.

Total Publications 320

Each circle represents an author affiliation

Each line represents non-neighbouring centres collaborating on 4+ articles

Location data from OpenStreetMap contributors, ODbL 1.0.
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A recurrent de novo MAX p.Arg60Gln variant causes a syndromic overgrowth disorder through differential expression of c-Myc target genes.

Harris EL; Roy V; Montagne M; Rose AMS; Livesey H; Reijnders MRF; Hobson E; Sansbury FH; Willemsen MH; Pfundt R; Warren D; Long V; Carr IM; Brunner HG; Sheridan EG; Firth HV; Lavigne P; Poulter JA

American journal of human genetics 2024;111;1;119-132

Cyclin D2 (CCND2) stabilization underpins a range of macrocephaly-associated disorders through mutation of CCND2 or activating mutations in upstream genes encoding PI3K-AKT pathway components. Here, we describe three individuals with overlapping macrocephaly-associated phenotypes who carry the same recurrent de novo c.179G>A (p.Arg60Gln) variant in Myc-associated factor X (MAX). The mutation, located in the b-HLH-LZ domain, causes increased intracellular CCND2 through increased transcription but it does not cause stabilization of CCND2. We show that the purified b-HLH-LZ domain of MAXArg60Gln (Max∗Arg60Gln) binds its target E-box sequence with a lower apparent affinity. This leads to a more efficient heterodimerization with c-Myc resulting in an increase in transcriptional activity of c-Myc in individuals carrying this mutation. The recent development of Omomyc-CPP, a cell-penetrating b-HLH-LZ-domain c-Myc inhibitor, provides a possible therapeutic option for MAXArg60Gln individuals, and others carrying similar germline mutations resulting in dysregulated transcriptional c-Myc activity.

Bi-allelic genetic variants in the translational GTPases GTPBP1 and GTPBP2 cause a distinct identical neurodevelopmental syndrome.

Salpietro V; Maroofian R; Zaki MS; Wangen J; Ciolfi A; Barresi S; Efthymiou S; Lamaze A; Aughey GN; Al Mutairi F; Rad A; Rocca C; Calì E; Accogli A; Zara F; Striano P; Mojarrad M; Tariq H; Giacopuzzi E; Taylor JC; Oprea G; Skrahina V; Rehman KU; Abd Elmaksoud M; Bassiony M; El Said HG; Abdel-Hamid MS; Al Shalan M; Seo G; Kim S; Lee H; Khang R; Issa MY; Elbendary HM; Rafat K; Marinakis NM; Traeger-Synodinos J; Ververi A; Sourmpi M; Eslahi A; Khadivi Zand F; Beiraghi Toosi M; Babaei M; Jackson A; ; Bertoli-Avella A; Pagnamenta AT; Niceta M; Battini R; Corsello A; Leoni C; Chiarelli F; Dallapiccola B; Faqeih EA; Tallur KK; Alfadhel M; Alobeid E; Maddirevula S; Mankad K; Banka S; Ghayoor-Karimiani E; Tartaglia M; Chung WK; Green R; Alkuraya FS; Jepson JEC; Houlden H

American journal of human genetics 2024;111;1;200-210

The homologous genes GTPBP1 and GTPBP2 encode GTP-binding proteins 1 and 2, which are involved in ribosomal homeostasis. Pathogenic variants in GTPBP2 were recently shown to be an ultra-rare cause of neurodegenerative or neurodevelopmental disorders (NDDs). Until now, no human phenotype has been linked to GTPBP1. Here, we describe individuals carrying bi-allelic GTPBP1 variants that display an identical phenotype with GTPBP2 and characterize the overall spectrum of GTP-binding protein (1/2)-related disorders. In this study, 20 individuals from 16 families with distinct NDDs and syndromic facial features were investigated by whole-exome (WES) or whole-genome (WGS) sequencing. To assess the functional impact of the identified genetic variants, semi-quantitative PCR, western blot, and ribosome profiling assays were performed in fibroblasts from affected individuals. We also investigated the effect of reducing expression of CG2017, an ortholog of human GTPBP1/2, in the fruit fly Drosophila melanogaster. Individuals with bi-allelic GTPBP1 or GTPBP2 variants presented with microcephaly, profound neurodevelopmental impairment, pathognomonic craniofacial features, and ectodermal defects. Abnormal vision and/or hearing, progressive spasticity, choreoathetoid movements, refractory epilepsy, and brain atrophy were part of the core phenotype of this syndrome. Cell line studies identified a loss-of-function (LoF) impact of the disease-associated variants but no significant abnormalities on ribosome profiling. Reduced expression of CG2017 isoforms was associated with locomotor impairment in Drosophila. In conclusion, bi-allelic GTPBP1 and GTPBP2 LoF variants cause an identical, distinct neurodevelopmental syndrome. Mutant CG2017 knockout flies display motor impairment, highlighting the conserved role for GTP-binding proteins in CNS development across species.

Investigating the role of common cis-regulatory variants in modifying penetrance of putatively damaging, inherited variants in severe neurodevelopmental disorders.

Wigdor EM; Samocha KE; Eberhardt RY; Chundru VK; Firth HV; Wright CF; Hurles ME; Martin HC

Scientific reports 2024;14;1;8708

Recent work has revealed an important role for rare, incompletely penetrant inherited coding variants in neurodevelopmental disorders (NDDs). Additionally, we have previously shown that common variants contribute to risk for rare NDDs. Here, we investigate whether common variants exert their effects by modifying gene expression, using multi-cis-expression quantitative trait loci (cis-eQTL) prediction models. We first performed a transcriptome-wide association study for NDDs using 6987 probands from the Deciphering Developmental Disorders (DDD) study and 9720 controls, and found one gene, RAB2A, that passed multiple testing correction (p = 6.7 × 10-7). We then investigated whether cis-eQTLs modify the penetrance of putatively damaging, rare coding variants inherited by NDD probands from their unaffected parents in a set of 1700 trios. We found no evidence that unaffected parents transmitting putatively damaging coding variants had higher genetically-predicted expression of the variant-harboring gene than their child. In probands carrying putatively damaging variants in constrained genes, the genetically-predicted expression of these genes in blood was lower than in controls (p = 2.7 × 10-3). However, results for proband-control comparisons were inconsistent across different sets of genes, variant filters and tissues. We find limited evidence that common cis-eQTLs modify penetrance of rare coding variants in a large cohort of NDD probands.

Refined preferences of prioritizers improve intelligent diagnosis for Mendelian diseases.

Yuan X; Su J; Wang J; Dai B; Sun Y; Zhang K; Li Y; Chuan J; Tang C; Yu Y; Gong Q

Scientific reports 2024;14;1;2845

Phenotype-guided gene prioritizers have proved a highly efficient approach to identifying causal genes for Mendelian diseases. In our previous study, we preliminarily evaluated the performance of ten prioritizers. However, all the selected software was run based on default settings and singleton mode. With a large-scale family dataset from Deciphering Developmental Disorders (DDD) project (N = 305) and an in-house trio cohort (N = 152), the four optimal performers in our prior study including Exomiser, PhenIX, AMELIE, and LIRCIAL were further assessed through parameter optimization and/or the utilization of trio mode. The in-depth assessment revealed high diagnostic yields of the four prioritizers with refined preferences, each alone or together: (1) 83.3-91.8% of the causal genes were presented among the first ten candidates in the final ranking lists of the four tools; (2) Over 97.7% of the causal genes were successfully captured within the top 50 by either of the four software. Exomiser did best in directly hitting the target (ranking the causal gene at the very top) while LIRICAL displayed a predominant overall detection capability. Besides, cases affected by low-penetrance and high-frequency pathogenic variants were found misjudged during the automated prioritization process. The discovery of the limitations shed light on the specific directions of future enhancement for causal-gene ranking tools.

Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt.

Shepherdson JL; Hutchison K; Don DW; McGillivray G; Choi TI; Allan CA; Amor DJ; Banka S; Basel DG; Buch LD; Carere DA; Carroll R; Clayton-Smith J; Crawford A; Dunø M; Faivre L; Gilfillan CP; Gold NB; Gripp KW; Hobson E; Holtz AM; Innes AM; Isidor B; Jackson A; Katsonis P; Amel Riazat Kesh L; ; Küry S; Lecoquierre F; Lockhart P; Maraval J; Matsumoto N; McCarrier J; McCarthy J; Miyake N; Moey LH; Németh AH; Østergaard E; Patel R; Pope K; Posey JE; Schnur RE; Shaw M; Stolerman E; Taylor JP; Wadman E; Wakeling E; White SM; Wong LC; Lupski JR; Lichtarge O; Corbett MA; Gecz J; Nicolet CM; Farnham PJ; Kim CH; Shinawi M

American journal of human genetics 2024

Pathogenic variants in multiple genes on the X chromosome have been implicated in syndromic and non-syndromic intellectual disability disorders. ZFX on Xp22.11 encodes a transcription factor that has been linked to diverse processes including oncogenesis and development, but germline variants have not been characterized in association with disease. Here, we present clinical and molecular characterization of 18 individuals with germline ZFX variants. Exome or genome sequencing revealed 11 variants in 18 subjects (14 males and 4 females) from 16 unrelated families. Four missense variants were identified in 11 subjects, with seven truncation variants in the remaining individuals. Clinical findings included developmental delay/intellectual disability, behavioral abnormalities, hypotonia, and congenital anomalies. Overlapping and recurrent facial features were identified in all subjects, including thickening and medial broadening of eyebrows, variations in the shape of the face, external eye abnormalities, smooth and/or long philtrum, and ear abnormalities. Hyperparathyroidism was found in four families with missense variants, and enrichment of different tumor types was observed. In molecular studies, DNA-binding domain variants elicited differential expression of a small set of target genes relative to wild-type ZFX in cultured cells, suggesting a gain or loss of transcriptional activity. Additionally, a zebrafish model of ZFX loss displayed an altered behavioral phenotype, providing additional evidence for the functional significance of ZFX. Our clinical and experimental data support that variants in ZFX are associated with an X-linked intellectual disability syndrome characterized by a recurrent facial gestalt, neurocognitive and behavioral abnormalities, and an increased risk for congenital anomalies and hyperparathyroidism.

VAMP2 Gene-Related Neurodevelopmental Disorder: A Differential Diagnosis for Rett/Angelman-Type Spectrum of Disorders.

Bogue D; Ryan G; Wassmer E; Research Consortium GE; Naik S

Molecular syndromology 2023;14;5;449-456

VAMP2 is an instrumental protein in neuronal synaptic transmission in the brain, facilitating neurotransmitter release. It is encoded by the VAMP2 gene, and pathogenic variants in this gene cause neurodevelopmental features including early onset axial hypotonia, intellectual disability, and features of autism spectrum disorder. To date, only three types of allelic variants (loss of function, in-frame deletions, and missense variants) in the VAMP2 gene have been previously reported in 11 patients with learning difficulties. Here, we describe a patient in whom a novel de novo pathogenic variant in the VAMP2 gene was identified.

A clustering of heterozygous missense variants in the crucial chromatin modifier WDR5 defines a new neurodevelopmental disorder.

Snijders Blok L; Verseput J; Rots D; Venselaar H; Innes AM; Stumpel C; Õunap K; Reinson K; Seaby EG; McKee S; Burton B; Kim K; van Hagen JM; Waisfisz Q; Joset P; Steindl K; Rauch A; Li D; Zackai EH; Sheppard SE; Keena B; Hakonarson H; Roos A; Kohlschmidt N; Cereda A; Iascone M; Rebessi E; Kernohan KD; Campeau PM; Millan F; Taylor JA; Lochmüller H; Higgs MR; Goula A; Bernhard B; Velasco DJ; Schmanski AA; Stark Z; Gallacher L; Pais L; Marcogliese PC; Yamamoto S; Raun N; Jakub TE; Kramer JM; den Hoed J; Fisher SE; Brunner HG; Kleefstra T

HGG advances 2023;4;1;100157

WDR5 is a broadly studied, highly conserved key protein involved in a wide array of biological functions. Among these functions, WDR5 is a part of several protein complexes that affect gene regulation via post-translational modification of histones. We collected data from 11 unrelated individuals with six different rare de novo germline missense variants in WDR5; one identical variant was found in five individuals and another variant in two individuals. All individuals had neurodevelopmental disorders including speech/language delays (n = 11), intellectual disability (n = 9), epilepsy (n = 7), and autism spectrum disorder (n = 4). Additional phenotypic features included abnormal growth parameters (n = 7), heart anomalies (n = 2), and hearing loss (n = 2). Three-dimensional protein structures indicate that all the residues affected by these variants are located at the surface of one side of the WDR5 protein. It is predicted that five out of the six amino acid substitutions disrupt interactions of WDR5 with RbBP5 and/or KMT2A/C, as part of the COMPASS (complex proteins associated with Set1) family complexes. Our experimental approaches in Drosophila melanogaster and human cell lines show normal protein expression, localization, and protein-protein interactions for all tested variants. These results, together with the clustering of variants in a specific region of WDR5 and the absence of truncating variants so far, suggest that dominant-negative or gain-of-function mechanisms might be at play. All in all, we define a neurodevelopmental disorder associated with missense variants in WDR5 and a broad range of features. This finding highlights the important role of genes encoding COMPASS family proteins in neurodevelopmental disorders.

Analysis of exome data in a UK cohort of 603 patients with syndromic orofacial clefting identifies causal molecular pathways.

Wilson K; Newbury DF; Kini U

Human molecular genetics 2023;32;11;1932-1942

Orofacial cleft (OC) is a common congenital anomaly in humans, which has lifelong implications for affected individuals. This disorder can be classified as syndromic or non-syndromic depending on the presence or absence of additional physical or neurodevelopmental abnormalities, respectively. Non-syndromic cleft is often non-familial in nature and has a complex aetiology, whereas syndromic forms tend to be monogenic. Although individual OC-related syndromes have been frequently described in the medical literature, there has not been a comprehensive review across syndromes, thereby leaving a gap in our knowledge, which this paper aims to address. Six hundred and three patients with cleft-related human phenotype ontology terms were identified within the Deciphering Developmental Disorders study. Genes carrying pathogenic/likely pathogenic variants were identified and reviewed enabling a diagnostic yield of 36.5%. In total, 124 candidate genes for syndromic OC were identified, including 34 new genes that should be considered for inclusion in clinical clefting panels. Functional enrichment and gene expression analyses identified three key processes that were significantly overrepresented in syndromic OC gene lists: embryonic morphogenesis, protein stability and chromatin organization. Comparison with non-syndromic OC gene networks led us to propose that chromatin remodelling specifically contributes to the aetiology of syndromic OC. Disease-driven gene discovery is a valid approach to gene identification and curation of gene panels. Through this approach, we have started to unravel common molecular pathways contributing to syndromic orofacial clefting.

Biallelic MED27 variants lead to variable ponto-cerebello-lental degeneration with movement disorders.

Maroofian R; Kaiyrzhanov R; Cali E; Zamani M; Zaki MS; Ferla M; Tortora D; Sadeghian S; Saadi SM; Abdullah U; Ghayoor Karimiani E; Efthymiou S; Yeşil G; Alavi S; Al Shamsi AM; Tajsharghi H; Abdel-Hamid MS; Saadi NW; Al Mutairi F; Alabdi L; Beetz C; Ali Z; Toosi MB; Rudnik-Schöneborn S; Babaei M; Isohanni P; Muhammad J; Sheraz K; Al Shalan M; Hickey SE; Marom D; Elhanan E; Kurian MA; Marafi D; Saberi A; Hamid M; Spaull R; Meng L; Lalani S; Maqbool S; Rahman F; Seeger J; Palculict TB; Lau T; Murphy D; Mencacci NE; Steindl K; Begemann A; Rauch A; Akbas S; Dilruba AA; Salpietro V; Yousaf H; Ben-Shachar S; Ejeskär K; Al Aqeel AI; High FA; Armstrong-Javors AE; Zahraei SM; Seifi T; Zeighami J; Shariati G; Sedaghat A; Asl SN; Shahrooei M; Zifarelli G; Burglen L; Ravelli C; Zschocke J; Schatz UA; Ghavideldarestani M; Kamel WA; Van Esch H; Hackenberg A; Taylor JC; Al-Gazali L; Bauer P; Gleeson JJ; Alkuraya FS; Lupski JR; Galehdari H; Azizimalamiri R; Chung WK; Baig SM; Houlden H; Severino M

Brain : a journal of neurology 2023

MED27 is a subunit of the Mediator multiprotein complex, which is involved in transcriptional regulation. Biallelic MED27 variants have recently been suggested to be responsible for an autosomal recessive neurodevelopmental disorder with spasticity, cataracts, and cerebellar hypoplasia. We further delineate the clinical phenotype of MED27-related disease by characterizing the clinical and radiological features of 57 affected individuals from 30 unrelated families with biallelic MED27 variants. Utilizing exome sequencing and extensive international genetic data sharing, 39 unpublished affected individuals from 18 independent families with biallelic missense variants in MED27 have been identified (29 females, mean age at last follow-up 17±12.4 years, range 0.1-45). Follow-up and hitherto unreported clinical features were obtained from the published 12 families. Brain MRI scans from 34 cases were reviewed. MED27-related disease manifests as a broad phenotypic continuum ranging from developmental and epileptic-dyskinestic encephalopathy to variable neurodevelopmental disorder with movement abnormalities. It is characterised by mild to profound global developmental delay/intellectual disability (100%), bilateral cataracts (89%), infantile hypotonia (74%), microcephaly (62%), gait ataxia (63%), dystonia (61%), variably combined with epilepsy (50%), limb spasticity (51%), facial dysmorphism (38%), and death before reaching adulthood (16%). Brain MRI revealed cerebellar atrophy (100%), white matter volume loss (76.4%), pontine hypoplasia (47.2%), and basal ganglia atrophy with signal alterations (44.4%). Previously unreported 39 affected individuals had seven homozygous pathogenic missense MED27 variants, five of which were recurrent. An emerging genotype-phenotype correlation was observed. This study provides a comprehensive clinical-radiological description of MED27-related disease, establishes genotype-phenotype and clinical-radiological correlations, and suggests a differential diagnosis with syndromes of cerebello-lental neurodegeneration and other subtypes of "neuro-MEDopathies".

Biallelic PRMT7 pathogenic variants are associated with a recognizable syndromic neurodevelopmental disorder with short stature, obesity, and craniofacial and digital abnormalities.

Cali E; Suri M; Scala M; Ferla MP; Alavi S; Faqeih EA; Bijlsma EK; Wigby KM; Baralle D; Mehrjardi MYV; Schwab J; Platzer K; Steindl K; Hashem M; Jones M; Niyazov DM; Jacober J; Littlejohn RO; Weis D; Zadeh N; Rodan L; Goldenberg A; Lecoquierre F; Dutra-Clarke M; Horvath G; Young D; Orenstein N; Bawazeer S; Vulto-van Silfhout AT; Herenger Y; Dehghani M; Seyedhassani SM; Bahreini A; Nasab ME; Ercan-Sencicek AG; Firoozfar Z; Movahedinia M; Efthymiou S; Striano P; Karimiani EG; Salpietro V; Taylor JC; Redman M; Stegmann APA; Laner A; Abdel-Salam G; Li M; Bengala M; Müller AJ; Digilio MC; Rauch A; Gunel M; Titheradge H; Schweitzer DN; Kraus A; Valenzuela I; McLean SD; Phornphutkul C; Salih M; Begtrup A; Schnur RE; Torti E; Haack TB; Prada CE; Alkuraya FS; Houlden H; Maroofian R

Genetics in medicine : official journal of the American College of Medical Genetics 2023;25;1;135-142

Protein arginine methyltransferase 7 (PRMT7) is a member of a family of enzymes that catalyzes the methylation of arginine residues on several protein substrates. Biallelic pathogenic PRMT7 variants have previously been associated with a syndromic neurodevelopmental disorder characterized by short stature, brachydactyly, intellectual developmental disability, and seizures. To our knowledge, no comprehensive study describes the detailed clinical characteristics of this syndrome. Thus, we aim to delineate the phenotypic spectrum of PRMT7-related disorder.

Biallelic variants in PIGN cause Fryns syndrome, multiple congenital anomalies-hypotonia-seizures syndrome, and neurologic phenotypes: A genotype-phenotype correlation study.

Loong L; Tardivo A; Knaus A; Hashim M; Pagnamenta AT; Alt K; Böhrer-Rabel H; Caro-Llopis A; Cole T; Distelmaier F; Edery P; Ferreira CR; Jezela-Stanek A; Kerr B; Kluger G; Krawitz PM; Kuhn M; Lemke JR; Lesca G; Lynch SA; Martinez F; Maxton C; Mierzewska H; Monfort S; Nicolai J; Orellana C; Pal DK; Płoski R; Quarrell OW; Rosello M; Rydzanicz M; Sabir A; Śmigiel R; Stegmann APA; Stewart H; Stumpel C; Szczepanik E; Tzschach A; Wolfe L; Taylor JC; Murakami Y; Kinoshita T; Bayat A; Kini U

Genetics in medicine : official journal of the American College of Medical Genetics 2023;25;1;37-48

Biallelic PIGN variants have been described in Fryns syndrome, multiple congenital anomalies-hypotonia-seizure syndrome (MCAHS), and neurologic phenotypes. The full spectrum of clinical manifestations in relation to the genotypes is yet to be reported.

Clinical and functional heterogeneity associated with the disruption of retinoic acid receptor beta.

Caron V; Chassaing N; Ragge N; Boschann F; Ngu AM; Meloche E; Chorfi S; Lakhani SA; Ji W; Steiner L; Marcadier J; Jansen PR; van de Pol LA; van Hagen JM; Russi AS; Le Guyader G; Nordenskjöld M; Nordgren A; Anderlid BM; Plaisancié J; Stoltenburg C; Horn D; Drenckhahn A; Hamdan FF; Lefebvre M; Attie-Bitach T; Forey P; Smirnov V; Ernould F; Jacquemont ML; Grotto S; Alcantud A; Coret A; Ferrer-Avargues R; Srivastava S; Vincent-Delorme C; Romoser S; Safina N; Saade D; Lupski JR; Calame DG; Geneviève D; Chatron N; Schluth-Bolard C; Myers KA; Dobyns WB; Calvas P; ; Salmon C; Holt R; Elmslie F; Allaire M; Prigozhin DM; Tremblay A; Michaud JL

Genetics in medicine : official journal of the American College of Medical Genetics 2023;25;8;100856

Dominant variants in the retinoic acid receptor beta (RARB) gene underlie a syndromic form of microphthalmia, known as MCOPS12, which is associated with other birth anomalies and global developmental delay with spasticity and/or dystonia. Here, we report 25 affected individuals with 17 novel pathogenic or likely pathogenic variants in RARB. This study aims to characterize the functional impact of these variants and describe the clinical spectrum of MCOPS12.

Clinical and genetic analysis further delineates the phenotypic spectrum of ALDH1A3-related anophthalmia and microphthalmia.

Kesim Y; Ceroni F; Damián A; Blanco-Kelly F; Ayuso C; Williamson K; Paquis-Flucklinger V; Bax DA; Plaisancié J; Rieubland C; Chamlal M; Cortón M; Chassaing N; Calvas P; Ragge NK

European journal of human genetics : EJHG 2023

Biallelic pathogenic variants in ALDH1A3 are responsible for approximately 11% of recessively inherited cases of severe developmental eye anomalies. Some individuals can display variable neurodevelopmental features, but the relationship to the ALDH1A3 variants remains unclear. Here, we describe seven unrelated families with biallelic pathogenic ALDH1A3 variants: four compound heterozygous and three homozygous. All affected individuals had bilateral anophthalmia/microphthalmia (A/M), three with additional intellectual or developmental delay, one with autism and seizures and three with facial dysmorphic features. This study confirms that individuals with biallelic pathogenic ALDH1A3 variants consistently manifest A/M, but additionally display neurodevelopmental features with significant intra- and interfamilial variability. Furthermore, we describe the first case with cataract and highlight the importance of screening ALDH1A3 variants in nonconsanguineous families with A/M.

Detailed Analysis of ITPR1 Missense Variants Guides Diagnostics and Therapeutic Design.

Tolonen JP; Parolin Schnekenberg R; McGowan S; Sims D; McEntagart M; Elmslie F; Shears D; Stewart H; Tofaris GK; Dabir T; Morrison PJ; Johnson D; Hadjivassiliou M; Ellard S; Shaw-Smith C; Znaczko A; Dixit A; Suri M; Sarkar A; Harrison RE; Jones G; Houlden H; Ceravolo G; Jarvis J; Williams J; Shanks ME; Clouston P; Rankin J; Blumkin L; Lerman-Sagie T; Ponger P; Raskin S; Granath K; Uusimaa J; Conti H; McCann E; Joss S; Blakes AJM; Metcalfe K; Kingston H; Bertoli M; Kneen R; Lynch SA; Martínez Albaladejo I; Moore AP; Jones WD; ; Becker EBE; Németh AH

Movement disorders : official journal of the Movement Disorder Society 2023

The ITPR1 gene encodes the inositol 1,4,5-trisphosphate (IP3 ) receptor type 1 (IP3 R1), a critical player in cerebellar intracellular calcium signaling. Pathogenic missense variants in ITPR1 cause congenital spinocerebellar ataxia type 29 (SCA29), Gillespie syndrome (GLSP), and severe pontine/cerebellar hypoplasia. The pathophysiological basis of the different phenotypes is poorly understood.

Developing a cluster-based approach for deciphering complexity in individuals with neurodevelopmental differences.

Cuppens T; Kaur M; Kumar AA; Shatto J; Ng AC; Leclercq M; Reformat MZ; Droit A; Dunham I; Bolduc FV

Frontiers in pediatrics 2023;11;1171920

Individuals with neurodevelopmental disorders such as global developmental delay (GDD) present both genotypic and phenotypic heterogeneity. This diversity has hampered developing of targeted interventions given the relative rarity of each individual genetic etiology. Novel approaches to clinical trials where distinct, but related diseases can be treated by a common drug, known as basket trials, which have shown benefits in oncology but have yet to be used in GDD. Nonetheless, it remains unclear how individuals with GDD could be clustered. Here, we assess two different approaches: agglomerative and divisive clustering.

diseaseGPS: auxiliary diagnostic system for genetic disorders based on genotype and phenotype.

Huang D; Jiang J; Zhao T; Wu S; Li P; Lyu Y; Feng J; Wei M; Zhu Z; Gu J; Ren Y; Yu G; Lu H

Bioinformatics (Oxford, England) 2023;39;9

The next-generation sequencing brought opportunities for the diagnosis of genetic disorders due to its high-throughput capabilities. However, the majority of existing methods were limited to only sequencing candidate variants, and the process of linking these variants to a diagnosis of genetic disorders still required medical professionals to consult databases. Therefore, we introduce diseaseGPS, an integrated platform for the diagnosis of genetic disorders that combines both phenotype and genotype data for analysis. It offers not only a user-friendly GUI web application for those without a programming background but also scripts that can be executed in batch mode for bioinformatics professionals. The genetic and phenotypic data are integrated using the ACMG-Bayes method and a novel phenotypic similarity method, to prioritize the results of genetic disorders. diseaseGPS was evaluated on 6085 cases from Deciphering Developmental Disorders project and 187 cases from Shanghai Children's hospital. The results demonstrated that diseaseGPS performed better than other commonly used methods.

Evaluation of in silico pathogenicity prediction tools for the classification of small in-frame indels.

Cannon S; Williams M; Gunning AC; Wright CF

BMC medical genomics 2023;16;1;36

The use of in silico pathogenicity predictions as evidence when interpreting genetic variants is widely accepted as part of standard variant classification guidelines. Although numerous algorithms have been developed and evaluated for classifying missense variants, in-frame insertions/deletions (indels) have been much less well studied.

Expanding SPTAN1 monoallelic variant associated disorders: From epileptic encephalopathy to pure spastic paraplegia and ataxia.

Morsy H; Benkirane M; Cali E; Rocca C; Zhelcheska K; Cipriani V; Galanaki E; Maroofian R; Efthymiou S; Murphy D; O'Driscoll M; Suri M; Banka S; Clayton-Smith J; Wright T; Redman M; Bassetti JA; Nizon M; Cogne B; Jamra RA; Bartolomaeus T; Heruth M; Krey I; Gburek-Augustat J; Wieczorek D; Gattermann F; Mcentagart M; Goldenberg A; Guyant-Marechal L; Garcia-Moreno H; Giunti P; Chabrol B; Bacrot S; Buissonnière R; Magry V; Gowda VK; Srinivasan VM; Melegh B; Szabó A; Sümegi K; Cossée M; Ziff M; Butterfield R; Hunt D; Bird-Lieberman G; Hanna M; Koenig M; Stankewich M; Vandrovcova J; Houlden H;

Genetics in medicine : official journal of the American College of Medical Genetics 2023;25;1;76-89

Nonerythrocytic αII-spectrin (SPTAN1) variants have been previously associated with intellectual disability and epilepsy. We conducted this study to delineate the phenotypic spectrum of SPTAN1 variants.

Expanding the neurodevelopmental phenotype associated with HK1 de novo heterozygous missense variants.

Poole RL; Badonyi M; Cozens A; Foulds N; Marsh JA; Rahman S; Ross A; Schooley J; Straub V; Quigley AJ; FitzPatrick D; Lampe A

European journal of medical genetics 2023;66;3;104696

Neurodevelopmental disorder with visual defects and brain anomalies (NEDVIBA) is a recently described genetic condition caused by de novo missense HK1 variants. Phenotypic data is currently limited; only seven patients have been published to date. This descriptive case series of a further four patients with de novo missense HK1 variants, alongside integration of phenotypic data with the reported cases, aims to improve our understanding of the associated phenotype. We provide further evidence that de novo HK1 variants located within the regulatory-terminal domain and alpha helix are associated with neurological problems and visual problems. We highlight for the first time an association with a raised cerebrospinal fluid lactate and specific abnormalities to the basal ganglia on brain magnetic resonance imaging, as well as associated respiratory issues and swallowing/feeding difficulties. We propose that this distinctive neurodevelopmental phenotype could arise through disruption of the regulatory glucose-6-phosphate binding site and subsequent gain of function of HK1 within the brain.

Further delineation of the rare GDACCF (global developmental delay, absent or hypoplastic corpus callosum, dysmorphic facies syndrome): genotype and phenotype of 22 patients with ZNF148 mutations.

Szakszon K; Lourenco CM; Callewaert BL; Geneviève D; Rouxel F; Morin D; Denommé-Pichon AS; Vitobello A; Patterson WG; Louie R; Pinto E Vairo F; Klee E; Kaiwar C; Gavrilova RH; Agre KE; Jacquemont S; Khadijé J; Giltay J; van Gassen K; Merő G; Gerkes E; Van Bon BW; Rinne T; Pfundt R; Brunner HG; Caluseriu O; Grasshoff U; Kehrer M; Haack TB; Khelifa MM; Bergmann AK; Cueto-González AM; Martorell AC; Ramachandrappa S; Sawyer LB; Fasel P; Braun D; Isis A; Superti-Furga A; McNiven V; Chitayat D; Ahmed SA; Brennenstuhl H; Schwaibolf EM; Battisti G; Parmentier B; Stevens SJC

Journal of medical genetics 2023

Pathogenic variants in the zinc finger protein coding genes are rare causes of intellectual disability and congenital malformations. Mutations in the ZNF148 gene causing GDACCF syndrome (global developmental delay, absent or hypoplastic corpus callosum, dysmorphic facies; MIM #617260) have been reported in five individuals so far.

Further delineation of the rare GDACCF (global developmental delay, absent or hypoplastic corpus callosum, dysmorphic facies syndrome): genotype and phenotype of 22 patients with ZNF148 mutations.

Szakszon K; Lourenco CM; Callewaert BL; Geneviève D; Rouxel F; Morin D; Denommé-Pichon AS; Vitobello A; Patterson WG; Louie R; Pinto E Vairo F; Klee E; Kaiwar C; Gavrilova RH; Agre KE; Jacquemont S; Khadijé J; Giltay J; van Gassen K; Merő G; Gerkes E; Van Bon BW; Rinne T; Pfundt R; Brunner HG; Caluseriu O; Grasshoff U; Kehrer M; Haack TB; Khelifa MM; Bergmann AK; Cueto-González AM; Martorell AC; Ramachandrappa S; Sawyer LB; Fasel P; Braun D; Isis A; Superti-Furga A; McNiven V; Chitayat D; Ahmed SA; Brennenstuhl H; Schwaibolf EM; Battisti G; Parmentier B; Stevens SJC

Journal of medical genetics 2023

Pathogenic variants in the zinc finger protein coding genes are rare causes of intellectual disability and congenital malformations. Mutations in the ZNF148 gene causing GDACCF syndrome (global developmental delay, absent or hypoplastic corpus callosum, dysmorphic facies; MIM #617260) have been reported in five individuals so far.

Genomic Diagnosis of Rare Pediatric Disease in the United Kingdom and Ireland.

Wright CF; Campbell P; Eberhardt RY; Aitken S; Perrett D; Brent S; Danecek P; Gardner EJ; Chundru VK; Lindsay SJ; Andrews K; Hampstead J; Kaplanis J; Samocha KE; Middleton A; Foreman J; Hobson RJ; Parker MJ; Martin HC; FitzPatrick DR; Hurles ME; Firth HV;

The New England journal of medicine 2023;388;17;1559-1571

Pediatric disorders include a range of highly penetrant, genetically heterogeneous conditions amenable to genomewide diagnostic approaches. Finding a molecular diagnosis is challenging but can have profound lifelong benefits.

Heterozygous rare variants in NR2F2 cause a recognizable multiple congenital anomaly syndrome with developmental delays.

Ganapathi M; Matsuoka LS; March M; Li D; Brokamp E; Benito-Sanz S; White SM; Lachlan K; Ahimaz P; Sewda A; Bastarache L; Thomas-Wilson A; Stoler JM; Bramswig NC; Baptista J; Stals K; Demurger F; Cogne B; Isidor B; Bedeschi MF; Peron A; Amiel J; Zackai E; Schacht JP; Iglesias AD; Morton J; Schmetz A; ; Seidel V; Lucia S; Baskin SM; Thiffault I; Cogan JD; Gordon CT; Chung WK; Bowdin S; Bhoj E

European journal of human genetics : EJHG 2023;31;10;1117-1124

Nuclear receptor subfamily 2 group F member 2 (NR2F2 or COUP-TF2) encodes a transcription factor which is expressed at high levels during mammalian development. Rare heterozygous Mendelian variants in NR2F2 were initially identified in individuals with congenital heart disease (CHD), then subsequently in cohorts of congenital diaphragmatic hernia (CDH) and 46,XX ovotesticular disorders/differences of sexual development (DSD); however, the phenotypic spectrum associated with pathogenic variants in NR2F2 remains poorly characterized. Currently, less than 40 individuals with heterozygous pathogenic variants in NR2F2 have been reported. Here, we review the clinical and molecular details of 17 previously unreported individuals with rare heterozygous NR2F2 variants, the majority of which were de novo. Clinical features were variable, including intrauterine growth restriction (IUGR), CHD, CDH, genital anomalies, DSD, developmental delays, hypotonia, feeding difficulties, failure to thrive, congenital and acquired microcephaly, dysmorphic facial features, renal failure, hearing loss, strabismus, asplenia, and vascular malformations, thus expanding the phenotypic spectrum associated with NR2F2 variants. The variants seen were predicted loss of function, including a nonsense variant inherited from a mildly affected mosaic mother, missense and a large deletion including the NR2F2 gene. Our study presents evidence for rare, heterozygous NR2F2 variants causing a highly variable syndrome of congenital anomalies, commonly associated with heart defects, developmental delays/intellectual disability, dysmorphic features, feeding difficulties, hypotonia, and genital anomalies. Based on the new and previous cases, we provide clinical recommendations for evaluating individuals diagnosed with an NR2F2-associated disorder.

Hypothesis-free phenotype prediction within a genetics-first framework.

Lu C; Zaucha J; Gam R; Fang H; Ben Smithers ; Oates ME; Bernabe-Rubio M; Williams J; Zelenka N; Pandurangan AP; Tandon H; Shihab H; Kalaivani R; Sung M; Sardar AJ; Tzovoras BG; Danovi D; Gough J

Nature Communications 2023;14;1;919

Cohort-wide sequencing studies have revealed that the largest category of variants is those deemed 'rare', even for the subset located in coding regions (99% of known coding variants are seen in less than 1% of the population. Associative methods give some understanding how rare genetic variants influence disease and organism-level phenotypes. But here we show that additional discoveries can be made through a knowledge-based approach using protein domains and ontologies (function and phenotype) that considers all coding variants regardless of allele frequency. We describe an ab initio, genetics-first method making molecular knowledge-based interpretations for exome-wide non-synonymous variants for phenotypes at the organism and cellular level. By using this reverse approach, we identify plausible genetic causes for developmental disorders that have eluded other established methods and present molecular hypotheses for the causal genetics of 40 phenotypes generated from a direct-to-consumer genotype cohort. This system offers a chance to extract further discovery from genetic data after standard tools have been applied.

IMPROVE-DD: Integrating multiple phenotype resources optimizes variant evaluation in genetically determined developmental disorders.

Aitken S; Firth HV; Wright CF; Hurles ME; FitzPatrick DR; Semple CA

HGG advances 2023;4;1;100162

Diagnosing rare developmental disorders using genome-wide sequencing data commonly necessitates review of multiple plausible candidate variants, often using ontologies of categorical clinical terms. We show that Integrating Multiple Phenotype Resources Optimizes Variant Evaluation in Developmental Disorders (IMPROVE-DD) by incorporating additional classes of data commonly available to clinicians and recorded in health records. In doing so, we quantify the distinct contributions of sex, growth, and development in addition to Human Phenotype Ontology (HPO) terms and demonstrate added value from these readily available information sources. We use likelihood ratios for nominal and quantitative data and propose a classifier for HPO terms in this framework. This Bayesian framework results in more robust diagnoses. Using data systematically collected in the Deciphering Developmental Disorders study, we considered 77 genes with pathogenic/likely pathogenic variants in ≥10 individuals. All genes showed at least a satisfactory prediction by receiver operating characteristic when testing on training data (AUC ≥ 0.6), and HPO terms were the best predictor for the majority of genes, though a minority (13/77) of genes were better predicted by other phenotypic data types. Overall, classifiers based upon multiple integrated phenotypic data sources performed better than those based upon any individual source, and importantly, integrated models produced notably fewer false positives. Finally, we show that IMPROVE-DD models with good predictive performance on cross-validation can be constructed from relatively few individuals. This suggests new strategies for candidate gene prioritization and highlights the value of systematic clinical data collection to support diagnostic programs.

Loss-of-Function Variants in DRD1 in Infantile Parkinsonism-Dystonia.

Reid KM; Steel D; Nair S; Bhate S; Biassoni L; Sudhakar S; Heys M; Burke E; Kamsteeg EJ; Genomics England Research Consortium ; Hameed B; Zech M; Mencacci NE; Barwick K; Topf M; Kurian MA

Cells 2023;12;7

The human dopaminergic system is vital for a broad range of neurological processes, including the control of voluntary movement. Here we report a proband presenting with clinical features of dopamine deficiency: severe infantile parkinsonism-dystonia, characterised by frequent oculogyric crises, dysautonomia and global neurodevelopmental impairment. CSF neurotransmitter analysis was unexpectedly normal. Triome whole-genome sequencing revealed a homozygous variant (c.110C>A, (p.T37K)) in DRD1, encoding the most abundant dopamine receptor (D1) in the central nervous system, most highly expressed in the striatum. This variant was absent from gnomAD, with a CADD score of 27.5. Using an in vitro heterologous expression system, we determined that DRD1-T37K results in loss of protein function. Structure-function modelling studies predicted reduced substrate binding, which was confirmed in vitro. Exposure of mutant protein to the selective D1 agonist Chloro APB resulted in significantly reduced cyclic AMP levels. Numerous D1 agonists failed to rescue the cellular defect, reflected clinically in the patient, who had no benefit from dopaminergic therapy. Our study identifies DRD1 as a new disease-associated gene, suggesting a crucial role for the D1 receptor in motor control.

Mechanism of KMT5B haploinsufficiency in neurodevelopment in humans and mice.

Sheppard SE; Bryant L; Wickramasekara RN; Vaccaro C; Robertson B; Hallgren J; Hulen J; Watson CJ; Faundes V; Duffourd Y; Lee P; Simon MC; de la Cruz X; Padilla N; Flores-Mendez M; Akizu N; Smiler J; Pellegrino Da Silva R; Li D; March M; Diaz-Rosado A; Peixoto de Barcelos I; Choa ZX; Lim CY; Dubourg C; Journel H; Demurger F; Mulhern M; Akman C; Lippa N; Andrews M; Baldridge D; Constantino J; van Haeringen A; Snoeck-Streef I; Chow P; Hing A; Graham JM; Au M; Faivre L; Shen W; Mao R; Palumbos J; Viskochil D; Gahl W; Tifft C; Macnamara E; Hauser N; Miller R; Maffeo J; Afenjar A; Doummar D; Keren B; Arn P; Macklin-Mantia S; Meerschaut I; Callewaert B; Reis A; Zweier C; Brewer C; Saggar A; Smeland MF; Kumar A; Elmslie F; Deshpande C; Nizon M; Cogne B; van Ierland Y; Wilke M; van Slegtenhorst M; Koudijs S; Chen JY; Dredge D; Pier D; Wortmann S; Kamsteeg EJ; Koch J; Haynes D; Pollack L; Titheradge H; Ranguin K; Denommé-Pichon AS; Weber S; Pérez de la Fuente R; Sánchez Del Pozo J; Lezana Rosales JM; Joset P; Steindl K; Rauch A; Mei D; Mari F; Guerrini R; Lespinasse J; Tran Mau-Them F; Philippe C; Dauriat B; Raymond L; Moutton S; Cueto-González AM; Tan TY; Mignot C; Grotto S; Renaldo F; Drivas TG; Hennessy L; Raper A; Parenti I; Kaiser FJ; Kuechler A; Busk ØL; Islam L; Siedlik JA; Henderson LB; Juusola J; Person R; Schnur RE; Vitobello A; Banka S; Bhoj EJ; Stessman HAF

Science advances 2023;9;10;eade1463

Pathogenic variants in KMT5B, a lysine methyltransferase, are associated with global developmental delay, macrocephaly, autism, and congenital anomalies (OMIM# 617788). Given the relatively recent discovery of this disorder, it has not been fully characterized. Deep phenotyping of the largest (n = 43) patient cohort to date identified that hypotonia and congenital heart defects are prominent features that were previously not associated with this syndrome. Both missense variants and putative loss-of-function variants resulted in slow growth in patient-derived cell lines. KMT5B homozygous knockout mice were smaller in size than their wild-type littermates but did not have significantly smaller brains, suggesting relative macrocephaly, also noted as a prominent clinical feature. RNA sequencing of patient lymphoblasts and Kmt5b haploinsufficient mouse brains identified differentially expressed pathways associated with nervous system development and function including axon guidance signaling. Overall, we identified additional pathogenic variants and clinical features in KMT5B-related neurodevelopmental disorder and provide insights into the molecular mechanisms of the disorder using multiple model systems.

Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease.

Calame DG; Guo T; Wang C; Garrett L; Jolly A; Dawood M; Kurolap A; Henig NZ; Fatih JM; Herman I; Du H; Mitani T; Becker L; Rathkolb B; Gerlini R; Seisenberger C; Marschall S; Hunter JV; Gerard A; Heidlebaugh A; Challman T; Spillmann RC; Jhangiani SN; Coban-Akdemir Z; Lalani S; Liu L; Revah-Politi A; Iglesias A; Guzman E; Baugh E; Boddaert N; Rondeau S; Ormieres C; Barcia G; Tan QKG; Thiffault I; Pastinen T; Sheikh K; Biliciler S; Mei D; Melani F; Shashi V; Yaron Y; Steele M; Wakeling E; Østergaard E; Nazaryan-Petersen L; ; Millan F; Santiago-Sim T; Thevenon J; Bruel AL; Thauvin-Robinet C; Popp D; Platzer K; Gawlinski P; Wiszniewski W; Marafi D; Pehlivan D; Posey JE; Gibbs RA; Gailus-Durner V; Guerrini R; Fuchs H; Hrabě de Angelis M; Hölter SM; Cheung HH; Gu S; Lupski JR

American journal of human genetics 2023;110;8;1394-1413

DExD/H-box RNA helicases (DDX/DHX) are encoded by a large paralogous gene family; in a subset of these human helicase genes, pathogenic variation causes neurodevelopmental disorder (NDD) traits and cancer. DHX9 encodes a BRCA1-interacting nuclear helicase regulating transcription, R-loops, and homologous recombination and exhibits the highest mutational constraint of all DDX/DHX paralogs but remains unassociated with disease traits in OMIM. Using exome sequencing and family-based rare-variant analyses, we identified 20 individuals with de novo, ultra-rare, heterozygous missense or loss-of-function (LoF) DHX9 variant alleles. Phenotypes ranged from NDDs to the distal symmetric polyneuropathy axonal Charcot-Marie-Tooth disease (CMT2). Quantitative Human Phenotype Ontology (HPO) analysis demonstrated genotype-phenotype correlations with LoF variants causing mild NDD phenotypes and nuclear localization signal (NLS) missense variants causing severe NDD. We investigated DHX9 variant-associated cellular phenotypes in human cell lines. Whereas wild-type DHX9 was restricted to the nucleus, NLS missense variants abnormally accumulated in the cytoplasm. Fibroblasts from an individual with an NLS variant also showed abnormal cytoplasmic DHX9 accumulation. CMT2-associated missense variants caused aberrant nucleolar DHX9 accumulation, a phenomenon previously associated with cellular stress. Two NDD-associated variants, p.Gly411Glu and p.Arg761Gln, altered DHX9 ATPase activity. The severe NDD-associated variant p.Arg141Gln did not affect DHX9 localization but instead increased R-loop levels and double-stranded DNA breaks. Dhx9-/- mice exhibited hypoactivity in novel environments, tremor, and sensorineural hearing loss. All together, these results establish DHX9 as a critical regulator of mammalian neurodevelopment and neuronal homeostasis.

Novel Variants of SOX4 in Patients with Intellectual Disability.

Grosse M; Kuechler A; Dabir T; Spranger S; Beck-Wödl S; Bertrand M; Haack TB; Grasemann C; Manka E; Depienne C; Kaiser FJ

International journal of molecular sciences 2023;24;4

SOX4 is a transcription factor with pleiotropic functions required for different developmental processes, such as corticogenesis. As with all SOX proteins, it contains a conserved high mobility group (HMG) and exerts its function via interaction with other transcription factors, such as POU3F2. Recently, pathogenic SOX4 variants have been identified in several patients who had clinical features overlapping with Coffin-Siris syndrome. In this study, we identified three novel variants in unrelated patients with intellectual disability, two of which were de novo (c.79G>T, p.Glu27*; c.182G>A p.Arg61Gln) and one inherited (c.355C>T, p.His119Tyr). All three variants affected the HMG box and were suspected to influence SOX4 function. We investigated the effects of these variants on transcriptional activation by co-expressing either wildtype (wt) or mutant SOX4 with its co-activator POU3F2 and measuring their activity in reporter assays. All variants abolished SOX4 activity. While our experiments provide further support for the pathogenicity of SOX4 loss-of-function (LOF) variants as a cause of syndromic intellectual disability (ID), our results also indicate incomplete penetrance associated with one variant. These findings will improve classification of novel, putatively pathogenic SOX4 variants.

Null and missense mutations of ERI1 cause a recessive phenotypic dichotomy in humans.

Guo L; Salian S; Xue JY; Rath N; Rousseau J; Kim H; Ehresmann S; Moosa S; Nakagawa N; Kuroda H; Clayton-Smith J; Wang J; Wang Z; Banka S; Jackson A; Zhang YM; Wei ZJ; Hüning I; Brunet T; Ohashi H; Thomas MF; Bupp C; Miyake N; Matsumoto N; Mendoza-Londono R; Costain G; Hahn G; Di Donato N; Yigit G; Yamada T; Nishimura G; Ansel KM; Wollnik B; Hrabě de Angelis M; Mégarbané A; Rosenfeld JA; Heissmeyer V; Ikegawa S; Campeau PM

American journal of human genetics 2023;110;7;1068-1085

ERI1 is a 3'-to-5' exoribonuclease involved in RNA metabolic pathways including 5.8S rRNA processing and turnover of histone mRNAs. Its biological and medical significance remain unclear. Here, we uncover a phenotypic dichotomy associated with bi-allelic ERI1 variants by reporting eight affected individuals from seven unrelated families. A severe spondyloepimetaphyseal dysplasia (SEMD) was identified in five affected individuals with missense variants but not in those with bi-allelic null variants, who showed mild intellectual disability and digital anomalies. The ERI1 missense variants cause a loss of the exoribonuclease activity, leading to defective trimming of the 5.8S rRNA 3' end and a decreased degradation of replication-dependent histone mRNAs. Affected-individual-derived induced pluripotent stem cells (iPSCs) showed impaired in vitro chondrogenesis with downregulation of genes regulating skeletal patterning. Our study establishes an entity previously unreported in OMIM and provides a model showing a more severe effect of missense alleles than null alleles within recessive genotypes, suggesting a key role of ERI1-mediated RNA metabolism in human skeletal patterning and chondrogenesis.

Null and missense mutations of ERI1 cause a recessive phenotypic dichotomy in humans.

Guo L; Salian S; Xue JY; Rath N; Rousseau J; Kim H; Ehresmann S; Moosa S; Nakagawa N; Kuroda H; Clayton-Smith J; Wang J; Wang Z; Banka S; Jackson A; Zhang YM; Wei ZJ; Hüning I; Brunet T; Ohashi H; Thomas MF; Bupp C; Miyake N; Matsumoto N; Mendoza-Londono R; Costain G; Hahn G; Di Donato N; Yigit G; Yamada T; Nishimura G; Ansel KM; Wollnik B; Hrabě de Angelis M; Mégarbané A; Rosenfeld JA; Heissmeyer V; Ikegawa S; Campeau PM

American journal of human genetics 2023;110;7;1068-1085

ERI1 is a 3'-to-5' exoribonuclease involved in RNA metabolic pathways including 5.8S rRNA processing and turnover of histone mRNAs. Its biological and medical significance remain unclear. Here, we uncover a phenotypic dichotomy associated with bi-allelic ERI1 variants by reporting eight affected individuals from seven unrelated families. A severe spondyloepimetaphyseal dysplasia (SEMD) was identified in five affected individuals with missense variants but not in those with bi-allelic null variants, who showed mild intellectual disability and digital anomalies. The ERI1 missense variants cause a loss of the exoribonuclease activity, leading to defective trimming of the 5.8S rRNA 3' end and a decreased degradation of replication-dependent histone mRNAs. Affected-individual-derived induced pluripotent stem cells (iPSCs) showed impaired in vitro chondrogenesis with downregulation of genes regulating skeletal patterning. Our study establishes an entity previously unreported in OMIM and provides a model showing a more severe effect of missense alleles than null alleles within recessive genotypes, suggesting a key role of ERI1-mediated RNA metabolism in human skeletal patterning and chondrogenesis.

Overlapping cortical malformations in patients with pathogenic variants in GRIN1 and GRIN2B.

Brock S; Laquerriere A; Marguet F; Myers SJ; Hongjie Y; Baralle D; Vanderhasselt T; Stouffs K; Keymolen K; Kim S; Allen J; Shaulsky G; Chelly J; Marcorelle P; Aziza J; Villard L; Sacaze E; de Wit MCY; Wilke M; Mancini GMS; Hehr U; Lim D; Mansour S; Traynelis SF; Beneteau C; Denis-Musquer M; Jansen AC; Fry AE; Bahi-Buisson N

Journal of medical genetics 2023;60;2;183-192

Malformations of cortical development (MCDs) have been reported in a subset of patients with pathogenic heterozygous variants in GRIN1 or GRIN2B, genes which encode for subunits of the N-methyl-D-aspartate receptor (NMDAR). The aim of this study was to further define the phenotypic spectrum of NMDAR-related MCDs.

PSMC3 proteasome subunit variants are associated with neurodevelopmental delay and type I interferon production.

Ebstein F; Küry S; Most V; Rosenfelt C; Scott-Boyer MP; van Woerden GM; Besnard T; Papendorf JJ; Studencka-Turski M; Wang T; Hsieh TC; Golnik R; Baldridge D; Forster C; de Konink C; Teurlings SMW; Vignard V; van Jaarsveld RH; Ades L; Cogné B; Mignot C; Deb W; Jongmans MCJ; Cole FS; van den Boogaard MH; Wambach JA; Wegner DJ; Yang S; Hannig V; Brault JA; Zadeh N; Bennetts B; Keren B; Gélineau AC; Powis Z; Towne M; Bachman K; Seeley A; Beck AE; Morrison J; Westman R; Averill K; Brunet T; Haasters J; Carter MT; Osmond M; Wheeler PG; Forzano F; Mohammed S; Trakadis Y; Accogli A; Harrison R; Guo Y; Hakonarson H; Rondeau S; Baujat G; Barcia G; Feichtinger RG; Mayr JA; Preisel M; Laumonnier F; Kallinich T; Knaus A; Isidor B; Krawitz P; Völker U; Hammer E; Droit A; Eichler EE; Elgersma Y; Hildebrand PW; Bolduc F; Krüger E; Bézieau S

Science translational medicine 2023;15;698;eabo3189

A critical step in preserving protein homeostasis is the recognition, binding, unfolding, and translocation of protein substrates by six AAA-ATPase proteasome subunits (ATPase-associated with various cellular activities) termed PSMC1-6, which are required for degradation of proteins by 26S proteasomes. Here, we identified 15 de novo missense variants in the PSMC3 gene encoding the AAA-ATPase proteasome subunit PSMC3/Rpt5 in 23 unrelated heterozygous patients with an autosomal dominant form of neurodevelopmental delay and intellectual disability. Expression of PSMC3 variants in mouse neuronal cultures led to altered dendrite development, and deletion of the PSMC3 fly ortholog Rpt5 impaired reversal learning capabilities in fruit flies. Structural modeling as well as proteomic and transcriptomic analyses of T cells derived from patients with PSMC3 variants implicated the PSMC3 variants in proteasome dysfunction through disruption of substrate translocation, induction of proteotoxic stress, and alterations in proteins controlling developmental and innate immune programs. The proteostatic perturbations in T cells from patients with PSMC3 variants correlated with a dysregulation in type I interferon (IFN) signaling in these T cells, which could be blocked by inhibition of the intracellular stress sensor protein kinase R (PKR). These results suggest that proteotoxic stress activated PKR in patient-derived T cells, resulting in a type I IFN response. The potential relationship among proteosome dysfunction, type I IFN production, and neurodevelopment suggests new directions in our understanding of pathogenesis in some neurodevelopmental disorders.

PUF60-related developmental disorder: A case series and phenotypic analysis of 10 additional patients with monoallelic PUF60 variants.

Grimes H; Ansari M; Ashraf T; Cueto-González AM; Calder A; Day M; Fernandez Alvarez P; Foster A; Lahiri N; Repetto GM; Scurr I; Varghese V; Low KJ

American journal of medical genetics. Part A 2023

PUF60-related developmental disorder (also referred to as Verheij syndrome), resulting from haploinsufficiency of PUF60, is associated with multiple congenital anomalies affecting a wide range of body systems. These anomalies include ophthalmic coloboma, and congenital anomalies of the heart, kidney, and musculoskeletal system. Behavioral and intellectual difficulties are also observed. While less common than other features associated with PUF60-related developmental disorder, for instance hearing impairment and short stature, identification of specific anomalies such as ophthalmic coloboma can aid with diagnostic identification given the limited spectrum of genes linked with this feature. We describe 10 patients with PUF60 gene variants, bringing the total number reported in the literature, to varying levels of details, to 56 patients. Patients were recruited both via locally based exome sequencing from international sites and from the DDD study in the United Kingdom. Eight of the variants reported were novel PUF60 variants. The addition of a further patient with a reported c449-457del variant to the existing literature highlights this as a recurrent variant. One variant was inherited from an affected parent. This is the first example in the literature of an inherited variant resulting in PUF60-related developmental disorder. Two patients (20%) were reported to have a renal anomaly consistent with 22% of cases in previously reported literature. Two patients received specialist endocrine treatment. More commonly observed were clinical features such as: cardiac anomalies (40%), ocular abnormalities (70%), intellectual disability (60%), and skeletal abnormalities (80%). Facial features did not demonstrate a recognizable gestalt. Of note, but remaining of unclear causality, we describe a single pediatric patient with pineoblastoma. We recommend that stature and pubertal progress should be monitored in PUF60-related developmental disorder with a low threshold for endocrine investigations as hormone therapy may be indicated. Our study reports an inherited case with PUF60-related developmental disorder which has important genetic counseling implications for families.

Saturation genome editing of DDX3X clarifies pathogenicity of germline and somatic variation.

Radford EJ; Tan HK; Andersson MHL; Stephenson JD; Gardner EJ; Ironfield H; Waters AJ; Gitterman D; Lindsay S; Abascal F; Martincorena I; Kolesnik-Taylor A; Ng-Cordell E; Firth HV; Baker K; Perry JRB; Adams DJ; Gerety SS; Hurles ME

Nature Communications 2023;14;1;7702

Loss-of-function of DDX3X is a leading cause of neurodevelopmental disorders (NDD) in females. DDX3X is also a somatically mutated cancer driver gene proposed to have tumour promoting and suppressing effects. We perform saturation genome editing of DDX3X, testing in vitro the functional impact of 12,776 nucleotide variants. We identify 3432 functionally abnormal variants, in three distinct classes. We train a machine learning classifier to identify functionally abnormal variants of NDD-relevance. This classifier has at least 97% sensitivity and 99% specificity to detect variants pathogenic for NDD, substantially out-performing in silico predictors, and resolving up to 93% of variants of uncertain significance. Moreover, functionally-abnormal variants can account for almost all of the excess nonsynonymous DDX3X somatic mutations seen in DDX3X-driven cancers. Systematic maps of variant effects generated in experimentally tractable cell types have the potential to transform clinical interpretation of both germline and somatic disease-associated variation.

Sex difference contributes to phenotypic diversity in individuals with neurodevelopmental disorders.

Cuppens T; Shatto J; Mangnier L; Kumar AA; Ng AC; Kaur M; Bui TA; Leclercq M; Droit A; Dunham I; Bolduc FV

Frontiers in pediatrics 2023;11;1172154

Gain a better understanding of sex-specific differences in individuals with global developmental delay (GDD), with a focus on phenotypes and genotypes.

SHORT syndrome with microcephaly and developmental delay.

Patel V; Cui W; Cobben JM

American journal of medical genetics. Part A 2023;191;3;850-854

We report a boy with typical clinical features of SHORT syndrome alongside a significant microcephaly and severe developmental delay associated with a de novo single nucleotide missense DNA variant resulting in a single amino acid change in codon 486 of the PIK3R1 gene (PIK3R1 c.1456G>A (p.Ala486Thr)). Our report strikingly coincides with another recently published case from Brazil, describing a 23-year-old woman with the same de novo PIK3R1 DNA variant, who also exhibits SHORT syndrome with severe secondary microcephaly and intellectual disability. On review of the literature, we have identified further cases of PIK3R1-related SHORT Syndrome with a similar phenotype. We note all these cases (including ours) have variants located in the -inter SH2 domain (iSH2); we speculate that pathogenic iSH2 located PIK3R1 variants are associated with a different and otherwise unreported clinical picture of SHORT syndrome that presents with microcephaly and/or significant developmental delay/intellectual disability. The pathogenic mechanism of why these variants apparently lead to a different clinical picture of SHORT syndrome remains unknown.

SOX5: Lamb-Shaffer syndrome-A case series further expanding the phenotypic spectrum.

Edgerley K; Bryson L; Hanington L; Irving R; Joss S; Lampe A; Maystadt I; Osio D; Richardson R; Split M; Sansbury FH; Scurr I; Stewart H; McNeil A; Low K

American journal of medical genetics. Part A 2023;191;5;1447-1458

To delineate further the clinical phenotype of Lamb-Shaffer Syndrome (LSS) 16 unpublished patients with heterozygous variation in SOX5 were identified either through the UK Decipher database or the study team was contacted by clinicians directly. Clinical phenotyping tables were completed for each patient by their responsible clinical geneticist. Photos and clinical features were compared to assess key phenotypes and genotype-phenotype correlation. We report 16 SOX5 variants all of which meet American College of Medical Genetics/Association for Clinical Genomic Science ACMG/ACGS criteria class IV or V. 7/16 have intragenic deletions of SOX5 and 9/16 have single nucleotide variants (including both truncating and missense variants). The cohort includes two sets of monozygotic twins and parental gonadal mosaicism is noted in one family. This cohort of 16 patients is compared with the 71 previously reported cases and corroborates previous phenotypic findings. As expected, the most common findings include global developmental delay with prominent speech delay, mild to moderate intellectual disability, behavioral abnormalities and sometimes subtle characteristic facial features. We expand in more detail on the behavioral phenotype and observe that there is a greater tendency toward lower growth parameters and microcephaly in patients with single nucleotide variants. This cohort provides further evidence of gonadal mosaicism in SOX5 variants; this should be considered when providing genetic counseling for couples with one affected child and an apparently de novo variant.

The PHF21A neurodevelopmental disorder: an evaluation of clinical data from 13 patients.

Poole RL; Bijlsma EK; Houge G; Jones G; Mikštienė V; Preikšaitienė E; Thompson L; Tatton-Brown K

Clinical dysmorphology 2023;32;2;49-54

Potocki-Shaffer syndrome (PSS) is a rare neurodevelopmental disorder caused by deletions involving the 11p11.2-p12 region, encompassing the plant homeodomain finger protein 21A (PHF21A) gene. PHF21A has an important role in epigenetic regulation and PHF21A variants have previously been associated with a specific disorder that, whilst sharing some features of PSS, has notable differences. This study aims to expand the phenotype, particularly in relation to overgrowth, associated with PHF21A variants. Analysis of phenotypic data was undertaken on 13 individuals with PHF21A constitutional variants including four individuals described in the current series. Of those individuals where data were recorded, postnatal overgrowth was reported in 5/6 (83%). In addition, all had both an intellectual disability and behavioural issues. Frequent associations included postnatal hypotonia (7/11, 64%); and at least one afebrile seizure episode (6/12, 50%). Although a recognizable facial gestalt was not associated, subtle dysmorphic features were shared amongst some individuals and included a tall broad forehead, broad nasal tip, anteverted nares and full cheeks. We provide further insight into the emerging neurodevelopmental syndrome associated with PHF21A disruption. We present some evidence that PHF21A might be considered a new member of the overgrowth-intellectual disability syndrome (OGID) family.

PTCHD1: Identification and Neurodevelopmental Contributions of an Autism Spectrum Disorder and Intellectual Disability Susceptibility Gene.

Pastore SF; Ko SY; Frankland PW; Hamel PA; Vincent JB

Genes 2022;13;3

Over the last one and a half decades, copy number variation and whole-genome sequencing studies have illuminated the considerable genetic heterogeneity that underlies the etiologies of autism spectrum disorder (ASD) and intellectual disability (ID). These investigations support the idea that ASD may result from complex interactions between susceptibility-related genetic variants (single nucleotide variants or copy number variants) and the environment. This review outlines the identification and neurobiological characterization of two such genes located in Xp22.11, Patched domain-containing 1 (PTCHD1), and its antisense lncRNA PTCHD1-AS. Animal models of Ptchd1 disruption have recapitulated a subset of clinical symptoms related to ASD as well as to ID. Furthermore, these Ptchd1 mouse knockout studies implicate the expression of Ptchd1 in both the thalamic and the hippocampal brain regions as being crucial for proper neurodevelopment and cognitive function. Altered kynurenine metabolic signalling has been postulated as a disease mechanism in one of these animal studies. Additionally, ASD patient-derived induced pluripotent stem cells (iPSCs) carrying a copy number loss impacting the antisense non-coding RNA PTCHD1-AS have been used to generate 2D neuronal cultures. While copy number loss of PTCHD1-AS does not affect the transcription of PTCHD1, the neurons exhibit diminished miniature excitatory postsynaptic current frequency, supporting its role in ASD etiology. A more thorough understanding of risk factor genes, such as PTCHD1 and PTCHD1-AS, will help to clarify the intricate genetic and biological mechanisms that underlie ASD and ID, providing a foundation for meaningful therapeutic interventions to enhance the quality of life of individuals who experience these conditions.

A severe case of Bosch-Boonstra-Schaaf optic atrophy syndrome with a novel description of coloboma and septo-optic dysplasia, owing to a start codon variant in the NR2F1 gene.

Gazdagh G; Mawby R; Self JE; Baralle D;

American journal of medical genetics. Part A 2022;188;3;900-906

Bosch-Boonstra-Schaaf optic atrophy syndrome (BBSOAS) is a rare congenital syndrome characterized by a range of phenotypes including optic atrophy and intellectual disability among other features. Pathogenic variants in the NR2F1 (nuclear receptor subfamily 2 group F member 1) gene have been linked to this condition. A recent report has shown that pathogenic variants in the start codon lead to decreased expression of the NR2F1 protein and a relatively mild phenotype, similar to that seen in whole gene deletions, and due to the lack of the dominant negative effect. Here we describe a severe case of BBSOAS with an initiation codon missense variant. The developmental delay, seizures, optic atrophy are in keeping with features observed in this condition, however this is the first report to describe colobomas and septo-optic dysplasia as associated features potentially extending the phenotype linked to BBSOAS. In addition, this is the first description of a severe phenotype linked to a de novo missense variant in the start codon of the NR2F1 gene.

Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders.

Yates TM; Lain A; Campbell J; FitzPatrick DR; Simpson TI

Database : the journal of biological databases and curation 2022;2022

There are >2500 different genetically determined developmental disorders (DD), which, as a group, show very high levels of both locus and allelic heterogeneity. This has led to the wide-spread use of evidence-based filtering of genome-wide sequence data as a diagnostic tool in DD. Determining whether the association of a filtered variant at a specific locus is a plausible explanation of the phenotype in the proband is crucial and commonly requires extensive manual literature review by both clinical scientists and clinicians. Access to a database of weighted clinical features extracted from rigorously curated literature would increase the efficiency of this process and facilitate the development of robust phenotypic similarity metrics. However, given the large and rapidly increasing volume of published information, conventional biocuration approaches are becoming impractical. Here, we present a scalable, automated method for the extraction of categorical phenotypic descriptors from the full-text literature. Papers identified through literature review were downloaded and parsed using the Cadmus custom retrieval package. Human Phenotype Ontology terms were extracted using MetaMap, with 76-84% precision and 65-73% recall. Mean terms per paper increased from 9 in title + abstract, to 68 using full text. We demonstrate that these literature-derived disease models plausibly reflect true disease expressivity more accurately than widely used manually curated models, through comparison with prospectively gathered data from the Deciphering Developmental Disorders study. The area under the curve for receiver operating characteristic (ROC) curves increased by 5-10% through the use of literature-derived models. This work shows that scalable automated literature curation increases performance and adds weight to the need for this strategy to be integrated into informatic variant analysis pipelines. Database URL:

De novo missense variants in FBXO11 alter its protein expression and subcellular localization.

Gregor A; Meerbrei T; Gerstner T; Toutain A; Lynch SA; Stals K; Maxton C; Lemke JR; Bernat JA; Bombei HM; Foulds N; Hunt D; Kuechler A; Beygo J; Stöbe P; Bouman A; Palomares-Bralo M; Santos-Simarro F; Garcia-Minaur S; Pacio-Miguez M; Popp B; Vasileiou G; Hebebrand M; Reis A; Schuhmann S; Krumbiegel M; Brown NJ; Sparber P; Melikyan L; Bessonova L; Cherevatova T; Sharkov A; Shcherbakova N; Dabir T; Kini U; Schwaibold EMC; Haack TB; Bertoli M; Hoffjan S; Falb R; Shinawi M; Sticht H; Zweier C

Human molecular genetics 2022;31;3;440-454

Recently, others and we identified de novo FBXO11 (F-Box only protein 11) variants as causative for a variable neurodevelopmental disorder (NDD). We now assembled clinical and mutational information on 23 additional individuals. The phenotypic spectrum remains highly variable, with developmental delay and/or intellectual disability as the core feature and behavioral anomalies, hypotonia and various facial dysmorphism as frequent aspects. The mutational spectrum includes intragenic deletions, likely gene disrupting and missense variants distributed across the protein. To further characterize the functional consequences of FBXO11 missense variants, we analyzed their effects on protein expression and localization by overexpression of 17 different mutant constructs in HEK293 and HeLa cells. We found that the majority of missense variants resulted in subcellular mislocalization and/or reduced FBXO11 protein expression levels. For instance, variants located in the nuclear localization signal and the N-terminal F-Box domain lead to altered subcellular localization with exclusion from the nucleus or the formation of cytoplasmic aggregates and to reduced protein levels in western blot. In contrast, variants localized in the C-terminal Zn-finger UBR domain lead to an accumulation in the cytoplasm without alteration of protein levels. Together with the mutational data, our functional results suggest that most missense variants likely lead to a loss of the original FBXO11 function and thereby highlight haploinsufficiency as the most likely disease mechanism for FBXO11-associated NDDs.

De novo variants in FRMD5 are associated with developmental delay, intellectual disability, ataxia, and abnormalities of eye movement.

Lu S; Ma M; Mao X; Bacino CA; Jankovic J; Sutton VR; Bartley JA; Wang X; Rosenfeld JA; Beleza-Meireles A; Chauhan J; Pan X; Li M; Liu P; Prescott K; Amin S; Davies G; Wangler MF; Dai Y; Bellen HJ

American journal of human genetics 2022;109;10;1932-1943

Proteins containing the FERM (four-point-one, ezrin, radixin, and moesin) domain link the plasma membrane with cytoskeletal structures at specific cellular locations and have been implicated in the localization of cell-membrane-associated proteins and/or phosphoinositides. FERM domain-containing protein 5 (FRMD5) localizes at cell adherens junctions and stabilizes cell-cell contacts. To date, variants in FRMD5 have not been associated with a Mendelian disease in OMIM. Here, we describe eight probands with rare heterozygous missense variants in FRMD5 who present with developmental delay, intellectual disability, ataxia, seizures, and abnormalities of eye movement. The variants are de novo in all for whom parental testing was available (six out of eight probands), and human genetic datasets suggest that FRMD5 is intolerant to loss of function (LoF). We found that the fly ortholog of FRMD5, CG5022 (dFrmd), is expressed in the larval and adult central nervous systems where it is present in neurons but not in glia. dFrmd LoF mutant flies are viable but are extremely sensitive to heat shock, which induces severe seizures. The mutants also exhibit defective responses to light. The human FRMD5 reference (Ref) cDNA rescues the fly dFrmd LoF phenotypes. In contrast, all the FRMD5 variants tested in this study (c.340T>C, c.1051A>G, c.1053C>G, c.1054T>C, c.1045A>C, and c.1637A>G) behave as partial LoF variants. In addition, our results indicate that two variants that were tested have dominant-negative effects. In summary, the evidence supports that the observed variants in FRMD5 cause neurological symptoms in humans.

Estimating the Prevalence of De Novo Monogenic Neurodevelopmental Disorders from Large Cohort Studies.

Gillentine MA; Wang T; Eichler EE

Biomedicines 2022;10;11

Rare diseases impact up to 400 million individuals globally. Of the thousands of known rare diseases, many are rare neurodevelopmental disorders (RNDDs) impacting children. RNDDs have proven to be difficult to assess epidemiologically for several reasons. The rarity of them makes it difficult to observe them in the population, there is clinical overlap among many disorders, making it difficult to assess the prevalence without genetic testing, and data have yet to be available to have accurate counts of cases. Here, we utilized large sequencing cohorts of individuals with rare, de novo monogenic disorders to estimate the prevalence of variation in over 11,000 genes among cohorts with developmental delay, autism spectrum disorder, and/or epilepsy. We found that the prevalence of many RNDDs is positively correlated to the previously estimated incidence. We identified the most often mutated genes among neurodevelopmental disorders broadly, as well as developmental delay and autism spectrum disorder independently. Finally, we assessed if social media group member numbers may be a valuable way to estimate prevalence. These data are critical for individuals and families impacted by these RNDDs, clinicians and geneticists in their understanding of how common diseases are, and for researchers to potentially prioritize research into particular genes or gene sets.

Evaluation of phenotype-driven gene prioritization methods for Mendelian diseases.

Yuan X; Wang J; Dai B; Sun Y; Zhang K; Chen F; Peng Q; Huang Y; Zhang X; Chen J; Xu X; Chuan J; Mu W; Li H; Fang P; Gong Q; Zhang P

Briefings in bioinformatics 2022;23;2

It's challenging work to identify disease-causing genes from the next-generation sequencing (NGS) data of patients with Mendelian disorders. To improve this situation, researchers have developed many phenotype-driven gene prioritization methods using a patient's genotype and phenotype information, or phenotype information only as input to rank the candidate's pathogenic genes. Evaluations of these ranking methods provide practitioners with convenience for choosing an appropriate tool for their workflows, but retrospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate. In this research, the performance of ten recognized causal-gene prioritization methods was benchmarked using 305 cases from the Deciphering Developmental Disorders (DDD) project and 209 in-house cases via a relatively unbiased methodology. The evaluation results show that methods using Human Phenotype Ontology (HPO) terms and Variant Call Format (VCF) files as input achieved better overall performance than those using phenotypic data alone. Besides, LIRICAL and AMELIE, two of the best methods in our benchmark experiments, complement each other in cases with the causal genes ranked highly, suggesting a possible integrative approach to further enhance the diagnostic efficiency. Our benchmarking provides valuable reference information to the computer-assisted rapid diagnosis in Mendelian diseases and sheds some light on the potential direction of future improvement on disease-causing gene prioritization methods.

Exome sequencing efficacy and phenotypic expansions involving esophageal atresia/tracheoesophageal fistula plus.

Sy MR; Chauhan J; Prescott K; Imam A; Kraus A; Beleza A; Salkeld L; Hosdurga S; Parker M; Vasudevan P; Islam L; Goel H; Bain N; Park SM; Mohammed S; Dieterich K; Coutton C; Satre V; Vieville G; Donaldson A; Beneteau C; Ghoumid J; Van Den Bogaert K; Boogaerts A; Boudry E; Vanlerberghe C; Petit F; Bernardini L; Torres B; Mattina T; Carli D; Mandrile G; Pinelli M; Brunetti-Pierri N; Neas K; Beddow R; Tørring PM; Faletra F; Spedicati B; Gasparini P; Mussa A; Ferrero GB; Lampe A; Lam W; Bi W; Bacino CA; Kuwahara A; Bush JO; Zhao X; Luna PN; Shaw CA; Rosenfeld JA; Scott DA

American journal of medical genetics. Part A 2022;188;12;3492-3504

Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a life-threatening birth defect that often occurs with other major birth defects (EA/TEF+). Despite advances in genetic testing, a molecular diagnosis can only be made in a minority of EA/TEF+ cases. Here, we analyzed clinical exome sequencing data and data from the DECIPHER database to determine the efficacy of exome sequencing in cases of EA/TEF+ and to identify phenotypic expansions involving EA/TEF. Among 67 individuals with EA/TEF+ referred for clinical exome sequencing, a definitive or probable diagnosis was made in 11 cases for an efficacy rate of 16% (11/67). This efficacy rate is significantly lower than that reported for other major birth defects, suggesting that polygenic, multifactorial, epigenetic, and/or environmental factors may play a particularly important role in EA/TEF pathogenesis. Our cohort included individuals with pathogenic or likely pathogenic variants that affect TCF4 and its downstream target NRXN1, and FANCA, FANCB, and FANCC, which are associated with Fanconi anemia. These cases, previously published case reports, and comparisons to other EA/TEF genes made using a machine learning algorithm, provide evidence in support of a potential pathogenic role for these genes in the development of EA/TEF.

Expanded cardiovascular phenotype of Myhre syndrome includes tetralogy of Fallot suggesting a role for SMAD4 in human neural crest defects.

Cappuccio G; Brunetti-Pierri N; Clift P; Learn C; Dykes JC; Mercer CL; Callewaert B; Meerschaut I; Spinelli AM; Bruno I; Gillespie MJ; Dorfman AT; Grimberg A; Lindsay ME; Lin AE

American journal of medical genetics. Part A 2022;188;5;1384-1395

Tetralogy of Fallot (ToF) can be associated with a wide range of extracardiac anomalies, with an underlying etiology identified in approximately 10% of cases. Individuals affected with Myhre syndrome due to recurrent SMAD4 mutations frequently have cardiovascular anomalies, including congenital heart defects. In addition to two patients in the literature with ToF, we describe five additional individuals with Myhre syndrome and classic ToF, ToF with pulmonary atresia and multiple aorto-pulmonary collaterals, and ToF with absent pulmonary valve. Aorta hypoplasia was documented in one patient and suspected in another two. In half of these individuals, postoperative cardiac dysfunction was thought to be more severe than classic postoperative ToF repair. There may be an increase in right ventricular pressure, and right ventricular dysfunction due to free pulmonic regurgitation. Noncardiac developmental abnormalities in our series and the literature, including corectopia, heterochromia iridis, and congenital miosis suggest an underlying defect of neural crest cell migration in Myhre syndrome. We advise clinicians that Myhre syndrome should be considered in the genetic evaluation of a child with ToF, short stature, unusual facial features, and developmental delay, as these children may be at risk for increased postoperative morbidity. Additional research is needed to investigate the hypothesis that postoperative hemodynamics in these patients may be consistent with restrictive myocardial physiology.

Expanding the genotype and phenotype spectrum of SYT1-associated neurodevelopmental disorder.

Melland H; Bumbak F; Kolesnik-Taylor A; Ng-Cordell E; John A; Constantinou P; Joss S; Larsen M; Fagerberg C; Laulund LW; Thies J; Emslie F; Willemsen M; Kleefstra T; Pfundt R; Barrick R; Chang R; Loong L; Alfadhel M; van der Smagt J; Nizon M; Kurian MA; Scott DJ; Ziarek JJ; Gordon SL; Baker K

Genetics in medicine : official journal of the American College of Medical Genetics 2022;24;4;880-893

Synaptotagmin-1 (SYT1) is a critical mediator of neurotransmitter release in the central nervous system. Previously reported missense SYT1 variants in the C2B domain are associated with severe intellectual disability, movement disorders, behavioral disturbances, and electroencephalogram abnormalities. In this study, we expand the genotypes and phenotypes and identify discriminating features of this disorder.

Expanding the phenotype of TAB2 variants and literature review.

Woods E; Marson I; Coci E; Spiller M; Kumar A; Brady A; Homfray T; Fisher R; Turnpenny P; Rankin J; Kanani F; Platzer K; Ververi A; Emmanouilidou E; Bourboun N; Giannakoulas G; Balasubramanian M

American journal of medical genetics. Part A 2022;188;11;3331-3342

TAB2 is a gene located on chromosome 6q25.1 and plays a key role in development of the heart. Existing literature describes congenital heart disease as a common recognized phenotype of TAB2 gene variants, with evidence of a distinct syndromic phenotype also existing beyond this. Here we describe 14 newly identified individuals with nine novel, pathogenic TAB2 variants. The majority of individuals were identified through the Deciphering Developmental Disorders study through trio whole exome sequencing. Eight individuals had de novo variants, the other six individuals were found to have maternally inherited, or likely maternally inherited, variants. Five individuals from the same family were identified following cardiac disease gene panel in the proband and subsequent targeted familial gene sequencing. The clinical features of this cohort were compared to the existing literature. Common clinical features include distinctive facial features, growth abnormalities, joint hypermobility, hypotonia, and developmental delay. Newly identified features included feeding difficulties, sleep problems, visual problems, genitourinary abnormality, and other anatomical variations. Here we report 14 new individuals, including novel TAB2 variants, in order to expand the emerging syndromic clinical phenotype and provide further genotype-phenotype correlation.

Further delineation of phenotypic spectrum of SCN2A-related disorder.

Richardson R; Baralle D; Bennett C; Briggs T; Bijlsma EK; Clayton-Smith J; Constantinou P; Foulds N; Jarvis J; Jewell R; Johnson DS; McEntagart M; Parker MJ; Radley JA; Robertson L; Ruivenkamp C; Rutten JW; Tellez J; Turnpenny PD; Wilson V; Wright M; Balasubramanian M

American journal of medical genetics. Part A 2022;188;3;867-877

SCN2A-related disorders include intellectual disability, autism spectrum disorder, seizures, episodic ataxia, and schizophrenia. In this study, the phenotype-genotype association in SCN2A-related disorders was further delineated by collecting detailed clinical and molecular characteristics. Using previously proposed genotype-phenotype hypotheses based on variant function and position, the potential of phenotype prediction from the variants found was examined. Patients were identified through the Deciphering Developmental Disorders study and gene matching strategies. Phenotypic information and variant interpretation evidence were collated. Seventeen previously unreported patients and five patients who had been previously reported (but with minimal phenotypic and segregation data) were included (10 males, 12 females; median age 10.5 years). All patients had developmental delays and the majority had intellectual disabilities. Seizures were reported in 15 of 22 (68.2%), four of 22 (18.2%) had autism spectrum disorder and no patients were reported with episodic ataxia. The majority of variants were de novo. One family had presumed gonadal mosaicism. The correlation of the use of sodium channel-blocking antiepileptic drugs with phenotype or genotype was variable. These data suggest that variant type and position alone can provide some predictive information about the phenotype in a proportion of cases, but more precise assessment of variant function is needed for meaningful phenotype prediction.

Gain-of-function mutations in KCNK3 cause a developmental disorder with sleep apnea.

Sörmann J; Schewe M; Proks P; Jouen-Tachoire T; Rao S; Riel EB; Agre KE; Begtrup A; Dean J; Descartes M; Fischer J; Gardham A; Lahner C; Mark PR; Muppidi S; Pichurin PN; Porrmann J; Schallner J; Smith K; Straub V; Vasudevan P; Willaert R; Carpenter EP; Rödström KEJ; Hahn MG; Müller T; Baukrowitz T; Hurles ME; Wright CF; Tucker SJ

Nature Genetics 2022;54;10;1534-1543

Sleep apnea is a common disorder that represents a global public health burden. KCNK3 encodes TASK-1, a K+ channel implicated in the control of breathing, but its link with sleep apnea remains poorly understood. Here we describe a new developmental disorder with associated sleep apnea (developmental delay with sleep apnea, or DDSA) caused by rare de novo gain-of-function mutations in KCNK3. The mutations cluster around the 'X-gate', a gating motif that controls channel opening, and produce overactive channels that no longer respond to inhibition by G-protein-coupled receptor pathways. However, despite their defective X-gating, these mutant channels can still be inhibited by a range of known TASK channel inhibitors. These results not only highlight an important new role for TASK-1 K+ channels and their link with sleep apnea but also identify possible therapeutic strategies.

Genetic and chemotherapeutic influences on germline hypermutation.

Kaplanis J; Ide B; Sanghvi R; Neville M; Danecek P; Coorens T; Prigmore E; Short P; Gallone G; McRae J; ; Carmichael J; Barnicoat A; Firth H; O'Brien P; Rahbari R; Hurles M

Nature 2022;605;7910;503-508

Mutations in the germline generates all evolutionary genetic variation and is a cause of genetic disease. Parental age is the primary determinant of the number of new germline mutations in an individual's genome1,2. Here we analysed the genome-wide sequences of 21,879 families with rare genetic diseases and identified 12 individuals with a hypermutated genome with between two and seven times more de novo single-nucleotide variants than expected. In most families (9 out of 12), the excess mutations came from the father. Two families had genetic drivers of germline hypermutation, with fathers carrying damaging genetic variation in DNA-repair genes. For five of the families, paternal exposure to chemotherapeutic agents before conception was probably a key driver of hypermutation. Our results suggest that the germline is well protected from mutagenic effects, hypermutation is rare, the number of excess mutations is relatively modest and most individuals with a hypermutated genome will not have a genetic disease.

Heterozygous variants in ZBTB7A cause a neurodevelopmental disorder associated with symptomatic overgrowth of pharyngeal lymphoid tissue, macrocephaly, and elevated fetal hemoglobin.

von der Lippe C; Tveten K; Prescott TE; Holla ØL; Busk ØL; Burke KB; Sansbury FH; Baptista J; Fry AE; Lim D; Jolles S; Evans J; Osio D; Macmillan C; Bruno I; Faletra F; Climent S; Urreitzi R; Hoenicka J; Palau F; Cohen ASA; Engleman K; Zhou D; Amudhavalli SM; Jeanne M; Bonnet-Brilhault F; Lévy J; Drunat S; Derive N; Haug MG; Thorstensen WM

American journal of medical genetics. Part A 2022;188;1;272-282

By clinical whole exome sequencing, we identified 12 individuals with ages 3 to 37 years, including three individuals from the same family, with a consistent phenotype of intellectual disability (ID), macrocephaly, and overgrowth of adenoid tissue. All 12 individuals harbored a rare heterozygous variant in ZBTB7A which encodes the transcription factor Zinc finger and BTB-domain containing protein 7A, known to play a role in lympho- and hematopoiesis. ID was generally mild. Fetal hemoglobin (HbF) fraction was elevated 2.2%-11.2% (reference value <2% in individuals > 6 months) in four of the five individuals for whom results were available. Ten of twelve individuals had undergone surgery at least once for lymphoid hypertrophy limited to the pharynx. In the most severely affected individual (individual 1), airway obstruction resulted in 17 surgical procedures before the age of 13 years. Sleep apnea was present in 8 of 10 individuals. In the nine unrelated individuals, ZBTB7A variants were novel and de novo. The six frameshift/nonsense and four missense variants were spread throughout the gene. This is the first report of a cohort of individuals with this novel syndromic neurodevelopmental disorder.

Integrated gene analyses of de novo variants from 46,612 trios with autism and developmental disorders.

Wang T; Kim CN; Bakken TE; Gillentine MA; Henning B; Mao Y; Gilissen C; ; Nowakowski TJ; Eichler EE

Proceedings of the National Academy of Sciences of the United States of America 2022;119;46;e2203491119

Most genetic studies consider autism spectrum disorder (ASD) and developmental disorder (DD) separately despite overwhelming comorbidity and shared genetic etiology. Here, we analyzed de novo variants (DNVs) from 15,560 ASD (6,557 from SPARK) and 31,052 DD trios independently and also combined as broader neurodevelopmental disorders (NDDs) using three models. We identify 615 NDD candidate genes (false discovery rate [FDR] < 0.05) supported by ≥1 models, including 138 reaching Bonferroni exome-wide significance (P < 3.64e-7) in all models. The genes group into five functional networks associating with different brain developmental lineages based on single-cell nuclei transcriptomic data. We find no evidence for ASD-specific genes in contrast to 18 genes significantly enriched for DD. There are 53 genes that show mutational bias, including enrichments for missense (n = 41) or truncating (n = 12) DNVs. We also find 10 genes with evidence of male- or female-bias enrichment, including 4 X chromosome genes with significant female burden (DDX3X, MECP2, WDR45, and HDAC8). This large-scale integrative analysis identifies candidates and functional subsets of NDD genes.

MED27, SLC6A7, and MPPE1 Variants in a Complex Neurodevelopmental Disorder with Severe Dystonia.

Reid KM; Spaull R; Salian S; Barwick K; Meyer E; Zhen J; Hirata H; Sheipouri D; Benkerroum H; Gorman KM; Papandreou A; Simpson MA; Hirano Y; Farabella I; Topf M; Grozeva D; Carss K; Smith M; Pall H; Lunt P; De Gressi S; Kamsteeg EJ; Haack TB; Carr L; Guerreiro R; Bras J; Maher ER; Scott RH; Vandenberg RJ; Raymond FL; Chong WK; Sudhakar S; Mankad K; Reith ME; Campeau PM; Harvey RJ; Kurian MA

Movement disorders : official journal of the Movement Disorder Society 2022;37;10;2139-2146

Despite advances in next generation sequencing technologies, the identification of variants of uncertain significance (VUS) can often hinder definitive diagnosis in patients with complex neurodevelopmental disorders.

Missense variants in ANKRD11 cause KBG syndrome by impairment of stability or transcriptional activity of the encoded protein.

de Boer E; Ockeloen CW; Kampen RA; Hampstead JE; Dingemans AJM; Rots D; Lütje L; Ashraf T; Baker R; Barat-Houari M; Angle B; Chatron N; Denommé-Pichon AS; Devinsky O; Dubourg C; Elmslie F; Elloumi HZ; Faivre L; Fitzgerald-Butt S; Geneviève D; Goos JAC; Helm BM; Kini U; Lasa-Aranzasti A; Lesca G; Lynch SA; Mathijssen IMJ; McGowan R; Monaghan KG; Odent S; Pfundt R; Putoux A; van Reeuwijk J; Santen GWE; Sasaki E; Sorlin A; van der Spek PJ; Stegmann APA; Swagemakers SMA; Valenzuela I; Viora-Dupont E; Vitobello A; Ware SM; Wéber M; Gilissen C; Low KJ; Fisher SE; Vissers LELM; Wong MMK; Kleefstra T

Genetics in medicine : official journal of the American College of Medical Genetics 2022;24;10;2051-2064

Although haploinsufficiency of ANKRD11 is among the most common genetic causes of neurodevelopmental disorders, the role of rare ANKRD11 missense variation remains unclear. We characterized clinical, molecular, and functional spectra of ANKRD11 missense variants.

Monogenic disorders as mimics of juvenile idiopathic arthritis.

Furness L; Riley P; Wright N; Banka S; Eyre S; Jackson A; Briggs TA

Pediatric rheumatology online journal 2022;20;1;44

Juvenile idiopathic arthritis is the most common chronic rheumatic disease of childhood. The term JIA encompasses a heterogenous group of diseases. The variability in phenotype of patients affected by the disease means it is not uncommon for mimics of JIA to be misdiagnosed.

Phenotypic and genetic spectrum of ATP6V1A encephalopathy: a disorder of lysosomal homeostasis.

Guerrini R; Mei D; Kerti-Szigeti K; Pepe S; Koenig MK; Von Allmen G; Cho MT; McDonald K; Baker J; Bhambhani V; Powis Z; Rodan L; Nabbout R; Barcia G; Rosenfeld JA; Bacino CA; Mignot C; Power LH; Harris CJ; Marjanovic D; Møller RS; Hammer TB; ; Keski Filppula R; Vieira P; Hildebrandt C; Sacharow S; ; Maragliano L; Benfenati F; Lachlan K; Benneche A; Petit F; de Sainte Agathe JM; Hallinan B; Si Y; Wentzensen IM; Zou F; Narayanan V; Matsumoto N; Boncristiano A; la Marca G; Kato M; Anderson K; Barba C; Sturiale L; Garozzo D; Bei R; ; Masuelli L; Conti V; Novarino G; Fassio A

Brain : a journal of neurology 2022;145;8;2687-2703

Vacuolar-type H+-ATPase (V-ATPase) is a multimeric complex present in a variety of cellular membranes that acts as an ATP-dependent proton pump and plays a key role in pH homeostasis and intracellular signalling pathways. In humans, 22 autosomal genes encode for a redundant set of subunits allowing the composition of diverse V-ATPase complexes with specific properties and expression. Sixteen subunits have been linked to human disease. Here we describe 26 patients harbouring 20 distinct pathogenic de novo missense ATP6V1A variants, mainly clustering within the ATP synthase α/β family-nucleotide-binding domain. At a mean age of 7 years (extremes: 6 weeks, youngest deceased patient to 22 years, oldest patient) clinical pictures included early lethal encephalopathies with rapidly progressive massive brain atrophy, severe developmental epileptic encephalopathies and static intellectual disability with epilepsy. The first clinical manifestation was early hypotonia, in 70%; 81% developed epilepsy, manifested as developmental epileptic encephalopathies in 58% of the cohort and with infantile spasms in 62%; 63% of developmental epileptic encephalopathies failed to achieve any developmental, communicative or motor skills. Less severe outcomes were observed in 23% of patients who, at a mean age of 10 years and 6 months, exhibited moderate intellectual disability, with independent walking and variable epilepsy. None of the patients developed communicative language. Microcephaly (38%) and amelogenesis imperfecta/enamel dysplasia (42%) were additional clinical features. Brain MRI demonstrated hypomyelination and generalized atrophy in 68%. Atrophy was progressive in all eight individuals undergoing repeated MRIs. Fibroblasts of two patients with developmental epileptic encephalopathies showed decreased LAMP1 expression, Lysotracker staining and increased organelle pH, consistent with lysosomal impairment and loss of V-ATPase function. Fibroblasts of two patients with milder disease, exhibited a different phenotype with increased Lysotracker staining, decreased organelle pH and no significant modification in LAMP1 expression. Quantification of substrates for lysosomal enzymes in cellular extracts from four patients revealed discrete accumulation. Transmission electron microscopy of fibroblasts of four patients with variable severity and of induced pluripotent stem cell-derived neurons from two patients with developmental epileptic encephalopathies showed electron-dense inclusions, lipid droplets, osmiophilic material and lamellated membrane structures resembling phospholipids. Quantitative assessment in induced pluripotent stem cell-derived neurons identified significantly smaller lysosomes. ATP6V1A-related encephalopathy represents a new paradigm among lysosomal disorders. It results from a dysfunctional endo-lysosomal membrane protein causing altered pH homeostasis. Its pathophysiology implies intracellular accumulation of substrates whose composition remains unclear, and a combination of developmental brain abnormalities and neurodegenerative changes established during prenatal and early postanal development, whose severity is variably determined by specific pathogenic variants.

Recurrent de novo missense variants in GNB2 can cause syndromic intellectual disability.

Tan NB; Pagnamenta AT; Ferla MP; Gadian J; Chung BH; Chan MC; Fung JL; Cook E; Guter S; Boschann F; Heinen A; Schallner J; Mignot C; Keren B; Whalen S; Sarret C; Mittag D; Demmer L; Stapleton R; Saida K; Matsumoto N; Miyake N; Sheffer R; Mor-Shaked H; Barnett CP; Byrne AB; Scott HS; Kraus A; Cappuccio G; Brunetti-Pierri N; Iorio R; Di Dato F; Pais LS; Yeung A; Tan TY; Taylor JC; Christodoulou J; White SM

Journal of medical genetics 2022;59;5;511-516

Binding proteins (G-proteins) mediate signalling pathways involved in diverse cellular functions and comprise Gα and Gβγ units. Human diseases have been reported for all five Gβ proteins. A de novo missense variant in GNB2 was recently reported in one individual with developmental delay/intellectual disability (DD/ID) and dysmorphism. We aim to confirm GNB2 as a neurodevelopmental disease gene, and elucidate the GNB2-associated neurodevelopmental phenotype in a patient cohort.

Recurrent de novo missense variants across multiple histone H4 genes underlie a neurodevelopmental syndrome.

Tessadori F; Duran K; Knapp K; Fellner M; ; Smithson S; Beleza Meireles A; Elting MW; Waisfisz Q; O'Donnell-Luria A; Nowak C; Douglas J; Ronan A; Brunet T; Kotzaeridou U; Svihovec S; Saenz MS; Thiffault I; Del Viso F; Devine P; Rego S; Tenney J; van Haeringen A; Ruivenkamp CAL; Koene S; Robertson SP; Deshpande C; Pfundt R; Verbeek N; van de Kamp JM; Weiss JMM; Ruiz A; Gabau E; Banne E; Pepler A; Bottani A; Laurent S; Guipponi M; Bijlsma E; Bruel AL; Sorlin A; Willis M; Powis Z; Smol T; Vincent-Delorme C; Baralle D; Colin E; Revencu N; Calpena E; Wilkie AOM; Chopra M; Cormier-Daire V; Keren B; Afenjar A; Niceta M; Terracciano A; Specchio N; Tartaglia M; Rio M; Barcia G; Rondeau S; Colson C; Bakkers J; Mace PD; Bicknell LS; van Haaften G

American journal of human genetics 2022;109;4;750-758

Chromatin is essentially an array of nucleosomes, each of which consists of the DNA double-stranded fiber wrapped around a histone octamer. This organization supports cellular processes such as DNA replication, DNA transcription, and DNA repair in all eukaryotes. Human histone H4 is encoded by fourteen canonical histone H4 genes, all differing at the nucleotide level but encoding an invariant protein. Here, we present a cohort of 29 subjects with de novo missense variants in six H4 genes (H4C3, H4C4, H4C5, H4C6, H4C9, and H4C11) identified by whole-exome sequencing and matchmaking. All individuals present with neurodevelopmental features of intellectual disability and motor and/or gross developmental delay, while non-neurological features are more variable. Ten amino acids are affected, six recurrently, and are all located within the H4 core or C-terminal tail. These variants cluster to specific regions of the core H4 globular domain, where protein-protein interactions occur with either other histone subunits or histone chaperones. Functional consequences of the identified variants were evaluated in zebrafish embryos, which displayed abnormal general development, defective head organs, and reduced body axis length, providing compelling evidence for the causality of the reported disorder(s). While multiple developmental syndromes have been linked to chromatin-associated factors, missense-bearing histone variants (e.g., H3 oncohistones) are only recently emerging as a major cause of pathogenicity. Our findings establish a broader involvement of H4 variants in developmental syndromes.

Report of two children with global developmental delay in association with de novo TLK2 variant and literature review.

Woods E; Spiller M; Balasubramanian M

American journal of medical genetics. Part A 2022;188;3;931-940

We describe clinical details, including novel findings, of two further children with the newly defined TLK2-related disorder. One patient was recruited to the Deciphering Developmental Delay (DDD) Study to identify underlying etiology of global developmental delay. The other was detected on whole-exome sequencing as part of second line investigations following normal microarray. Both patients were found to have de novo heterozygous pathogenic TLK2 variants. A novel c.6del p.(Glu3Lysfs*) loss-of-function frameshift variant was found in Patient 1. A c.1121+1G>A splice-donor variant was detected in Patient 2. TLK2-related neurodevelopmental disorder is a specific syndrome that has been recently described. Global developmental delay, behavioral problems, gastrointestinal disorders, and typical facial dysmorphism are common features. Neuropsychiatric disorders, ophthalmic, musculoskeletal and cranial abnormalities, as well as short stature, have also all been described. The novel findings we describe include sleep disturbance, nondifferentiation of lateral semi-circular canals (where asymmetric semi-circular canals were a feature in the previous cohort), vesico-ureteric reflux, and bilateral periauricular skin tags. Here, we report a novel TLK2 variant and previously undescribed features of TLK2-related disorder, to expand the clinical phenotype and provide further genotype-phenotype correlation.

Structural mapping of GABRB3 variants reveals genotype-phenotype correlations.

Johannesen KM; Iqbal S; Guazzi M; Mohammadi NA; Pérez-Palma E; Schaefer E; De Saint Martin A; Abiwarde MT; McTague A; Pons R; Piton A; Kurian MA; Ambegaonkar G; Firth H; Sanchis-Juan A; Deprez M; Jansen K; De Waele L; Briltra EH; Verbeek NE; van Kempen M; Fazeli W; Striano P; Zara F; Visser G; Braakman HMH; Haeusler M; Elbracht M; Vaher U; Smol T; Lemke JR; Platzer K; Kennedy J; Klein KM; Au PYB; Smyth K; Kaplan J; Thomas M; Dewenter MK; Dinopoulos A; Campbell AJ; Lal D; Lederer D; Liao VWY; Ahring PK; Møller RS; Gardella E

Genetics in medicine : official journal of the American College of Medical Genetics 2022;24;3;681-693

Pathogenic variants in GABRB3 have been associated with a spectrum of phenotypes from severe developmental disorders and epileptic encephalopathies to milder epilepsy syndromes and mild intellectual disability (ID). In this study, we analyzed a large cohort of individuals with GABRB3 variants to deepen the phenotypic understanding and investigate genotype-phenotype correlations.

The Phenotypic Continuum of ATP1A3-Related Disorders.

Vezyroglou A; Akilapa R; Barwick K; Koene S; Brownstein CA; Holder-Espinasse M; Fry AE; Németh AH; Tofaris GK; Hay E; Hughes I; Mansour S; Mordekar SR; Splitt M; Turnpenny PD; Demetriou D; Koopmann TT; Ruivenkamp CAL; Agrawal PB; Carr L; Clowes V; Ghali N; Holder SE; Radley J; Male A; Sisodiya SM; Kurian MA; Cross JH; Balasubramanian M

Neurology 2022;99;14;e1511-e1526

ATP1A3 is associated with a broad spectrum of predominantly neurologic disorders, which continues to expand beyond the initially defined phenotypes of alternating hemiplegia of childhood, rapid-onset dystonia parkinsonism, and cerebellar ataxia, areflexia, pes cavus, optic atrophy, sensorineural hearing loss syndrome. This phenotypic variability makes it challenging to assess the pathogenicity of an ATP1A3 variant found in an undiagnosed patient. We describe the phenotypic features of individuals carrying a pathogenic/likely pathogenic ATP1A3 variant and perform a literature review of all ATP1A3 variants published thus far in association with human neurologic disease. Our aim is to demonstrate the heterogeneous clinical spectrum of the gene and look for phenotypic overlap between patients that will streamline the diagnostic process.

Traboulsi syndrome caused by mutations in ASPH: An autosomal recessive disorder with overlapping features of Marfan syndrome.

Jones G; Johnson K; Eason J; Hamilton M; Osio D; Kanani F; Baptista J; Suri M

European journal of medical genetics 2022;65;10;104572

Traboulsi syndrome, otherwise known as facial dysmorphism, lens dislocation, anterior-segment abnormalities and spontaneous filtering blebs, is an autosomal recessive condition associated with characteristic ocular features including dislocated crystalline lenses, anterior segment abnormalities and in some individuals, non-traumatic conjunctival cysts. There is a distinctive facial appearance which includes flattened malar region with convex nasal ridge. Alterations in the aspartate beta-hydroxylase (ASPH) gene are known to be the cause of the condition. We report seven further individuals from six unrelated families with characteristic ocular and facial features. Five individuals had aortic root dilatation, with childhood onset in some, and one undergoing aortic root repair aged 47 years for severe aortic regurgitation and aortic root dilatation. Interestingly, inguinal hernias were commonly reported. Although some skeletal features were seen, these were not consistent. One of the patients had mild deficiency of factor VII on clotting studies. The ASPH protein hydroxylates specific asparagine- and aspartate-residues in epidermal growth factor (EGF)-domain containing proteins including coagulation factors and associated genes including FBN1. We propose this as an explanation for the overlap in clinical features with Marfan syndrome and conclude that Traboulsi syndrome is an important differential diagnosis. We strongly recommend echocardiography surveillance for patients with Traboulsi syndrome.

TRAPPC11-related muscular dystrophy with hypoglycosylation of alpha-dystroglycan in skeletal muscle and brain.

Munot P; McCrea N; Torelli S; Manzur A; Sewry C; Chambers D; Feng L; Ala P; Zaharieva I; Ragge N; Roper H; Marton T; Cox P; Milev MP; Liang WC; Maruyama S; Nishino I; Sacher M; Phadke R; Muntoni F

Neuropathology and applied neurobiology 2022;48;2;e12771

TRAPPC11, a subunit of the transport protein particle (TRAPP) complex, is important for complex integrity and anterograde membrane transport from the endoplasmic reticulum (ER) to the ER-Golgi intermediate compartment. Several individuals with TRAPPC11 mutations have been reported with muscle weakness and other features including brain, liver, skeletal and eye involvement. A detailed analysis of brain and muscle pathology will further our understanding of the presentation and aetiology of TRAPPC11 disease.

Variants in PHF8 cause a spectrum of X-linked neurodevelopmental disorders and facial dysmorphology.

Sobering AK; Bryant LM; Li D; McGaughran J; Maystadt I; Moortgat S; Graham JM; van Haeringen A; Ruivenkamp C; Cuperus R; Vogt J; Morton J; Brasch-Andersen C; Steenhof M; Hansen LK; Adler É; Lyonnet S; Pingault V; Sandrine M; Ziegler A; Donald T; Nelson B; Holt B; Petryna O; Firth H; McWalter K; Zyskind J; Telegrafi A; Juusola J; Person R; Bamshad MJ; Earl D; ; Tsai AC; Yearwood KR; Marco E; Nowak C; Douglas J; Hakonarson H; Bhoj EJ

HGG advances 2022;3;3;100102

Loss-of-function variants in PHD Finger Protein 8 (PHF8) cause Siderius X-linked intellectual disability (ID) syndrome, hereafter called PHF8-XLID. PHF8 is a histone demethylase that is important for epigenetic regulation of gene expression. PHF8-XLID is an under-characterized disorder with only five previous reports describing different PHF8 predicted loss-of-function variants in eight individuals. Features of PHF8-XLID include ID and craniofacial dysmorphology. In this report we present 16 additional individuals with PHF8-XLID from 11 different families of diverse ancestry. We also present five individuals from four different families who have ID and a variant of unknown significance in PHF8 with no other explanatory variant in another gene. All affected individuals exhibited developmental delay and all but two had borderline to severe ID. Of the two who did not have ID, one had dyscalculia and the other had mild learning difficulties. Craniofacial findings such as hypertelorism, microcephaly, elongated face, ptosis, and mild facial asymmetry were found in some affected individuals. Orofacial clefting was seen in three individuals from our cohort, suggesting that this feature is less common than previously reported. Autism spectrum disorder and attention deficit hyperactivity disorder, which were not previously emphasized in PHF8-XLID, were frequently observed in affected individuals. This series expands the clinical phenotype of this rare ID syndrome caused by loss of PHF8 function.

AHDC1 missense mutations in Xia-Gibbs syndrome.

Khayat MM; Hu J; Jiang Y; Li H; Chander V; Dawood M; Hansen AW; Li S; Friedman J; Cross L; Bijlsma EK; Ruivenkamp CAL; Sansbury FH; Innis JW; O'Shea JO; Meng Q; Rosenfeld JA; McWalter K; Wangler MF; Lupski JR; Posey JE; Murdock D; Gibbs RA

HGG advances 2021;2;4

Xia-Gibbs syndrome (XGS; MIM: 615829) is a phenotypically heterogeneous neurodevelopmental disorder (NDD) caused by newly arising mutations in the AT-Hook DNA-Binding Motif-Containing 1 (AHDC1) gene that are predicted to lead to truncated AHDC1 protein synthesis. More than 270 individuals have been diagnosed with XGS worldwide. Despite the absence of an independent assay for AHDC1 protein function to corroborate potential functional consequences of rare variant genetic findings, there are also reports of individuals with XGS-like trait manifestations who have de novo missense AHDC1 mutations and who have been provided a molecular diagnosis of the disorder. To investigate a potential contribution of missense mutations to XGS, we mapped the missense mutations from 10 such individuals to the AHDC1 conserved protein domain structure and detailed the observed phenotypes. Five newly identified individuals were ascertained from a local XGS Registry, and an additional five were taken from external reports or databases, including one publication. Where clinical data were available, individuals with missense mutations all displayed phenotypes consistent with those observed in individuals with AHDC1 truncating mutations, including delayed motor milestones, intellectual disability (ID), hypotonia, and speech delay. A subset of the 10 reported missense mutations cluster in two regions of the AHDC1 protein with known conserved domains, likely representing functional motifs. Variants outside the clustered regions score lower for computational prediction of their likely damaging effects. Overall, de novo missense variants in AHDC1 are likely diagnostic of XGS when in silico analysis of their position relative to conserved regions is considered together with disease trait manifestations.

PTPN4 germline variants result in aberrant neurodevelopment and growth.

Chmielewska JJ; Burkardt D; Granadillo JL; Slaugh R; Morgan S; Rotenberg J; Keren B; Mignot C; Escobar L; Turnpenny P; Zuteck M; Seaver LH; Ploski R; Dziembowska M; Wynshaw-Boris A; Adegbola A

HGG advances 2021;2;3

Protein-tyrosine phosphatases (PTPs) are pleomorphic regulators of eukaryotic cellular responses to extracellular signals that function by modulating the phosphotyrosine of specific proteins. A handful of PTPs have been implicated in germline and somatic human disease. Using exome sequencing, we identified missense and truncating variants in PTPN4 in six unrelated individuals with varying degrees of intellectual disability or developmental delay. The variants occurred de novo in all five subjects in whom segregation analysis was possible. Recurring features include postnatal growth deficiency or excess, seizures, and, less commonly, structural CNS, heart, or skeletal anomalies. PTPN4 is a widely expressed protein tyrosine phosphatase that regulates neuronal cell homeostasis by protecting neurons against apoptosis. We suggest that pathogenic variants in PTPN4 confer risk for growth and cognitive abnormalities in humans.

ALG13 X-linked intellectual disability: New variants, glycosylation analysis, and expanded phenotypes.

Alsharhan H; He M; Edmondson AC; Daniel EJP; Chen J; Donald T; Bakhtiari S; Amor DJ; Jones EA; Vassallo G; Vincent M; Cogné B; Deb W; Werners AH; Jin SC; Bilguvar K; Christodoulou J; Webster RI; Yearwood KR; Ng BG; Freeze HH; Kruer MC; Li D; Raymond KM; Bhoj EJ; Sobering AK

Journal of inherited metabolic disease 2021;44;4;1001-1012

Pathogenic variants in ALG13 (ALG13 UDP-N-acetylglucosaminyltransferase subunit) cause an X-linked congenital disorder of glycosylation (ALG13-CDG) where individuals have variable clinical phenotypes that include developmental delay, intellectual disability, infantile spasms, and epileptic encephalopathy. Girls with a recurrent de novo c.3013C>T; p.(Asn107Ser) variant have normal transferrin glycosylation. Using a highly sensitive, semi-quantitative flow injection-electrospray ionization-quadrupole time-of-flight mass spectrometry (ESI-QTOF/MS) N-glycan assay, we report subtle abnormalities in N-glycans that normally account for <0.3% of the total plasma glycans that may increase up to 0.5% in females with the p.(Asn107Ser) variant. Among our 11 unrelated ALG13-CDG individuals, one male had abnormal serum transferrin glycosylation. We describe seven previously unreported subjects including three novel variants in ALG13 and report a milder neurodevelopmental course. We also summarize the molecular, biochemical, and clinical data for the 53 previously reported ALG13-CDG individuals. We provide evidence that ALG13 pathogenic variants may mildly alter N-linked protein glycosylation in both female and male subjects, but the underlying mechanism remains unclear.

Assessing performance of pathogenicity predictors using clinically relevant variant datasets.

Gunning AC; Fryer V; Fasham J; Crosby AH; Ellard S; Baple EL; Wright CF

Journal of medical genetics 2021;58;8;547-555

Pathogenicity predictors are integral to genomic variant interpretation but, despite their widespread usage, an independent validation of performance using a clinically relevant dataset has not been undertaken.

BDV Syndrome: An Emerging Syndrome With Profound Obesity and Neurodevelopmental Delay Resembling Prader-Willi Syndrome.

Bosch E; Hebebrand M; Popp B; Penger T; Behring B; Cox H; Towner S; Kraus C; Wilson WG; Khan S; Krumbiegel M; Ekici AB; Uebe S; Trollmann R; Woelfle J; Reis A; Vasileiou G

The Journal of clinical endocrinology and metabolism 2021;106;12;3413-3427

CPE encodes carboxypeptidase E, an enzyme that converts proneuropeptides and propeptide hormones to bioactive forms. It is widely expressed in the endocrine and central nervous system. To date, 4 individuals from 2 families with core clinical features including morbid obesity, neurodevelopmental delay, and hypogonadotropic hypogonadism, harboring biallelic loss-of-function (LoF) CPE variants, have been reported.

Clinical delineation, sex differences, and genotype-phenotype correlation in pathogenic KDM6A variants causing X-linked Kabuki syndrome type 2.

Faundes V; Goh S; Akilapa R; Bezuidenhout H; Bjornsson HT; Bradley L; Brady AF; Brischoux-Boucher E; Brunner H; Bulk S; Canham N; Cody D; Dentici ML; Digilio MC; Elmslie F; Fry AE; Gill H; Hurst J; Johnson D; Julia S; Lachlan K; Lebel RR; Byler M; Gershon E; Lemire E; Gnazzo M; Lepri FR; Marchese A; McEntagart M; McGaughran J; Mizuno S; Okamoto N; Rieubland C; Rodgers J; Sasaki E; Scalais E; Scurr I; Suri M; van der Burgt I; Matsumoto N; Miyake N; Benoit V; Lederer D; Banka S

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;7;1202-1210

The variant spectrum and the phenotype of X-linked Kabuki syndrome type 2 (KS2) are poorly understood.

Comprehensive study of 28 individuals with SIN3A-related disorder underscoring the associated mild cognitive and distinctive facial phenotype.

Balasubramanian M; Dingemans AJM; Albaba S; Richardson R; Yates TM; Cox H; Douzgou S; Armstrong R; Sansbury FH; Burke KB; Fry AE; Ragge N; Sharif S; Foster A; De Sandre-Giovannoli A; Elouej S; Vasudevan P; Mansour S; Wilson K; Stewart H; Heide S; Nava C; Keren B; Demirdas S; Brooks AS; Vincent M; Isidor B; Küry S; Schouten M; Leenders E; Chung WK; Haeringen AV; Scheffner T; Debray FG; White SM; Palafoll MIV; Pfundt R; Newbury-Ecob R; Kleefstra T

European journal of human genetics : EJHG 2021;29;4;625-636

Witteveen-Kolk syndrome (OMIM 613406) is a recently defined neurodevelopmental syndrome caused by heterozygous loss-of-function variants in SIN3A. We define the clinical and neurodevelopmental phenotypes related to SIN3A-haploinsufficiency in 28 unreported patients. Patients with SIN3A variants adversely affecting protein function have mild intellectual disability, growth and feeding difficulties. Involvement of a multidisciplinary team including a geneticist, paediatrician and neurologist should be considered in managing these patients. Patients described here were identified through a combination of clinical evaluation and gene matching strategies (GeneMatcher and Decipher). All patients consented to participate in this study. Mean age of this cohort was 8.2 years (17 males, 11 females). Out of 16 patients ≥ 8 years old assessed, eight (50%) had mild intellectual disability (ID), four had moderate ID (22%), and one had severe ID (6%). Four (25%) did not have any cognitive impairment. Other neurological symptoms such as seizures (4/28) and hypotonia (12/28) were common. Behaviour problems were reported in a minority. In patients ≥2 years, three were diagnosed with Autism Spectrum Disorder (ASD) and four with Attention Deficit Hyperactivity Disorder (ADHD). We report 27 novel variants and one previously reported variant. 24 were truncating variants; three were missense variants and one large in-frame gain including exons 10-12.

Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood.

Levy MA; Beck DB; Metcalfe K; Douzgou S; Sithambaram S; Cottrell T; Ansar M; Kerkhof J; Mignot C; Nougues MC; Keren B; Moore HW; Oegema R; Giltay JC; Simon M; van Jaarsveld RH; Bos J; van Haelst M; Motazacker MM; Boon EMJ; Santen GWE; Ruivenkamp CAL; Alders M; Luperchio TR; Boukas L; Ramsey K; Narayanan V; Schaefer GB; Bonasio R; Doheny KF; Stevenson RE; Banka S; Sadikovic B; Fahrner JA

NPJ genomic medicine 2021;6;1;92

TET3 encodes an essential dioxygenase involved in epigenetic regulation through DNA demethylation. TET3 deficiency, or Beck-Fahrner syndrome (BEFAHRS; MIM: 618798), is a recently described neurodevelopmental disorder of the DNA demethylation machinery with a nonspecific phenotype resembling other chromatin-modifying disorders, but inconsistent variant types and inheritance patterns pose diagnostic challenges. Given TET3's direct role in regulating 5-methylcytosine and recent identification of syndrome-specific DNA methylation profiles, we analyzed genome-wide DNA methylation in whole blood of TET3-deficient individuals and identified an episignature that distinguishes affected and unaffected individuals and those with mono-allelic and bi-allelic pathogenic variants. Validation and testing of the episignature correctly categorized known TET3 variants and determined pathogenicity of variants of uncertain significance. Clinical utility was demonstrated when the episignature alone identified an affected individual from over 1000 undiagnosed cases and was confirmed upon distinguishing TET3-deficient individuals from those with 46 other disorders. The TET3-deficient signature - and the signature resulting from activating mutations in DNMT1 which normally opposes TET3 - are characterized by hypermethylation, which for BEFAHRS involves CpG sites that may be biologically relevant. This work expands the role of epi-phenotyping in molecular diagnosis and reveals genome-wide DNA methylation profiling as a quantitative, functional readout for characterization of this new biochemical category of disease.

Delineating the Smith-Kingsmore syndrome phenotype: Investigation of 16 patients with the MTOR c.5395G > A p.(Glu1799Lys) missense variant.

Poole RL; Curry PDK; Marcinkute R; Brewer C; Coman D; Hobson E; Johnson D; Lynch SA; Saggar A; Searle C; Scurr I; Turnpenny PD; Vasudevan P; Tatton-Brown K

American journal of medical genetics. Part A 2021;185;8;2445-2454

Smith-Kingsmore Syndrome (SKS) is a rare genetic syndrome associated with megalencephaly, a variable intellectual disability, autism spectrum disorder, and MTOR gain of function variants. Only 30 patients with MTOR missense variants are published, including 14 (47%) with the MTOR c.5395G>A p.(Glu1799Lys) variant. Limited phenotypic data impacts the quality of information delivered to families and the robustness of interpretation of novel MTOR missense variation. This study aims to improve our understanding of the SKS phenotype through the investigation of 16 further patients with the MTOR c.5395G>A p.(Glu1799Lys) variant. Through the careful phenotypic evaluation of these 16 patients and integration with data from 14 previously reported patients, we have defined major (100% patients) and frequent (>15%) SKS clinical characteristics and, using these data, proposed guidance for evidence-based management. In addition, in the absence of functional studies, we suggest that the combination of the SKS major clinical features of megalencephaly (where the head circumference is at least 3SD) and an intellectual disability with a de novo MTOR missense variant (absent from population databases) should be considered diagnostic for SKS.

Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders.

Gardner EJ; Sifrim A; Lindsay SJ; Prigmore E; Rajan D; Danecek P; Gallone G; Eberhardt RY; Martin HC; Wright CF; FitzPatrick DR; Firth HV; Hurles ME

American journal of human genetics 2021;108;11;2186-2194

Structural variation (SV) describes a broad class of genetic variation greater than 50 bp in size. SVs can cause a wide range of genetic diseases and are prevalent in rare developmental disorders (DDs). Individuals presenting with DDs are often referred for diagnostic testing with chromosomal microarrays (CMAs) to identify large copy-number variants (CNVs) and/or with single-gene, gene-panel, or exome sequencing (ES) to identify single-nucleotide variants, small insertions/deletions, and CNVs. However, individuals with pathogenic SVs undetectable by conventional analysis often remain undiagnosed. Consequently, we have developed the tool InDelible, which interrogates short-read sequencing data for split-read clusters characteristic of SV breakpoints. We applied InDelible to 13,438 probands with severe DDs recruited as part of the Deciphering Developmental Disorders (DDD) study and discovered 63 rare, damaging variants in genes previously associated with DDs missed by standard SNV, indel, or CNV discovery approaches. Clinical review of these 63 variants determined that about half (30/63) were plausibly pathogenic. InDelible was particularly effective at ascertaining variants between 21 and 500 bp in size and increased the total number of potentially pathogenic variants identified by DDD in this size range by 42.9%. Of particular interest were seven confirmed de novo variants in MECP2, which represent 35.0% of all de novo protein-truncating variants in MECP2 among DDD study participants. InDelible provides a framework for the discovery of pathogenic SVs that are most likely missed by standard analytical workflows and has the potential to improve the diagnostic yield of ES across a broad range of genetic diseases.

Disruption of RFX family transcription factors causes autism, attention-deficit/hyperactivity disorder, intellectual disability, and dysregulated behavior.

Harris HK; Nakayama T; Lai J; Zhao B; Argyrou N; Gubbels CS; Soucy A; Genetti CA; Suslovitch V; Rodan LH; Tiller GE; Lesca G; Gripp KW; Asadollahi R; Hamosh A; Applegate CD; Turnpenny PD; Simon MEH; Volker-Touw CML; Gassen KLIV; Binsbergen EV; Pfundt R; Gardeitchik T; Vries BBA; Immken LL; Buchanan C; Willing M; Toler TL; Fassi E; Baker L; Vansenne F; Wang X; Ambrus JL; Fannemel M; Posey JE; Agolini E; Novelli A; Rauch A; Boonsawat P; Fagerberg CR; Larsen MJ; Kibaek M; Labalme A; Poisson A; Payne KK; Walsh LE; Aldinger KA; Balciuniene J; Skraban C; Gray C; Murrell J; Bupp CP; Pascolini G; Grammatico P; Broly M; Küry S; Nizon M; Rasool IG; Zahoor MY; Kraus C; Reis A; Iqbal M; Uguen K; Audebert-Bellanger S; Ferec C; Redon S; Baker J; Wu Y; Zampino G; Syrbe S; Brosse I; Jamra RA; Dobyns WB; Cohen LL; Blomhoff A; Mignot C; Keren B; Courtin T; Agrawal PB; Beggs AH; Yu TW

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;6;1028-1040

We describe a novel neurobehavioral phenotype of autism spectrum disorder (ASD), intellectual disability, and/or attention-deficit/hyperactivity disorder (ADHD) associated with de novo or inherited deleterious variants in members of the RFX family of genes. RFX genes are evolutionarily conserved transcription factors that act as master regulators of central nervous system development and ciliogenesis.

Evaluating variants classified as pathogenic in ClinVar in the DDD Study.

Wright CF; Eberhardt RY; Constantinou P; Hurles ME; FitzPatrick DR; Firth HV;

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;3;571-575

Automated variant filtering is an essential part of diagnostic genome-wide sequencing but may generate false negative results. We sought to investigate whether some previously identified pathogenic variants may be being routinely excluded by standard variant filtering pipelines.

Extracellular LGALS3BP regulates neural progenitor position and relates to human cortical complexity.

Kyrousi C; O'Neill AC; Brazovskaja A; He Z; Kielkowski P; Coquand L; Di Giaimo R; D' Andrea P; Belka A; Forero Echeverry A; Mei D; Lenge M; Cruceanu C; Buchsbaum IY; Khattak S; Fabien G; Binder E; Elmslie F; Guerrini R; Baffet AD; Sieber SA; Treutlein B; Robertson SP; Cappello S

Nature Communications 2021;12;1;6298

Basal progenitors (BPs), including intermediate progenitors and basal radial glia, are generated from apical radial glia and are enriched in gyrencephalic species like humans, contributing to neuronal expansion. Shortly after generation, BPs delaminate towards the subventricular zone, where they further proliferate before differentiation. Gene expression alterations involved in BP delamination and function in humans are poorly understood. Here, we study the role of LGALS3BP, so far known as a cancer biomarker, which is a secreted protein enriched in human neural progenitors (NPCs). We show that individuals with LGALS3BP de novo variants exhibit altered local gyrification, sulcal depth, surface area and thickness in their cortex. Additionally, using cerebral organoids, human fetal tissues and mice, we show that LGALS3BP regulates the position of NPCs. Single-cell RNA-sequencing and proteomics reveal that LGALS3BP-mediated mechanisms involve the extracellular matrix in NPCs' anchoring and migration within the human brain. We propose that its temporal expression influences NPCs' delamination, corticogenesis and gyrification extrinsically.

Haploinsufficiency of ARFGEF1 is associated with developmental delay, intellectual disability, and epilepsy with variable expressivity.

Thomas Q; Gautier T; Marafi D; Besnard T; Willems M; Moutton S; Isidor B; Cogné B; Conrad S; Tenconi R; Iascone M; Sorlin A; Masurel A; Dabir T; Jackson A; Banka S; Delanne J; Lupski JR; Saadi NW; Alkuraya FS; Zahrani FA; Agrawal PB; England E; Madden JA; Posey JE; Burglen L; Rodriguez D; Chevarin M; Nguyen S; Mau-Them FT; Duffourd Y; Garret P; Bruel AL; Callier P; Marle N; Denomme-Pichon AS; Duplomb L; Philippe C; Thauvin-Robinet C; Govin J; Faivre L; Vitobello A

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;10;1901-1911

ADP ribosylation factor guanine nucleotide exchange factors (ARFGEFs) are a family of proteins implicated in cellular trafficking between the Golgi apparatus and the plasma membrane through vesicle formation. Among them is ARFGEF1/BIG1, a protein involved in axon elongation, neurite development, and polarization processes. ARFGEF1 has been previously suggested as a candidate gene for different types of epilepsies, although its implication in human disease has not been well characterized.

Heterozygous De Novo Truncating Mutation of Nucleolin in an ASD Individual Disrupts Its Nucleolar Localization.

Sheikh TI; Harripaul R; Vasli N; Ghadami M; Santangelo SL; Ayub M; Sasanfar R; Vincent JB

Genes 2021;13;1

Nucleolin (NCL/C23; OMIM: 164035) is a major nucleolar protein that plays a critical role in multiple processes, including ribosome assembly and maturation, chromatin decondensation, and pre-rRNA transcription. Due to its diverse functions, nucleolin has frequently been implicated in pathological processes, including cancer and viral infection. We recently identified a de novo frameshifting indel mutation of NCL, p.Gly664Glufs*70, through whole-exome sequencing of autism spectrum disorder trios. Through the transfection of constructs encoding either a wild-type human nucleolin or a mutant nucleolin with the same C-terminal sequence predicted for the autism proband, and by using co-localization with the nucleophosmin (NPM; B23) protein, we have shown that the nucleolin mutation leads to mislocalization of the NCL protein from the nucleolus to the nucleoplasm. Moreover, a construct with a nonsense mutation at the same residue, p.Gly664*, shows a very similar effect on the location of the NCL protein, thus confirming the presence of a predicted nucleolar location signal in this region of the NCL protein. Real-time fluorescence recovery experiments show significant changes in the kinetics and mobility of mutant NCL protein in the nucleoplasm of HEK293Tcells. Several other studies also report de novoNCL mutations in ASD or neurodevelopmental disorders. The altered mislocalization and dynamics of mutant NCL (p.G664Glufs*70/p.G664*) may have relevance to the etiopathlogy of NCL-related ASD and other neurodevelopmental phenotypes.

Heterozygous lamin B1 and lamin B2 variants cause primary microcephaly and define a novel laminopathy.

Parry DA; Martin CA; Greene P; Marsh JA; ; Blyth M; Cox H; Donnelly D; Greenhalgh L; Greville-Heygate S; Harrison V; Lachlan K; McKenna C; Quigley AJ; Rea G; Robertson L; Suri M; Jackson AP

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;2;408-414

Lamins are the major component of nuclear lamina, maintaining structural integrity of the nucleus. Lamin A/C variants are well established to cause a spectrum of disorders ranging from myopathies to progeria, termed laminopathies. Phenotypes resulting from variants in LMNB1 and LMNB2 have been much less clearly defined.

Heterozygous variants in SPTBN1 cause intellectual disability and autism.

Rosenfeld JA; Xiao R; Bekheirnia MR; Kanani F; Parker MJ; Koenig MK; van Haeringen A; Ruivenkamp C; Rosmaninho-Salgado J; Almeida PM; Sá J; Pinto Basto J; Palen E; Oetjens KF; Burrage LC; Xia F; Liu P; Eng CM; ; Yang Y; Posey JE; Lee BH

American journal of medical genetics. Part A 2021;185;7;2037-2045

Spectrins are common components of cytoskeletons, binding to cytoskeletal elements and the plasma membrane, allowing proper localization of essential membrane proteins, signal transduction, and cellular scaffolding. Spectrins are assembled from α and β subunits, encoded by SPTA1 and SPTAN1 (α) and SPTB, SPTBN1, SPTBN2, SPTBN4, and SPTBN5 (β). Pathogenic variants in various spectrin genes are associated with erythroid cell disorders (SPTA1, SPTB) and neurologic disorders (SPTAN1, SPTBN2, and SPTBN4), but no phenotypes have been definitively associated with variants in SPTBN1 or SPTBN5. Through exome sequencing and case matching, we identified seven unrelated individuals with heterozygous SPTBN1 variants: two with de novo missense variants and five with predicted loss-of-function variants (found to be de novo in two, while one was inherited from a mother with a history of learning disabilities). Common features include global developmental delays, intellectual disability, and behavioral disturbances. Autistic features (4/6) and epilepsy (2/7) or abnormal electroencephalogram without overt seizures (1/7) were present in a subset. Identification of loss-of-function variants suggests a haploinsufficiency mechanism, but additional functional studies are required to fully elucidate disease pathogenesis. Our findings support the essential roles of SPTBN1 in human neurodevelopment and expand the knowledge of human spectrinopathy disorders.

Identification of LAMA1 mutations ends diagnostic odyssey and has prognostic implications for patients with presumed Joubert syndrome.

Powell L; Olinger E; Wedderburn S; Ramakumaran VS; Kini U; Clayton-Smith J; Ramsden SC; Rice SJ; Barroso-Gil M; Wilson I; Cowley L; Johnson S; Harris E; Montgomery T; Bertoli M; ; Boltshauser E; Sayer JA

Brain communications 2021;3;3;fcab163

Paediatric neurology syndromes are a broad and complex group of conditions with a large spectrum of clinical phenotypes. Joubert syndrome is a genetically heterogeneous neurological ciliopathy syndrome with molar tooth sign as the neuroimaging hallmark. We reviewed the clinical, radiological and genetic data for several families with a clinical diagnosis of Joubert syndrome but negative genetic analysis. We detected biallelic pathogenic variants in LAMA1, including novel alleles, in each of the four cases we report, thereby establishing a firm diagnosis of Poretti-Boltshauser syndrome. Analysis of brain MRI revealed cerebellar dysplasia and cerebellar cysts, associated with Poretti-Boltshauser syndrome and the absence of typical molar tooth signs. Using large UK patient cohorts, the relative prevalence of Joubert syndrome as a cause of intellectual disability was 0.2% and of Poretti-Boltshauser syndrome was 0.02%. We conclude that children with congenital brain disorders that mimic Joubert syndrome may have a delayed diagnosis due to poor recognition of key features on brain imaging and the lack of inclusion of LAMA1 on molecular genetic gene panels. We advocate the inclusion of LAMA1 genetic analysis on all intellectual disability and Joubert syndrome gene panels and promote a wider awareness of the clinical and radiological features of these syndromes.

Impaired eIF5A function causes a Mendelian disorder that is partially rescued in model systems by spermidine.

Faundes V; Jennings MD; Crilly S; Legraie S; Withers SE; Cuvertino S; Davies SJ; Douglas AGL; Fry AE; Harrison V; Amiel J; Lehalle D; Newman WG; Newkirk P; Ranells J; Splitt M; Cross LA; Saunders CJ; Sullivan BR; Granadillo JL; Gordon CT; Kasher PR; Pavitt GD; Banka S

Nature Communications 2021;12;1;833

The structure of proline prevents it from adopting an optimal position for rapid protein synthesis. Poly-proline-tract (PPT) associated ribosomal stalling is resolved by highly conserved eIF5A, the only protein to contain the amino acid hypusine. We show that de novo heterozygous EIF5A variants cause a disorder characterized by variable combinations of developmental delay, microcephaly, micrognathia and dysmorphism. Yeast growth assays, polysome profiling, total/hypusinated eIF5A levels and PPT-reporters studies reveal that the variants impair eIF5A function, reduce eIF5A-ribosome interactions and impair the synthesis of PPT-containing proteins. Supplementation with 1 mM spermidine partially corrects the yeast growth defects, improves the polysome profiles and restores expression of PPT reporters. In zebrafish, knockdown eif5a partly recapitulates the human phenotype that can be rescued with 1 µM spermidine supplementation. In summary, we uncover the role of eIF5A in human development and disease, demonstrate the mechanistic complexity of EIF5A-related disorder and raise possibilities for its treatment.

MED27 Variants Cause Developmental Delay, Dystonia, and Cerebellar Hypoplasia.

Meng L; Isohanni P; Shao Y; Graham BH; Hickey SE; Brooks S; Suomalainen A; Joset P; Steindl K; Rauch A; Hackenberg A; High FA; Armstrong-Javors A; Mencacci NE; Gonzàlez-Latapi P; Kamel WA; Al-Hashel JY; Bustos BI; Hernandez AV; Krainc D; Lubbe SJ; Van Esch H; De Luca C; Ballon K; Ravelli C; Burglen L; Qebibo L; Calame DG; Mitani T; Marafi D; Pehlivan D; Saadi NW; Sahin Y; Maroofian R; Efthymiou S; Houlden H; Maqbool S; Rahman F; Gu S; Posey JE; Lupski JR; Hunter JV; Wangler MF; Carroll CJ; Yang Y

Annals of neurology 2021;89;4;828-833

The Mediator multiprotein complex functions as a regulator of RNA polymerase II-catalyzed gene transcription. In this study, exome sequencing detected biallelic putative disease-causing variants in MED27, encoding Mediator complex subunit 27, in 16 patients from 11 families with a novel neurodevelopmental syndrome. Patient phenotypes are highly homogeneous, including global developmental delay, intellectual disability, axial hypotonia with distal spasticity, dystonic movements, and cerebellar hypoplasia. Seizures and cataracts were noted in severely affected individuals. Identification of multiple patients with biallelic MED27 variants supports the critical role of MED27 in normal human neural development, particularly for the cerebellum. ANN NEUROL 2021;89:828-833.

Missense variants in DPYSL5 cause a neurodevelopmental disorder with corpus callosum agenesis and cerebellar abnormalities.

Jeanne M; Demory H; Moutal A; Vuillaume ML; Blesson S; Thépault RA; Marouillat S; Halewa J; Maas SM; Motazacker MM; Mancini GMS; van Slegtenhorst MA; Andreou A; Cox H; Vogt J; Laufman J; Kostandyan N; Babikyan D; Hancarova M; Bendova S; Sedlacek Z; Aldinger KA; Sherr EH; Argilli E; England EM; Audebert-Bellanger S; Bonneau D; Colin E; Denommé-Pichon AS; Gilbert-Dussardier B; Isidor B; Küry S; Odent S; Redon R; Khanna R; Dobyns WB; Bézieau S; Honnorat J; Lohkamp B; Toutain A; Laumonnier F

American journal of human genetics 2021;108;5;951-961

The collapsin response mediator protein (CRMP) family proteins are intracellular mediators of neurotrophic factors regulating neurite structure/spine formation and are essential for dendrite patterning and directional axonal pathfinding during brain developmental processes. Among this family, CRMP5/DPYSL5 plays a significant role in neuronal migration, axonal guidance, dendrite outgrowth, and synapse formation by interacting with microtubules. Here, we report the identification of missense mutations in DPYSL5 in nine individuals with brain malformations, including corpus callosum agenesis and/or posterior fossa abnormalities, associated with variable degrees of intellectual disability. A recurrent de novo p.Glu41Lys variant was found in eight unrelated patients, and a p.Gly47Arg variant was identified in one individual from the first family reported with Ritscher-Schinzel syndrome. Functional analyses of the two missense mutations revealed impaired dendritic outgrowth processes in young developing hippocampal primary neuronal cultures. We further demonstrated that these mutations, both located in the same loop on the surface of DPYSL5 monomers and oligomers, reduced the interaction of DPYSL5 with neuronal cytoskeleton-associated proteins MAP2 and βIII-tubulin. Our findings collectively indicate that the p.Glu41Lys and p.Gly47Arg variants impair DPYSL5 function on dendritic outgrowth regulation by preventing the formation of the ternary complex with MAP2 and βIII-tubulin, ultimately leading to abnormal brain development. This study adds DPYSL5 to the list of genes implicated in brain malformation and in neurodevelopmental disorders.

Missense variants in the N-terminal domain of the A isoform of FHF2/FGF13 cause an X-linked developmental and epileptic encephalopathy.

Fry AE; Marra C; Derrick AV; Pickrell WO; Higgins AT; Te Water Naude J; McClatchey MA; Davies SJ; Metcalfe KA; Tan HJ; Mohanraj R; Avula S; Williams D; Brady LI; Mesterman R; Tarnopolsky MA; Zhang Y; Yang Y; Wang X; ; Rees MI; Goldfarb M; Chung SK

American journal of human genetics 2021;108;1;176-185

Fibroblast growth factor homologous factors (FHFs) are intracellular proteins which regulate voltage-gated sodium (Nav) channels in the brain and other tissues. FHF dysfunction has been linked to neurological disorders including epilepsy. Here, we describe two sibling pairs and three unrelated males who presented in infancy with intractable focal seizures and severe developmental delay. Whole-exome sequencing identified hemi- and heterozygous variants in the N-terminal domain of the A isoform of FHF2 (FHF2A). The X-linked FHF2 gene (also known as FGF13) has alternative first exons which produce multiple protein isoforms that differ in their N-terminal sequence. The variants were located at highly conserved residues in the FHF2A inactivation particle that competes with the intrinsic fast inactivation mechanism of Nav channels. Functional characterization of mutant FHF2A co-expressed with wild-type Nav1.6 (SCN8A) revealed that mutant FHF2A proteins lost the ability to induce rapid-onset, long-term blockade of the channel while retaining pro-excitatory properties. These gain-of-function effects are likely to increase neuronal excitability consistent with the epileptic potential of FHF2 variants. Our findings demonstrate that FHF2 variants are a cause of infantile-onset developmental and epileptic encephalopathy and underline the critical role of the FHF2A isoform in regulating Nav channel function.

New insights into the clinical and molecular spectrum of the novel CYFIP2-related neurodevelopmental disorder and impairment of the WRC-mediated actin dynamics.

Begemann A; Sticht H; Begtrup A; Vitobello A; Faivre L; Banka S; Alhaddad B; Asadollahi R; Becker J; Bierhals T; Brown KE; Bruel AL; Brunet T; Carneiro M; Cremer K; Day R; Denommé-Pichon AS; Dyment DA; Engels H; Fisher R; Goh ES; Hajianpour MJ; Haertel LRM; Hauer N; Hempel M; Herget T; Johannsen J; Kraus C; Le Guyader G; Lesca G; Mau-Them FT; McDermott JH; McWalter K; Meyer P; Õunap K; Popp B; Reimand T; Riedhammer KM; Russo M; Sadleir LG; Saenz M; Schiff M; Schuler E; Syrbe S; Van der Ven AT; Verloes A; Willems M; Zweier C; Steindl K; Zweier M; Rauch A

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;3;543-554

A few de novo missense variants in the cytoplasmic FMRP-interacting protein 2 (CYFIP2) gene have recently been described as a novel cause of severe intellectual disability, seizures, and hypotonia in 18 individuals, with p.Arg87 substitutions in the majority.

Non-coding region variants upstream of MEF2C cause severe developmental disorder through three distinct loss-of-function mechanisms.

Wright CF; Quaife NM; Ramos-Hernández L; Danecek P; Ferla MP; Samocha KE; Kaplanis J; Gardner EJ; Eberhardt RY; Chao KR; Karczewski KJ; Morales J; Gallone G; Balasubramanian M; Banka S; Gompertz L; Kerr B; Kirby A; Lynch SA; Morton JEV; Pinz H; Sansbury FH; Stewart H; Zuccarelli BD; ; Cook SA; Taylor JC; Juusola J; Retterer K; Firth HV; Hurles ME; Lara-Pezzi E; Barton PJR; Whiffin N

American journal of human genetics 2021;108;6;1083-1094

Clinical genetic testing of protein-coding regions identifies a likely causative variant in only around half of developmental disorder (DD) cases. The contribution of regulatory variation in non-coding regions to rare disease, including DD, remains very poorly understood. We screened 9,858 probands from the Deciphering Developmental Disorders (DDD) study for de novo mutations in the 5' untranslated regions (5' UTRs) of genes within which variants have previously been shown to cause DD through a dominant haploinsufficient mechanism. We identified four single-nucleotide variants and two copy-number variants upstream of MEF2C in a total of ten individual probands. We developed multiple bespoke and orthogonal experimental approaches to demonstrate that these variants cause DD through three distinct loss-of-function mechanisms, disrupting transcription, translation, and/or protein function. These non-coding region variants represent 23% of likely diagnoses identified in MEF2C in the DDD cohort, but these would all be missed in standard clinical genetics approaches. Nonetheless, these variants are readily detectable in exome sequence data, with 30.7% of 5' UTR bases across all genes well covered in the DDD dataset. Our analyses show that non-coding variants upstream of genes within which coding variants are known to cause DD are an important cause of severe disease and demonstrate that analyzing 5' UTRs can increase diagnostic yield. We also show how non-coding variants can help inform both the disease-causing mechanism underlying protein-coding variants and dosage tolerance of the gene.

Pathogenic variants causing ABL1 malformation syndrome cluster in a myristoyl-binding pocket and increase tyrosine kinase activity.

Blakes AJM; Gaul E; Lam W; Shannon N; Knapp KM; Bicknell LS; Jackson MR; Wade EM; Robertson S; White SM; Heller R; Chase A; Baralle D; Douglas AGL

European journal of human genetics : EJHG 2021;29;4;593-603

ABL1 is a proto-oncogene encoding a nonreceptor tyrosine kinase, best known in the somatic BCR-ABL fusion gene associated with chronic myeloid leukaemia. Recently, germline missense variants in ABL1 have been found to cause an autosomal dominant developmental syndrome with congenital heart disease, skeletal malformations and characteristic facies. Here, we describe a series of six new unrelated individuals with heterozygous missense variants in ABL1 (including four novel variants) identified via whole exome sequencing. All the affected individuals in this series recapitulate the phenotype of the ABL1 developmental syndrome and additionally we affirm that hearing impairment is a common feature of the condition. Four of the variants cluster in the myristoyl-binding pocket of ABL1, a region critical for auto-inhibitory regulation of the kinase domain. Bio-informatic analysis of transcript-wide conservation and germline/somatic variation reveals that this pocket region is subject to high missense constraint and evolutionary conservation. Functional work to investigate ABL1 kinase activity in vitro by transient transfection of HEK293T cells with variant ABL1 plasmid constructs revealed increased phosphorylation of ABL1-specific substrates compared to wild-type. The increased tyrosine kinase activity was suppressed by imatinib treatment. This case series of six new patients with germline heterozygous ABL1 missense variants further delineates the phenotypic spectrum of this condition and recognises microcephaly as a common finding. Our analysis supports an ABL1 gain-of-function mechanism due to loss of auto-inhibition, and demonstrates the potential for pharmacological inhibition using imatinib.

Pathogenic variants in SMARCA5, a chromatin remodeler, cause a range of syndromic neurodevelopmental features.

Li D; Wang Q; Gong NN; Kurolap A; Feldman HB; Boy N; Brugger M; Grand K; McWalter K; Guillen Sacoto MJ; Wakeling E; Hurst J; March ME; Bhoj EJ; Nowaczyk MJM; Gonzaga-Jauregui C; Mathew M; Dava-Wala A; Siemon A; Bartholomew D; Huang Y; Lee H; Martinez-Agosto JA; Schwaibold EMC; Brunet T; Choukair D; Pais LS; White SM; Christodoulou J; Brown D; Lindstrom K; Grebe T; Tiosano D; Kayser MS; Tan TY; Deardorff MA; Song Y; Hakonarson H

Science advances 2021;7;20

Intellectual disability encompasses a wide spectrum of neurodevelopmental disorders, with many linked genetic loci. However, the underlying molecular mechanism for more than 50% of the patients remains elusive. We describe pathogenic variants in SMARCA5, encoding the ATPase motor of the ISWI chromatin remodeler, as a cause of a previously unidentified neurodevelopmental disorder, identifying 12 individuals with de novo or dominantly segregating rare heterozygous variants. Accompanying phenotypes include mild developmental delay, frequent postnatal short stature and microcephaly, and recurrent dysmorphic features. Loss of function of the SMARCA5 Drosophila ortholog Iswi led to smaller body size, reduced sensory dendrite complexity, and tiling defects in larvae. In adult flies, Iswi neural knockdown caused decreased brain size, aberrant mushroom body morphology, and abnormal locomotor function. Iswi loss of function was rescued by wild-type but not mutant SMARCA5. Our results demonstrate that SMARCA5 pathogenic variants cause a neurodevelopmental syndrome with mild facial dysmorphia.

SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females.

Radio FC; Pang K; Ciolfi A; Levy MA; Hernández-García A; Pedace L; Pantaleoni F; Liu Z; de Boer E; Jackson A; Bruselles A; McConkey H; Stellacci E; Lo Cicero S; Motta M; Carrozzo R; Dentici ML; McWalter K; Desai M; Monaghan KG; Telegrafi A; Philippe C; Vitobello A; Au M; Grand K; Sanchez-Lara PA; Baez J; Lindstrom K; Kulch P; Sebastian J; Madan-Khetarpal S; Roadhouse C; MacKenzie JJ; Monteleone B; Saunders CJ; Jean Cuevas JK; Cross L; Zhou D; Hartley T; Sawyer SL; Monteiro FP; Secches TV; Kok F; Schultz-Rogers LE; Macke EL; Morava E; Klee EW; Kemppainen J; Iascone M; Selicorni A; Tenconi R; Amor DJ; Pais L; Gallacher L; Turnpenny PD; Stals K; Ellard S; Cabet S; Lesca G; Pascal J; Steindl K; Ravid S; Weiss K; Castle AMR; Carter MT; Kalsner L; de Vries BBA; van Bon BW; Wevers MR; Pfundt R; Stegmann APA; Kerr B; Kingston HM; Chandler KE; Sheehan W; Elias AF; Shinde DN; Towne MC; Robin NH; Goodloe D; Vanderver A; Sherbini O; Bluske K; Hagelstrom RT; Zanus C; Faletra F; Musante L; Kurtz-Nelson EC; Earl RK; Anderlid BM; Morin G; van Slegtenhorst M; Diderich KEM; Brooks AS; Gribnau J; Boers RG; Finestra TR; Carter LB; Rauch A; Gasparini P; Boycott KM; Barakat TS; Graham JM; Faivre L; Banka S; Wang T; Eichler EE; Priolo M; Dallapiccola B; Vissers LELM; Sadikovic B; Scott DA; Holder JL; Tartaglia M

American journal of human genetics 2021;108;3;502-516

Deletion 1p36 (del1p36) syndrome is the most common human disorder resulting from a terminal autosomal deletion. This condition is molecularly and clinically heterogeneous. Deletions involving two non-overlapping regions, known as the distal (telomeric) and proximal (centromeric) critical regions, are sufficient to cause the majority of the recurrent clinical features, although with different facial features and dysmorphisms. SPEN encodes a transcriptional repressor commonly deleted in proximal del1p36 syndrome and is located centromeric to the proximal 1p36 critical region. Here, we used clinical data from 34 individuals with truncating variants in SPEN to define a neurodevelopmental disorder presenting with features that overlap considerably with those of proximal del1p36 syndrome. The clinical profile of this disease includes developmental delay/intellectual disability, autism spectrum disorder, anxiety, aggressive behavior, attention deficit disorder, hypotonia, brain and spine anomalies, congenital heart defects, high/narrow palate, facial dysmorphisms, and obesity/increased BMI, especially in females. SPEN also emerges as a relevant gene for del1p36 syndrome by co-expression analyses. Finally, we show that haploinsufficiency of SPEN is associated with a distinctive DNA methylation episignature of the X chromosome in affected females, providing further evidence of a specific contribution of the protein to the epigenetic control of this chromosome, and a paradigm of an X chromosome-specific episignature that classifies syndromic traits. We conclude that SPEN is required for multiple developmental processes and SPEN haploinsufficiency is a major contributor to a disorder associated with deletions centromeric to the previously established 1p36 critical regions.

Syndromic disorders caused by gain-of-function variants in KCNH1, KCNK4, and KCNN3-a subgroup of K+ channelopathies.

Gripp KW; Smithson SF; Scurr IJ; Baptista J; Majumdar A; Pierre G; Williams M; Henderson LB; Wentzensen IM; McLaughlin H; Leeuwen L; Simon MEH; van Binsbergen E; Dinulos MBP; Kaplan JD; McRae A; Superti-Furga A; Good JM; Kutsche K

European journal of human genetics : EJHG 2021;29;9;1384-1395

Decreased or increased activity of potassium channels caused by loss-of-function and gain-of-function (GOF) variants in the corresponding genes, respectively, underlies a broad spectrum of human disorders affecting the central nervous system, heart, kidney, and other organs. While the association of epilepsy and intellectual disability (ID) with variants affecting function in genes encoding potassium channels is well known, GOF missense variants in K+ channel encoding genes in individuals with syndromic developmental disorders have only recently been recognized. These syndromic phenotypes include Zimmermann-Laband and Temple-Baraitser syndromes, caused by dominant variants in KCNH1, FHEIG syndrome due to dominant variants in KCNK4, and the clinical picture associated with dominant variants in KCNN3. Here we review the presentation of these individuals, including five newly reported with variants in KCNH1 and three additional individuals with KCNN3 variants, all variants likely affecting function. There is notable overlap in the phenotypic findings of these syndromes associated with dominant KCNN3, KCNH1, and KCNK4 variants, sharing developmental delay and/or ID, coarse facial features, gingival enlargement, distal digital hypoplasia, and hypertrichosis. We suggest to combine the phenotypes and define a new subgroup of potassium channelopathies caused by increased K+ conductance, referred to as syndromic neurodevelopmental K+ channelopathies due to dominant variants in KCNH1, KCNK4, or KCNN3.

Syndromic Forms of Hyperinsulinaemic Hypoglycaemia-A 15-year follow-up Study.

Kostopoulou E; Dastamani A; Güemes M; Clement E; Caiulo S; Shanmugananda P; Dattani M; Gilbert C; Hurst JA; Shah P

Clinical endocrinology 2021;94;3;399-412

Hyperinsulinaemic hypoglycaemia (HH) is one of the commonest causes of hypoglycaemia in children. The molecular basis includes defects in pathways that regulate insulin release. Syndromic conditions like Beckwith-Wiedemann (BWS), Kabuki (KS) and Turner (TS) are known to be associated with a higher risk for HH. This systematic review of children with HH referred to a tertiary centre aims at estimating the frequency of a syndromic/multisystem condition to help address stratification of genetic analysis in infants with HH.

Systematic assessment of outcomes following a genetic diagnosis identified through a large-scale research study into developmental disorders.

Copeland H; Kivuva E; Firth HV; Wright CF

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;6;1058-1064

The clinical and psychosocial outcomes associated with receiving a genetic diagnosis for developmental disorders are wide-ranging but under-studied. We sought to investigate outcomes from a subset of families who received a diagnosis through the Deciphering Developmental Disorders (DDD) study.

The broad phenotypic spectrum of PPP2R1A-related neurodevelopmental disorders correlates with the degree of biochemical dysfunction.

Lenaerts L; Reynhout S; Verbinnen I; Laumonnier F; Toutain A; Bonnet-Brilhault F; Hoorne Y; Joss S; Chassevent AK; Smith-Hicks C; Loeys B; Joset P; Steindl K; Rauch A; Mehta SG; Chung WK; Devriendt K; Holder SE; Jewett T; Baldwin LM; Wilson WG; Towner S; Srivastava S; Johnson HF; Daumer-Haas C; Baethmann M; Ruiz A; Gabau E; Jain V; Varghese V; Al-Beshri A; Fulton S; Wechsberg O; Orenstein N; Prescott K; Childs AM; Faivre L; Moutton S; Sullivan JA; Shashi V; Koudijs SM; Heijligers M; Kivuva E; McTague A; Male A; van Ierland Y; Plecko B; Maystadt I; Hamid R; Hannig VL; Houge G; Janssens V

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;2;352-362

Neurodevelopmental disorders (NDD) caused by protein phosphatase 2A (PP2A) dysfunction have mainly been associated with de novo variants in PPP2R5D and PPP2CA, and more rarely in PPP2R1A. Here, we aimed to better understand the latter by characterizing 30 individuals with de novo and often recurrent variants in this PP2A scaffolding Aα subunit.

The contribution of X-linked coding variation to severe developmental disorders.

Martin HC; Gardner EJ; Samocha KE; Kaplanis J; Akawi N; Sifrim A; Eberhardt RY; Tavares ALT; Neville MDC; Niemi MEK; Gallone G; McRae J; ; Wright CF; FitzPatrick DR; Firth HV; Hurles ME

Nature Communications 2021;12;1;627

Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders.

Truncating variants in the SHANK1 gene are associated with a spectrum of neurodevelopmental disorders.

May HJ; Jeong J; Revah-Politi A; Cohen JS; Chassevent A; Baptista J; Baugh EH; Bier L; Bottani A; Carminho A Rodrigues MT; Conlon C; Fluss J; Guipponi M; Kim CA; Matsumoto N; Person R; Primiano M; Rankin J; Shinawi M; Smith-Hicks C; Telegrafi A; Toy S; Uchiyama Y; Aggarwal V; Goldstein DB; Roche KW; Anyane-Yeboa K

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;10;1912-1921

In this study, we aimed to characterize the clinical phenotype of a SHANK1-related disorder and define the functional consequences of SHANK1 truncating variants.

Variants in GNAI1 cause a syndrome associated with variable features including developmental delay, seizures, and hypotonia.

Muir AM; Gardner JF; van Jaarsveld RH; de Lange IM; van der Smagt JJ; Wilson GN; Dubbs H; Goldberg EM; Zitano L; Bupp C; Martinez J; Srour M; Accogli A; Alhakeem A; Meltzer M; Gropman A; Brewer C; Caswell RC; Montgomery T; McKenna C; McKee S; Powell C; Vasudevan PC; Brady AF; Joss S; Tysoe C; Noh G; Tarnopolsky M; Brady L; Zafar M; Schrier Vergano SA; Murray B; Sawyer L; Hainline BE; Sapp K; DeMarzo D; Huismann DJ; Wentzensen IM; Schnur RE; Monaghan KG; Juusola J; Rhodes L; Dobyns WB; Lecoquierre F; Goldenberg A; Polster T; Axer-Schaefer S; Platzer K; Klöckner C; Hoffman TL; MacArthur DG; O'Leary MC; VanNoy GE; England E; Varghese VC; Mefford HC

Genetics in medicine : official journal of the American College of Medical Genetics 2021;23;5;881-887

Neurodevelopmental disorders (NDDs) encompass a spectrum of genetically heterogeneous disorders with features that commonly include developmental delay, intellectual disability, and autism spectrum disorders. We sought to delineate the molecular and phenotypic spectrum of a novel neurodevelopmental disorder caused by variants in the GNAI1 gene.

Variants in the degron of AFF3 are associated with intellectual disability, mesomelic dysplasia, horseshoe kidney, and epileptic encephalopathy.

Voisin N; Schnur RE; Douzgou S; Hiatt SM; Rustad CF; Brown NJ; Earl DL; Keren B; Levchenko O; Geuer S; Verheyen S; Johnson D; Zarate YA; Hančárová M; Amor DJ; Bebin EM; Blatterer J; Brusco A; Cappuccio G; Charrow J; Chatron N; Cooper GM; Courtin T; Dadali E; Delafontaine J; Del Giudice E; Doco M; Douglas G; Eisenkölbl A; Funari T; Giannuzzi G; Gruber-Sedlmayr U; Guex N; Heron D; Holla ØL; Hurst ACE; Juusola J; Kronn D; Lavrov A; Lee C; Lorrain S; Merckoll E; Mikhaleva A; Norman J; Pradervand S; Prchalová D; Rhodes L; Sanders VR; Sedláček Z; Seebacher HA; Sellars EA; Sirchia F; Takenouchi T; Tanaka AJ; Taska-Tench H; Tønne E; Tveten K; Vitiello G; Vlčková M; Uehara T; Nava C; Yalcin B; Kosaki K; Donnai D; Mundlos S; Brunetti-Pierri N; Chung WK; Reymond A

American journal of human genetics 2021;108;5;857-873

The ALF transcription factor paralogs, AFF1, AFF2, AFF3, and AFF4, are components of the transcriptional super elongation complex that regulates expression of genes involved in neurogenesis and development. We describe an autosomal dominant disorder associated with de novo missense variants in the degron of AFF3, a nine amino acid sequence important for its binding to ubiquitin ligase, or with de novo deletions of this region. The sixteen affected individuals we identified, along with two previously reported individuals, present with a recognizable pattern of anomalies, which we named KINSSHIP syndrome (KI for horseshoe kidney, NS for Nievergelt/Savarirayan type of mesomelic dysplasia, S for seizures, H for hypertrichosis, I for intellectual disability, and P for pulmonary involvement), partially overlapping the AFF4-associated CHOPS syndrome. Whereas homozygous Aff3 knockout mice display skeletal anomalies, kidney defects, brain malformations, and neurological anomalies, knockin animals modeling one of the microdeletions and the most common of the missense variants identified in affected individuals presented with lower mesomelic limb deformities like KINSSHIP-affected individuals and early lethality, respectively. Overexpression of AFF3 in zebrafish resulted in body axis anomalies, providing some support for the pathological effect of increased amount of AFF3. The only partial phenotypic overlap of AFF3- and AFF4-associated syndromes and the previously published transcriptome analyses of ALF transcription factors suggest that these factors are not redundant and each contributes uniquely to proper development.

ZTTK syndrome: Clinical and molecular findings of 15 cases and a review of the literature.

Kushary ST; Revah-Politi A; Barua S; Ganapathi M; Accogli A; Aggarwal V; Brunetti-Pierri N; Cappuccio G; Capra V; Fagerberg CR; Gazdagh G; Guzman E; Hadonou M; Harrison V; Havelund K; Iancu D; Kraus A; Lippa NC; Mansukhani M; McBrian D; McEntagart M; Pacio-Míguez M; Palomares-Bralo M; Pottinger C; Ruivenkamp CAL; Sacco O; Santen GWE; Santos-Simarro F; Scala M; Short J; Sørensen KP; Woods CG; ; ; Anyane Yeboa K

American journal of medical genetics. Part A 2021;185;12;3740-3753

Zhu-Tokita-Takenouchi-Kim (ZTTK) syndrome is caused by de novo loss-of-function variants in the SON gene (MIM #617140). This multisystemic disorder is characterized by intellectual disability, seizures, abnormal brain imaging, variable dysmorphic features, and various congenital anomalies. The wide application and increasing accessibility of whole exome sequencing (WES) has helped to identify new cases of ZTTK syndrome over the last few years. To date, there have been approximately 45 cases reported in the literature. Here, we describe 15 additional individuals with variants in the SON gene, including those with missense variants bringing the total number of known cases to 60. We have reviewed the clinical and molecular data of these new cases and all previously reported cases to further delineate the most common as well as emerging clinical findings related to this syndrome. Furthermore, we aim to delineate any genotype-phenotype correlations specifically for a recurring pathogenic four base pair deletion (c.5753_5756del) along with discussing the impact of missense variants seen in the SON gene.

A restricted spectrum of missense KMT2D variants cause a multiple malformations disorder distinct from Kabuki syndrome.

Cuvertino S; Hartill V; Colyer A; Garner T; Nair N; Al-Gazali L; Canham N; Faundes V; Flinter F; Hertecant J; Holder-Espinasse M; Jackson B; Lynch SA; Nadat F; Narasimhan VM; Peckham M; Sellers R; Seri M; Montanari F; Southgate L; Squeo GM; Trembath R; van Heel D; Venuto S; Weisberg D; Stals K; Ellard S; ; Barton A; Kimber SJ; Sheridan E; Merla G; Stevens A; Johnson CA; Banka S

Genetics in medicine : official journal of the American College of Medical Genetics 2020;22;5;867-877

To investigate if specific exon 38 or 39 KMT2D missense variants (MVs) cause a condition distinct from Kabuki syndrome type 1 (KS1).

A synonymous UPF3B variant causing a speech disorder implicates NMD as a regulator of neurodevelopmental disorder gene networks.

Domingo D; Nawaz U; Corbett M; Espinoza JL; Tatton-Brown K; Coman D; Wilkinson MF; Gecz J; Jolly LA

Human molecular genetics 2020;29;15;2568-2578

Loss-of-function mutations of the X-chromosome gene UPF3B cause male neurodevelopmental disorders (NDDs) via largely unknown mechanisms. We investigated initially by interrogating a novel synonymous UPF3B variant in a male with absent speech. In silico and functional studies using cell lines derived from this individual show altered UPF3B RNA splicing. The resulting mRNA species encodes a frame-shifted protein with a premature termination codon (PTC) predicted to elicit degradation via nonsense-mediated mRNA decay (NMD). UPF3B mRNA was reduced in the cell line, and no UPF3B protein was produced, confirming a loss-of-function allele. UPF3B is itself involved in the NMD mechanism which degrades both PTC-bearing mutant transcripts and also many physiological transcripts. RNAseq analysis showed that ~1.6% of mRNAs exhibited altered expression. These mRNA changes overlapped and correlated with those we identified in additional cell lines obtained from individuals harbouring other UPF3B mutations, permitting us to interrogate pathogenic mechanisms of UPF3B-associated NDDs. We identified 102 genes consistently deregulated across all UPF3B mutant cell lines. Of the 51 upregulated genes, 75% contained an NMD-targeting feature, thus identifying high-confidence direct NMD targets. Intriguingly, 22 of the dysregulated genes encoded known NDD genes, suggesting UPF3B-dependent NMD regulates gene networks critical for cognition and behaviour. Indeed, we show that 78.5% of all NDD genes encode a transcript predicted to be targeted by NMD. These data describe the first synonymous UPF3B mutation in a patient with prominent speech and language disabilities and identify plausible mechanisms of pathology downstream of UPF3B mutations involving the deregulation of NDD-gene networks.

AMELIE speeds Mendelian diagnosis by matching patient phenotype and genotype to primary literature.

Birgmeier J; Haeussler M; Deisseroth CA; Steinberg EH; Jagadeesh KA; Ratner AJ; Guturu H; Wenger AM; Diekhans ME; Stenson PD; Cooper DN; Ré C; Beggs AH; Bernstein JA; Bejerano G

Science translational medicine 2020;12;544

The diagnosis of Mendelian disorders requires labor-intensive literature research. Trained clinicians can spend hours looking for the right publication(s) supporting a single gene that best explains a patient's disease. AMELIE (Automatic Mendelian Literature Evaluation) greatly accelerates this process. AMELIE parses all 29 million PubMed abstracts and downloads and further parses hundreds of thousands of full-text articles in search of information supporting the causality and associated phenotypes of most published genetic variants. AMELIE then prioritizes patient candidate variants for their likelihood of explaining any patient's given set of phenotypes. Diagnosis of singleton patients (without relatives' exomes) is the most time-consuming scenario, and AMELIE ranked the causative gene at the very top for 66% of 215 diagnosed singleton Mendelian patients from the Deciphering Developmental Disorders project. Evaluating only the top 11 AMELIE-scored genes of 127 (median) candidate genes per patient resulted in a rapid diagnosis in more than 90% of cases. AMELIE-based evaluation of all cases was 3 to 19 times more efficient than hand-curated database-based approaches. We replicated these results on a retrospective cohort of clinical cases from Stanford Children's Health and the Manton Center for Orphan Disease Research. An analysis web portal with our most recent update, programmatic interface, and code is available at

Atypical, milder presentation in a child with CC2D2A and KIDINS220 variants.

Lam Z; Albaba S; Study D; Balasubramanian M

Clinical dysmorphology 2020;29;1;10-16

With the increasing availability and clinical use of exome and whole-genome sequencing, reverse phenotyping is now becoming common practice in clinical genetics. Here, we report a patient identified through the Wellcome Trust Deciphering Developmental Disorders study who has homozygous pathogenic variants in CC2D2A and a de-novo heterozygous pathogenic variant in KIDINS220. He presents with developmental delay, intellectual disability, and oculomotor apraxia. Reverse phenotyping has demonstrated that he likely has a composite phenotype with contributions from both variants. The patient is much more mildly affected than those with Joubert Syndrome or Spastic paraplegia, intellectual disability, nystagmus, and obesity, the conditions associated with CC2D2A and KIDINS220 respectively, and therefore, contributes to the phenotypic variability associated with the two conditions.

AVADA: toward automated pathogenic variant evidence retrieval directly from the full-text literature.

Birgmeier J; Deisseroth CA; Hayward LE; Galhardo LMT; Tierno AP; Jagadeesh KA; Stenson PD; Cooper DN; Bernstein JA; Haeussler M; Bejerano G

Genetics in medicine : official journal of the American College of Medical Genetics 2020;22;2;362-370

Both monogenic pathogenic variant cataloging and clinical patient diagnosis start with variant-level evidence retrieval followed by expert evidence integration in search of diagnostic variants and genes. Here, we try to accelerate pathogenic variant evidence retrieval by an automatic approach.

Biallelic mutations in NRROS cause an early onset lethal microgliopathy.

Smith C; McColl BW; Patir A; Barrington J; Armishaw J; Clarke A; Eaton J; Hobbs V; Mansour S; Nolan M; Rice GI; Rodero MP; Seabra L; Uggenti C; Livingston JH; Bridges LR; Jeffrey IJM; Crow YJ

Acta neuropathologica 2020;139;5;947-951

Biallelic variants in GLE1 with survival beyond neonatal period.

Yates TM; Campeau PM; Ghoumid J; Kibaek M; Larsen MJ; Smol T; Albaba S; Hertz JM; Balasubramanian M

Clinical genetics 2020;98;6;622-625

Biallelic variants in the small optic lobe calpain CAPN15 are associated with congenital eye anomalies, deafness and other neurodevelopmental deficits.

Zha C; Farah CA; Holt RJ; Ceroni F; Al-Abdi L; Thuriot F; Khan AO; Helaby R; Lévesque S; Alkuraya FS; Kraus A; Ragge NK; Sossin WS

Human molecular genetics 2020;29;18;3054-3063

Microphthalmia, coloboma and cataract are part of a spectrum of developmental eye disorders in humans affecting ~12 per 100 000 live births. Currently, variants in over 100 genes are known to underlie these conditions. However, at least 40% of affected individuals remain without a clinical genetic diagnosis, suggesting variants in additional genes may be responsible. Calpain 15 (CAPN15) is an intracellular cysteine protease belonging to the non-classical small optic lobe (SOL) family of calpains, an important class of developmental proteins, as yet uncharacterized in vertebrates. We identified five individuals with microphthalmia and/or coloboma from four independent families carrying homozygous or compound heterozygous predicted damaging variants in CAPN15. Several individuals had additional phenotypes including growth deficits, developmental delay and hearing loss. We generated Capn15 knockout mice that exhibited similar severe developmental eye defects, including anophthalmia, microphthalmia and cataract, and diminished growth. We demonstrate widespread Capn15 expression throughout the brain and central nervous system, strongest during early development, and decreasing postnatally. Together, these findings demonstrate a critical role of CAPN15 in vertebrate developmental eye disorders, and may signify a new developmental pathway.

Biophysical classification of a CACNA1D de novo mutation as a high-risk mutation for a severe neurodevelopmental disorder.

Hofer NT; Tuluc P; Ortner NJ; Nikonishyna YV; Fernándes-Quintero ML; Liedl KR; Flucher BE; Cox H; Striessnig J

Molecular autism 2020;11;1;4

There is increasing evidence that de novo CACNA1D missense mutations inducing increased Cav1.3 L-type Ca2+-channel-function confer a high risk for neurodevelopmental disorders (autism spectrum disorder with and without neurological and endocrine symptoms). Electrophysiological studies demonstrating the presence or absence of typical gain-of-function gating changes could therefore serve as a tool to distinguish likely disease-causing from non-pathogenic de novo CACNA1D variants in affected individuals. We tested this hypothesis for mutation S652L, which has previously been reported in twins with a severe neurodevelopmental disorder in the Deciphering Developmental Disorder Study, but has not been classified as a novel disease mutation.

Clinical findings of 21 previously unreported probands with HNRNPU-related syndrome and comprehensive literature review.

Durkin A; Albaba S; Fry AE; Morton JE; Douglas A; Beleza A; Williams D; Volker-Touw CML; Lynch SA; Canham N; Clowes V; Straub V; Lachlan K; Gibbon F; El Gamal M; Varghese V; Parker MJ; Newbury-Ecob R; Turnpenny PD; Gardham A; Ghali N; Balasubramanian M

American journal of medical genetics. Part A 2020;182;7;1637-1654

With advances in genetic testing and improved access to such advances, whole exome sequencing is becoming a first-line investigation in clinical work-up of children with developmental delay/intellectual disability (ID). As a result, the need to understand the importance of genetic variants and its effect on the clinical phenotype is increasing. Here, we report on the largest cohort of patients with HNRNPU variants. These 21 patients follow on from the previous study published by Yates et al. in 2017 from our group predominantly identified from the Deciphering Developmental Disorders study that reported seven patients with HNRNPU variants. All the probands reported here have a de novo loss-of-function variant. These probands have craniofacial dysmorphic features, in the majority including widely spaced teeth, microcephaly, high arched eyebrows, and palpebral fissure abnormalities. Many of the patients in the group also have moderate to severe ID and seizures that tend to start in early childhood. This series has allowed us to define a novel neurodevelopmental syndrome, with a likely mechanism of haploinsufficiency, and expand substantially on already published literature on HNRNPU-related neurodevelopmental syndrome.

De novo SMARCA2 variants clustered outside the helicase domain cause a new recognizable syndrome with intellectual disability and blepharophimosis distinct from Nicolaides-Baraitser syndrome.

Cappuccio G; Sayou C; Tanno PL; Tisserant E; Bruel AL; Kennani SE; Sá J; Low KJ; Dias C; Havlovicová M; Hančárová M; Eichler EE; Devillard F; Moutton S; Van-Gils J; Dubourg C; Odent S; Gerard B; Piton A; Yamamoto T; Okamoto N; Firth H; Metcalfe K; Moh A; Chapman KA; Aref-Eshghi E; Kerkhof J; Torella A; Nigro V; Perrin L; Piard J; Le Guyader G; Jouan T; Thauvin-Robinet C; Duffourd Y; George-Abraham JK; Buchanan CA; Williams D; Kini U; Wilson K; ; Sousa SB; Hennekam RCM; Sadikovic B; Thevenon J; Govin J; Vitobello A; Brunetti-Pierri N

Genetics in medicine : official journal of the American College of Medical Genetics 2020;22;11;1838-1850

Nontruncating variants in SMARCA2, encoding a catalytic subunit of SWI/SNF chromatin remodeling complex, cause Nicolaides-Baraitser syndrome (NCBRS), a condition with intellectual disability and multiple congenital anomalies. Other disorders due to SMARCA2 are unknown.

Delineation of a Human Mendelian Disorder of the DNA Demethylation Machinery: TET3 Deficiency.

Beck DB; Petracovici A; He C; Moore HW; Louie RJ; Ansar M; Douzgou S; Sithambaram S; Cottrell T; Santos-Cortez RLP; Prijoles EJ; Bend R; Keren B; Mignot C; Nougues MC; Õunap K; Reimand T; Pajusalu S; Zahid M; Saqib MAN; Buratti J; Seaby EG; McWalter K; Telegrafi A; Baldridge D; Shinawi M; Leal SM; Schaefer GB; Stevenson RE; Banka S; Bonasio R; Fahrner JA

American journal of human genetics 2020;106;2;234-245

Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.

Evidence for 28 genetic disorders discovered by combining healthcare and research data.

Kaplanis J; Samocha KE; Wiel L; Zhang Z; Arvai KJ; Eberhardt RY; Gallone G; Lelieveld SH; Martin HC; McRae JF; Short PJ; Torene RI; de Boer E; Danecek P; Gardner EJ; Huang N; Lord J; Martincorena I; Pfundt R; Reijnders MRF; Yeung A; Yntema HG; ; Vissers LELM; Juusola J; Wright CF; Brunner HG; Firth HV; FitzPatrick DR; Barrett JC; Hurles ME; Gilissen C; Retterer K

Nature 2020;586;7831;757-762

De novo mutations in protein-coding genes are a well-established cause of developmental disorders1. However, genes known to be associated with developmental disorders account for only a minority of the observed excess of such de novo mutations1,2. Here, to identify previously undescribed genes associated with developmental disorders, we integrate healthcare and research exome-sequence data from 31,058 parent-offspring trios of individuals with developmental disorders, and develop a simulation-based statistical test to identify gene-specific enrichment of de novo mutations. We identified 285 genes that were significantly associated with developmental disorders, including 28 that had not previously been robustly associated with developmental disorders. Although we detected more genes associated with developmental disorders, much of the excess of de novo mutations in protein-coding genes remains unaccounted for. Modelling suggests that more than 1,000 genes associated with developmental disorders have not yet been described, many of which are likely to be less penetrant than the currently known genes. Research access to clinical diagnostic datasets will be critical for completing the map of genes associated with developmental disorders.

Exome sequencing in patients with antiepileptic drug exposure and complex phenotypes.

Jackson A; Ward H; Bromley RL; Deshpande C; Vasudevan P; Scurr I; Dean J; Shannon N; Berg J; Holder S; Baralle D; Clayton-Smith J;

Archives of disease in childhood 2020;105;4;384-389

Fetal anticonvulsant syndrome (FACS) describes the pattern of physical and developmental problems seen in those children exposed to certain antiepileptic drugs (AEDs) in utero. The diagnosis of FACS is a clinical one and so excluding alternative diagnoses such as genetic disorders is essential.

Genotype-phenotype correlation at codon 1740 of SETD2.

Rabin R; Radmanesh A; Glass IA; Dobyns WB; Aldinger KA; Shieh JT; Romoser S; Bombei H; Dowsett L; Trapane P; Bernat JA; Baker J; Mendelsohn NJ; Popp B; Siekmeyer M; Sorge I; Sansbury FH; Watts P; Foulds NC; Burton J; Hoganson G; Hurst JA; Menzies L; Osio D; Kerecuk L; Cobben JM; Jizi K; Jacquemont S; Bélanger SA; Löhner K; Veenstra-Knol HE; Lemmink HH; Keller-Ramey J; Wentzensen IM; Punj S; McWalter K; Lenberg J; Ellsworth KA; Radtke K; Akbarian S; Pappas J

American journal of medical genetics. Part A 2020;182;9;2037-2048

The SET domain containing 2, histone lysine methyltransferase encoded by SETD2 is a dual-function methyltransferase for histones and microtubules and plays an important role for transcriptional regulation, genomic stability, and cytoskeletal functions. Specifically, SETD2 is associated with trimethylation of histone H3 at lysine 36 (H3K36me3) and methylation of α-tubulin at lysine 40. Heterozygous loss of function and missense variants have previously been described with Luscan-Lumish syndrome (LLS), which is characterized by overgrowth, neurodevelopmental features, and absence of overt congenital anomalies. We have identified 15 individuals with de novo variants in codon 1740 of SETD2 whose features differ from those with LLS. Group 1 consists of 12 individuals with heterozygous variant c.5218C>T p.(Arg1740Trp) and Group 2 consists of 3 individuals with heterozygous variant c.5219G>A p.(Arg1740Gln). The phenotype of Group 1 includes microcephaly, profound intellectual disability, congenital anomalies affecting several organ systems, and similar facial features. Individuals in Group 2 had moderate to severe intellectual disability, low normal head circumference, and absence of additional major congenital anomalies. While LLS is likely due to loss of function of SETD2, the clinical features seen in individuals with variants affecting codon 1740 are more severe suggesting an alternative mechanism, such as gain of function, effects on epigenetic regulation, or posttranslational modification of the cytoskeleton. Our report is a prime example of different mutations in the same gene causing diverging phenotypes and the features observed in Group 1 suggest a new clinically recognizable syndrome uniquely associated with the heterozygous variant c.5218C>T p.(Arg1740Trp) in SETD2.

Human and mouse essentiality screens as a resource for disease gene discovery.

Cacheiro P; Muñoz-Fuentes V; Murray SA; Dickinson ME; Bucan M; Nutter LMJ; Peterson KA; Haselimashhadi H; Flenniken AM; Morgan H; Westerberg H; Konopka T; Hsu CW; Christiansen A; Lanza DG; Beaudet AL; Heaney JD; Fuchs H; Gailus-Durner V; Sorg T; Prochazka J; Novosadova V; Lelliott CJ; Wardle-Jones H; Wells S; Teboul L; Cater H; Stewart M; Hough T; Wurst W; Sedlacek R; Adams DJ; Seavitt JR; Tocchini-Valentini G; Mammano F; Braun RE; McKerlie C; Herault Y; de Angelis MH; Mallon AM; Lloyd KCK; Brown SDM; Parkinson H; Meehan TF; Smedley D; ;

Nature Communications 2020;11;1;655

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery.

Lysine acetyltransferase 8 is involved in cerebral development and syndromic intellectual disability.

Li L; Ghorbani M; Weisz-Hubshman M; Rousseau J; Thiffault I; Schnur RE; Breen C; Oegema R; Weiss MM; Waisfisz Q; Welner S; Kingston H; Hills JA; Boon EM; Basel-Salmon L; Konen O; Goldberg-Stern H; Bazak L; Tzur S; Jin J; Bi X; Bruccoleri M; McWalter K; Cho MT; Scarano M; Schaefer GB; Brooks SS; Hughes SS; van Gassen KLI; van Hagen JM; Pandita TK; Agrawal PB; Campeau PM; Yang XJ

The Journal of clinical investigation 2020;130;3;1431-1445

Epigenetic integrity is critical for many eukaryotic cellular processes. An important question is how different epigenetic regulators control development and influence disease. Lysine acetyltransferase 8 (KAT8) is critical for acetylation of histone H4 at lysine 16 (H4K16), an evolutionarily conserved epigenetic mark. It is unclear what roles KAT8 plays in cerebral development and human disease. Here, we report that cerebrum-specific knockout mice displayed cerebral hypoplasia in the neocortex and hippocampus, along with improper neural stem and progenitor cell (NSPC) development. Mutant cerebrocortical neuroepithelia exhibited faulty proliferation, aberrant neurogenesis, massive apoptosis, and scant H4K16 propionylation. Mutant NSPCs formed poor neurospheres, and pharmacological KAT8 inhibition abolished neurosphere formation. Moreover, we describe KAT8 variants in 9 patients with intellectual disability, seizures, autism, dysmorphisms, and other anomalies. The variants altered chromobarrel and catalytic domains of KAT8, thereby impairing nucleosomal H4K16 acetylation. Valproate was effective for treating epilepsy in at least 2 of the individuals. This study uncovers a critical role of KAT8 in cerebral and NSPC development, identifies 9 individuals with KAT8 variants, and links deficient H4K16 acylation directly to intellectual disability, epilepsy, and other developmental anomalies.

MN1 C-terminal truncation syndrome is a novel neurodevelopmental and craniofacial disorder with partial rhombencephalosynapsis.

Mak CCY; Doherty D; Lin AE; Vegas N; Cho MT; Viot G; Dimartino C; Weisfeld-Adams JD; Lessel D; Joss S; Li C; Gonzaga-Jauregui C; Zarate YA; Ehmke N; Horn D; Troyer C; Kant SG; Lee Y; Ishak GE; Leung G; Barone Pritchard A; Yang S; Bend EG; Filippini F; Roadhouse C; Lebrun N; Mehaffey MG; Martin PM; Apple B; Millan F; Puk O; Hoffer MJV; Henderson LB; McGowan R; Wentzensen IM; Pei S; Zahir FR; Yu M; Gibson WT; Seman A; Steeves M; Murrell JR; Luettgen S; Francisco E; Strom TM; Amlie-Wolf L; Kaindl AM; Wilson WG; Halbach S; Basel-Salmon L; Lev-El N; Denecke J; Vissers LELM; Radtke K; Chelly J; Zackai E; Friedman JM; Bamshad MJ; Nickerson DA; ; Reid RR; Devriendt K; Chae JH; Stolerman E; McDougall C; Powis Z; Bienvenu T; Tan TY; Orenstein N; Dobyns WB; Shieh JT; Choi M; Waggoner D; Gripp KW; Parker MJ; Stoler J; Lyonnet S; Cormier-Daire V; Viskochil D; Hoffman TL; Amiel J; Chung BHY; Gordon CT

Brain : a journal of neurology 2020;143;1;55-68

MN1 encodes a transcriptional co-regulator without homology to other proteins, previously implicated in acute myeloid leukaemia and development of the palate. Large deletions encompassing MN1 have been reported in individuals with variable neurodevelopmental anomalies and non-specific facial features. We identified a cluster of de novo truncating mutations in MN1 in a cohort of 23 individuals with strikingly similar dysmorphic facial features, especially midface hypoplasia, and intellectual disability with severe expressive language delay. Imaging revealed an atypical form of rhombencephalosynapsis, a distinctive brain malformation characterized by partial or complete loss of the cerebellar vermis with fusion of the cerebellar hemispheres, in 8/10 individuals. Rhombencephalosynapsis has no previously known definitive genetic or environmental causes. Other frequent features included perisylvian polymicrogyria, abnormal posterior clinoid processes and persistent trigeminal artery. MN1 is encoded by only two exons. All mutations, including the recurrent variant p.Arg1295* observed in 8/21 probands, fall in the terminal exon or the extreme 3' region of exon 1, and are therefore predicted to result in escape from nonsense-mediated mRNA decay. This was confirmed in fibroblasts from three individuals. We propose that the condition described here, MN1 C-terminal truncation (MCTT) syndrome, is not due to MN1 haploinsufficiency but rather is the result of dominantly acting C-terminally truncated MN1 protein. Our data show that MN1 plays a critical role in human craniofacial and brain development, and opens the door to understanding the biological mechanisms underlying rhombencephalosynapsis.

Mosaicism in ASXL3-related syndrome: Description of five patients from three families.

Schirwani S; Hauser N; Platt A; Punj S; Prescott K; Canham N; Study DDD; Mansour S; Balasubramanian M

European journal of medical genetics 2020;63;6;103925

De novo pathogenic variants in the additional sex combs-like 3 (ASXL3) gene cause a rare multi-systemic neurodevelopmental disorder. There is growing evidence that germline and somatic mosaicism are more common and play a greater role in genetic disorders than previously acknowledged. There is one previous report of ASXL3-related syndrome caused by de novo pathogenic variants in two siblings suggesting gonadal mosaicism. In this report, we present five patients with ASXL3-related syndrome, describing two families comprising two non-twin siblings harbouring apparent de novo pathogenic variants in ASXL3. Parents were clinically unaffected and there was no evidence of mosaicism from genomic DNA on exome-trio data, suggesting germline mosaicism in one of the parents. We also describe clinical details of a patient with typical features of ASXL3-related syndrome and mosaic de novo pathogenic variant in ASXL3 in 30-35% of both blood and saliva sample on trio-exome sequencing. We expand the known genetic basis of ASXL3-related syndromes and discuss mosaicism as a disease mechanism in five patients from three unrelated families. The findings of this report highlight the importance of taking gonadal mosaicism into consideration when counselling families regarding recurrence risk. We also discuss postzygotic mosaicism as a cause of fully penetrant ASXL3-related syndrome.

Novel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome.

Alharatani R; Ververi A; Beleza-Meireles A; Ji W; Mis E; Patterson QT; Griffin JN; Bhujel N; Chang CA; Dixit A; Konstantino M; Healy C; Hannan S; Neo N; Cash A; Li D; Bhoj E; Zackai EH; Cleaver R; Baralle D; McEntagart M; Newbury-Ecob R; Scott R; Hurst JA; Au PYB; Hosey MT; Khokha M; Marciano DK; Lakhani SA; Liu KJ

Human molecular genetics 2020;29;11;1900-1921

CTNND1 encodes the p120-catenin (p120) protein, which has a wide range of functions, including the maintenance of cell-cell junctions, regulation of the epithelial-mesenchymal transition and transcriptional signalling. Due to advances in next-generation sequencing, CTNND1 has been implicated in human diseases including cleft palate and blepharocheilodontic (BCD) syndrome albeit only recently. In this study, we identify eight novel protein-truncating variants, six de novo, in 13 participants from nine families presenting with craniofacial dysmorphisms including cleft palate and hypodontia, as well as congenital cardiac anomalies, limb dysmorphologies and neurodevelopmental disorders. Using conditional deletions in mice as well as CRISPR/Cas9 approaches to target CTNND1 in Xenopus, we identified a subset of phenotypes that can be linked to p120-catenin in epithelial integrity and turnover, and additional phenotypes that suggest mesenchymal roles of CTNND1. We propose that CTNND1 variants have a wider developmental role than previously described and that variations in this gene underlie not only cleft palate and BCD but may be expanded to a broader velocardiofacial-like syndrome.

Opposite Modulation of RAC1 by Mutations in TRIO Is Associated with Distinct, Domain-Specific Neurodevelopmental Disorders.

Barbosa S; Greville-Heygate S; Bonnet M; Godwin A; Fagotto-Kaufmann C; Kajava AV; Laouteouet D; Mawby R; Wai HA; Dingemans AJM; Hehir-Kwa J; Willems M; Capri Y; Mehta SG; Cox H; Goudie D; Vansenne F; Turnpenny P; Vincent M; Cogné B; Lesca G; Hertecant J; Rodriguez D; Keren B; Burglen L; Gérard M; Putoux A; ; Cantagrel V; Siquier-Pernet K; Rio M; Banka S; Sarkar A; Steeves M; Parker M; Clement E; Moutton S; Tran Mau-Them F; Piton A; de Vries BBA; Guille M; Debant A; Schmidt S; Baralle D

American journal of human genetics 2020;106;3;338-355

The Rho-guanine nucleotide exchange factor (RhoGEF) TRIO acts as a key regulator of neuronal migration, axonal outgrowth, axon guidance, and synaptogenesis by activating the GTPase RAC1 and modulating actin cytoskeleton remodeling. Pathogenic variants in TRIO are associated with neurodevelopmental diseases, including intellectual disability (ID) and autism spectrum disorders (ASD). Here, we report the largest international cohort of 24 individuals with confirmed pathogenic missense or nonsense variants in TRIO. The nonsense mutations are spread along the TRIO sequence, and affected individuals show variable neurodevelopmental phenotypes. In contrast, missense variants cluster into two mutational hotspots in the TRIO sequence, one in the seventh spectrin repeat and one in the RAC1-activating GEFD1. Although all individuals in this cohort present with developmental delay and a neuro-behavioral phenotype, individuals with a pathogenic variant in the seventh spectrin repeat have a more severe ID associated with macrocephaly than do most individuals with GEFD1 variants, who display milder ID and microcephaly. Functional studies show that the spectrin and GEFD1 variants cause a TRIO-mediated hyper- or hypo-activation of RAC1, respectively, and we observe a striking correlation between RAC1 activation levels and the head size of the affected individuals. In addition, truncations in TRIO GEFD1 in the vertebrate model X. tropicalis induce defects that are concordant with the human phenotype. This work demonstrates distinct clinical and molecular disorders clustering in the GEFD1 and seventh spectrin repeat domains and highlights the importance of tight control of TRIO-RAC1 signaling in neuronal development.

Partial Loss of USP9X Function Leads to a Male Neurodevelopmental and Behavioral Disorder Converging on Transforming Growth Factor β Signaling.

Johnson BV; Kumar R; Oishi S; Alexander S; Kasherman M; Vega MS; Ivancevic A; Gardner A; Domingo D; Corbett M; Parnell E; Yoon S; Oh T; Lines M; Lefroy H; Kini U; Van Allen M; Grønborg S; Mercier S; Küry S; Bézieau S; Pasquier L; Raynaud M; Afenjar A; Billette de Villemeur T; Keren B; Désir J; Van Maldergem L; Marangoni M; Dikow N; Koolen DA; VanHasselt PM; Weiss M; Zwijnenburg P; Sa J; Reis CF; López-Otín C; Santiago-Fernández O; Fernández-Jaén A; Rauch A; Steindl K; Joset P; Goldstein A; Madan-Khetarpal S; Infante E; Zackai E; Mcdougall C; Narayanan V; Ramsey K; Mercimek-Andrews S; Pena L; Shashi V; ; Schoch K; Sullivan JA; Pinto E Vairo F; Pichurin PN; Ewing SA; Barnett SS; Klee EW; Perry MS; Koenig MK; Keegan CE; Schuette JL; Asher S; Perilla-Young Y; Smith LD; Rosenfeld JA; Bhoj E; Kaplan P; Li D; Oegema R; van Binsbergen E; van der Zwaag B; Smeland MF; Cutcutache I; Page M; Armstrong M; Lin AE; Steeves MA; Hollander ND; Hoffer MJV; Reijnders MRF; Demirdas S; Koboldt DC; Bartholomew D; Mosher TM; Hickey SE; Shieh C; Sanchez-Lara PA; Graham JM; Tezcan K; Schaefer GB; Danylchuk NR; Asamoah A; Jackson KE; Yachelevich N; Au M; Pérez-Jurado LA; Kleefstra T; Penzes P; Wood SA; Burne T; Pierson TM; Piper M; Gécz J; Jolly LA

Biological psychiatry 2020;87;2;100-112

The X-chromosome gene USP9X encodes a deubiquitylating enzyme that has been associated with neurodevelopmental disorders primarily in female subjects. USP9X escapes X inactivation, and in female subjects de novo heterozygous copy number loss or truncating mutations cause haploinsufficiency culminating in a recognizable syndrome with intellectual disability and signature brain and congenital abnormalities. In contrast, the involvement of USP9X in male neurodevelopmental disorders remains tentative.

Phenotypic and biochemical analysis of an international cohort of individuals with variants in NAA10 and NAA15.

Cheng H; Gottlieb L; Marchi E; Kleyner R; Bhardwaj P; Rope AF; Rosenheck S; Moutton S; Philippe C; Eyaid W; Alkuraya FS; Toribio J; Mena R; Prada CE; Stessman H; Bernier R; Wermuth M; Kauffmann B; Blaumeiser B; Kooy RF; Baralle D; Mancini GMS; Conway SJ; Xia F; Chen Z; Meng L; Mihajlovic L; Marmorstein R; Lyon GJ

Human molecular genetics 2020;29;5;877-878

Phenotypic expansion of POGZ-related intellectual disability syndrome (White-Sutton syndrome).

Assia Batzir N; Posey JE; Song X; Akdemir ZC; Rosenfeld JA; Brown CW; Chen E; Holtrop SG; Mizerik E; Nieto Moreno M; Payne K; Raas-Rothschild A; Scott R; Vernon HJ; Zadeh N; ; Lupski JR; Sutton VR

American journal of medical genetics. Part A 2020;182;1;38-52

White-Sutton syndrome (WHSUS) is a recently-identified genetic disorder resulting from de novo heterozygous pathogenic variants in POGZ. Thus far, over 50 individuals have been reported worldwide, however phenotypic characterization and data regarding the natural history are still incomplete. Here we report the clinical features of 22 individuals with 21 unique loss of function POGZ variants. We observed a broad spectrum of intellectual disability and/or developmental delay with or without autism, and speech delay in all individuals. Other common problems included ocular abnormalities, hearing loss and gait abnormalities. A validated sleep disordered breathing questionnaire identified symptoms of obstructive sleep apnea in 4/12 (33%) individuals. A higher-than-expected proportion of cases also had gastrointestinal phenotypes, both functional and anatomical, as well as genitourinary anomalies. In line with previous publications, we observed an increased body mass index (BMI) z-score compared to the general population (mean 0.59, median 0.9; p 0.0253). Common facial features included microcephaly, broad forehead, midface hypoplasia, triangular mouth, broad nasal root and flat nasal bridge. Analysis of the Baylor Genetics clinical laboratory database revealed that POGZ variants were implicated in approximately 0.14% of cases who underwent clinical exome sequencing for neurological indications with or without involvement of other body systems. This study describes a greater allelic series and expands the phenotypic spectrum of this new syndromic form of intellectual disability and autism.

Phenotypic spectrum and transcriptomic profile associated with germline variants in TRAF7.

Castilla-Vallmanya L; Selmer KK; Dimartino C; Rabionet R; Blanco-Sánchez B; Yang S; Reijnders MRF; van Essen AJ; Oufadem M; Vigeland MD; Stadheim B; Houge G; Cox H; Kingston H; Clayton-Smith J; Innis JW; Iascone M; Cereda A; Gabbiadini S; Chung WK; Sanders V; Charrow J; Bryant E; Millichap J; Vitobello A; Thauvin C; Mau-Them FT; Faivre L; Lesca G; Labalme A; Rougeot C; Chatron N; Sanlaville D; Christensen KM; Kirby A; Lewandowski R; Gannaway R; Aly M; Lehman A; Clarke L; Graul-Neumann L; Zweier C; Lessel D; Lozic B; Aukrust I; Peretz R; Stratton R; Smol T; Dieux-Coëslier A; Meira J; Wohler E; Sobreira N; Beaver EM; Heeley J; Briere LC; High FA; Sweetser DA; Walker MA; Keegan CE; Jayakar P; Shinawi M; Kerstjens-Frederikse WS; Earl DL; Siu VM; Reesor E; Yao T; Hegele RA; Vaske OM; Rego S; ; Shapiro KA; Wong B; Gambello MJ; McDonald M; Karlowicz D; Colombo R; Serretti A; Pais L; O'Donnell-Luria A; Wray A; Sadedin S; Chong B; Tan TY; Christodoulou J; White SM; Slavotinek A; Barbouth D; Morel Swols D; Parisot M; Bole-Feysot C; Nitschké P; Pingault V; Munnich A; Cho MT; Cormier-Daire V; Balcells S; Lyonnet S; Grinberg D; Amiel J; Urreizti R; Gordon CT

Genetics in medicine : official journal of the American College of Medical Genetics 2020;22;7;1215-1226

Somatic variants in tumor necrosis factor receptor-associated factor 7 (TRAF7) cause meningioma, while germline variants have recently been identified in seven patients with developmental delay and cardiac, facial, and digital anomalies. We aimed to define the clinical and mutational spectrum associated with TRAF7 germline variants in a large series of patients, and to determine the molecular effects of the variants through transcriptomic analysis of patient fibroblasts.

PRIM1 deficiency causes a distinctive primordial dwarfism syndrome.

Parry DA; Tamayo-Orrego L; Carroll P; Marsh JA; Greene P; Murina O; Uggenti C; Leitch A; ; Káposzta R; Merő G; Nagy A; Orlik B; Kovács-Pászthy B; Quigley AJ; Riszter M; Rankin J; Reijns MAM; Szakszon K; Jackson AP;

Genes & development 2020;34;21-22;1520-1533

DNA replication is fundamental for cell proliferation in all organisms. Nonetheless, components of the replisome have been implicated in human disease, and here we report PRIM1 encoding the catalytic subunit of DNA primase as a novel disease gene. Using a variant classification agnostic approach, biallelic mutations in PRIM1 were identified in five individuals. PRIM1 protein levels were markedly reduced in patient cells, accompanied by replication fork asymmetry, increased interorigin distances, replication stress, and prolonged S-phase duration. Consequently, cell proliferation was markedly impaired, explaining the patients' extreme growth failure. Notably, phenotypic features distinct from those previously reported with DNA polymerase genes were evident, highlighting differing developmental requirements for this core replisome component that warrant future investigation.

Recurrent De Novo NAHR Reciprocal Duplications in the ATAD3 Gene Cluster Cause a Neurogenetic Trait with Perturbed Cholesterol and Mitochondrial Metabolism.

Gunning AC; Strucinska K; Muñoz Oreja M; Parrish A; Caswell R; Stals KL; Durigon R; Durlacher-Betzer K; Cunningham MH; Grochowski CM; Baptista J; Tysoe C; Baple E; Lahiri N; Homfray T; Scurr I; Armstrong C; Dean J; Fernandez Pelayo U; Jones AWE; Taylor RW; Misra VK; Yoon WH; Wright CF; Lupski JR; Spinazzola A; Harel T; Holt IJ; Ellard S

American journal of human genetics 2020;106;2;272-279

Recent studies have identified both recessive and dominant forms of mitochondrial disease that result from ATAD3A variants. The recessive form includes subjects with biallelic deletions mediated by non-allelic homologous recombination. We report five unrelated neonates with a lethal metabolic disorder characterized by cardiomyopathy, corneal opacities, encephalopathy, hypotonia, and seizures in whom a monoallelic reciprocal duplication at the ATAD3 locus was identified. Analysis of the breakpoint junction fragment indicated that these 67 kb heterozygous duplications were likely mediated by non-allelic homologous recombination at regions of high sequence identity in ATAD3A exon 11 and ATAD3C exon 7. At the recombinant junction, the duplication allele produces a fusion gene derived from ATAD3A and ATAD3C, the protein product of which lacks key functional residues. Analysis of fibroblasts derived from two affected individuals shows that the fusion gene product is expressed and stable. These cells display perturbed cholesterol and mitochondrial DNA organization similar to that observed for individuals with severe ATAD3A deficiency. We hypothesize that the fusion protein acts through a dominant-negative mechanism to cause this fatal mitochondrial disorder. Our data delineate a molecular diagnosis for this disorder, extend the clinical spectrum associated with structural variation at the ATAD3 locus, and identify a third mutational mechanism for ATAD3 gene cluster variants. These results further affirm structural variant mutagenesis mechanisms in sporadic disease traits, emphasize the importance of copy number analysis in molecular genomic diagnosis, and highlight some of the challenges of detecting and interpreting clinically relevant rare gene rearrangements from next-generation sequencing data.

Recurrent heterozygous PAX6 missense variants cause severe bilateral microphthalmia via predictable effects on DNA-protein interaction.

Williamson KA; Hall HN; Owen LJ; Livesey BJ; Hanson IM; Adams GGW; Bodek S; Calvas P; Castle B; Clarke M; Deng AT; Edery P; Fisher R; Gillessen-Kaesbach G; Heon E; Hurst J; Josifova D; Lorenz B; McKee S; Meire F; Moore AT; Parker M; Reiff CM; Self J; Tobias ES; Verheij JBGM; Willems M; Williams D; van Heyningen V; Marsh JA; FitzPatrick DR

Genetics in medicine : official journal of the American College of Medical Genetics 2020;22;3;598-609

Most classical aniridia is caused by PAX6 haploinsufficiency. PAX6 missense variants can be hypomorphic or mimic haploinsufficiency. We hypothesized that missense variants also cause previously undescribed disease by altering the affinity and/or specificity of PAX6 genomic interactions.

SCN3A-Related Neurodevelopmental Disorder: A Spectrum of Epilepsy and Brain Malformation.

Zaman T; Helbig KL; Clatot J; Thompson CH; Kang SK; Stouffs K; Jansen AE; Verstraete L; Jacquinet A; Parrini E; Guerrini R; Fujiwara Y; Miyatake S; Ben-Zeev B; Bassan H; Reish O; Marom D; Hauser N; Vu TA; Ackermann S; Spencer CE; Lippa N; Srinivasan S; Charzewska A; Hoffman-Zacharska D; Fitzpatrick D; Harrison V; Vasudevan P; Joss S; Pilz DT; Fawcett KA; Helbig I; Matsumoto N; Kearney JA; Fry AE; Goldberg EM

Annals of neurology 2020;88;2;348-362

Pathogenic variants in SCN3A, encoding the voltage-gated sodium channel subunit Nav1.3, cause severe childhood onset epilepsy and malformation of cortical development. Here, we define the spectrum of clinical, genetic, and neuroimaging features of SCN3A-related neurodevelopmental disorder.

SLC12A2 variants cause a neurodevelopmental disorder or cochleovestibular defect.

McNeill A; Iovino E; Mansard L; Vache C; Baux D; Bedoukian E; Cox H; Dean J; Goudie D; Kumar A; Newbury-Ecob R; Fallerini C; Renieri A; Lopergolo D; Mari F; Blanchet C; Willems M; Roux AF; Pippucci T; Delpire E

Brain : a journal of neurology 2020;143;8;2380-2387

The SLC12 gene family consists of SLC12A1-SLC12A9, encoding electroneutral cation-coupled chloride co-transporters. SCL12A2 has been shown to play a role in corticogenesis and therefore represents a strong candidate neurodevelopmental disorder gene. Through trio exome sequencing we identified de novo mutations in SLC12A2 in six children with neurodevelopmental disorders. All had developmental delay or intellectual disability ranging from mild to severe. Two had sensorineural deafness. We also identified SLC12A2 variants in three individuals with non-syndromic bilateral sensorineural hearing loss and vestibular areflexia. The SLC12A2 de novo mutation rate was demonstrated to be significantly elevated in the deciphering developmental disorders cohort. All tested variants were shown to reduce co-transporter function in Xenopus laevis oocytes. Analysis of SLC12A2 expression in foetal brain at 16-18 weeks post-conception revealed high expression in radial glial cells, compatible with a role in neurogenesis. Gene co-expression analysis in cells robustly expressing SLC12A2 at 16-18 weeks post-conception identified a transcriptomic programme associated with active neurogenesis. We identify SLC12A2 de novo mutations as the cause of a novel neurodevelopmental disorder and bilateral non-syndromic sensorineural hearing loss and provide further data supporting a role for this gene in human neurodevelopment.

The CHD4-related syndrome: a comprehensive investigation of the clinical spectrum, genotype-phenotype correlations, and molecular basis.

Weiss K; Lazar HP; Kurolap A; Martinez AF; Paperna T; Cohen L; Smeland MF; Whalen S; Heide S; Keren B; Terhal P; Irving M; Takaku M; Roberts JD; Petrovich RM; Schrier Vergano SA; Kenney A; Hove H; DeChene E; Quinonez SC; Colin E; Ziegler A; Rumple M; Jain M; Monteil D; Roeder ER; Nugent K; van Haeringen A; Gambello M; Santani A; Medne L; Krock B; Skraban CM; Zackai EH; Dubbs HA; Smol T; Ghoumid J; Parker MJ; Wright M; Turnpenny P; Clayton-Smith J; Metcalfe K; Kurumizaka H; Gelb BD; Baris Feldman H; Campeau PM; Muenke M; Wade PA; Lachlan K

Genetics in medicine : official journal of the American College of Medical Genetics 2020;22;2;389-397

Sifrim-Hitz-Weiss syndrome (SIHIWES) is a recently described multisystemic neurodevelopmental disorder caused by de novo variants inCHD4. In this study, we investigated the clinical spectrum of the disorder, genotype-phenotype correlations, and the effect of different missense variants on CHD4 function.

Trappc9 deficiency causes parent-of-origin dependent microcephaly and obesity.

Liang ZS; Cimino I; Yalcin B; Raghupathy N; Vancollie VE; Ibarra-Soria X; Firth HV; Rimmington D; Farooqi IS; Lelliott CJ; Munger SC; O'Rahilly S; Ferguson-Smith AC; Coll AP; Logan DW

PLoS genetics 2020;16;9;e1008916

Some imprinted genes exhibit parental origin specific expression bias rather than being transcribed exclusively from one copy. The physiological relevance of this remains poorly understood. In an analysis of brain-specific allele-biased expression, we identified that Trappc9, a cellular trafficking factor, was expressed predominantly (~70%) from the maternally inherited allele. Loss-of-function mutations in human TRAPPC9 cause a rare neurodevelopmental syndrome characterized by microcephaly and obesity. By studying Trappc9 null mice we discovered that homozygous mutant mice showed a reduction in brain size, exploratory activity and social memory, as well as a marked increase in body weight. A role for Trappc9 in energy balance was further supported by increased ad libitum food intake in a child with TRAPPC9 deficiency. Strikingly, heterozygous mice lacking the maternal allele (70% reduced expression) had pathology similar to homozygous mutants, whereas mice lacking the paternal allele (30% reduction) were phenotypically normal. Taken together, we conclude that Trappc9 deficient mice recapitulate key pathological features of TRAPPC9 mutations in humans and identify a role for Trappc9 and its imprinting in controlling brain development and metabolism.

Widening of the genetic and clinical spectrum of Lamb-Shaffer syndrome, a neurodevelopmental disorder due to SOX5 haploinsufficiency.

Zawerton A; Mignot C; Sigafoos A; Blackburn PR; Haseeb A; McWalter K; Ichikawa S; Nava C; Keren B; Charles P; Marey I; Tabet AC; Levy J; Perrin L; Hartmann A; Lesca G; Schluth-Bolard C; Monin P; Dupuis-Girod S; Guillen Sacoto MJ; Schnur RE; Zhu Z; Poisson A; El Chehadeh S; Alembik Y; Bruel AL; Lehalle D; Nambot S; Moutton S; Odent S; Jaillard S; Dubourg C; Hilhorst-Hofstee Y; Barbaro-Dieber T; Ortega L; Bhoj EJ; Masser-Frye D; Bird LM; Lindstrom K; Ramsey KM; Narayanan V; Fassi E; Willing M; Cole T; Salter CG; Akilapa R; Vandersteen A; Canham N; Rump P; Gerkes EH; Klein Wassink-Ruiter JS; Bijlsma E; Hoffer MJV; Vargas M; Wojcik A; Cherik F; Francannet C; Rosenfeld JA; Machol K; Scott DA; Bacino CA; Wang X; Clark GD; Bertoli M; Zwolinski S; Thomas RH; Akay E; Chang RC; Bressi R; Sanchez Russo R; Srour M; Russell L; Goyette AE; Dupuis L; Mendoza-Londono R; Karimov C; Joseph M; Nizon M; Cogné B; Kuechler A; Piton A; ; Klee EW; Lefebvre V; Clark KJ; Depienne C

Genetics in medicine : official journal of the American College of Medical Genetics 2020;22;3;524-537

Lamb-Shaffer syndrome (LAMSHF) is a neurodevelopmental disorder described in just over two dozen patients with heterozygous genetic alterations involving SOX5, a gene encoding a transcription factor regulating cell fate and differentiation in neurogenesis and other discrete developmental processes. The genetic alterations described so far are mainly microdeletions. The present study was aimed at increasing our understanding of LAMSHF, its clinical and genetic spectrum, and the pathophysiological mechanisms involved.

ZMYND11-related syndromic intellectual disability: 16 patients delineating and expanding the phenotypic spectrum.

Yates TM; Drucker M; Barnicoat A; Low K; Gerkes EH; Fry AE; Parker MJ; O'Driscoll M; Charles P; Cox H; Marey I; Keren B; Rinne T; McEntagart M; Ramachandran V; Drury S; Vansenne F; Sival DA; Herkert JC; Callewaert B; Tan WH; Balasubramanian M

Human mutation 2020;41;5;1042-1050

Pathogenic variants in ZMYND11, which acts as a transcriptional repressor, have been associated with intellectual disability, behavioral abnormalities, and seizures. Only 11 affected individuals have been reported to date, and the phenotype associated with pathogenic variants in this gene have not been fully defined. Here, we present 16 additional patients with predicted pathogenic heterozygous variants in including four individuals from the same family, to further delineate and expand the genotypic and phenotypic spectrum of ZMYND11-related syndromic intellectual disability. The associated phenotype includes developmental delay, particularly affecting speech, mild-moderate intellectual disability, significant behavioral abnormalities, seizures, and hypotonia. There are subtle shared dysmorphic features, including prominent eyelashes and eyebrows, a depressed nasal bridge with bulbous nasal tip, anteverted nares, thin vermilion of the upper lip, and wide mouth. Novel features include brachydactyly and tooth enamel hypoplasia. Most identified variants are likely to result in premature truncation and/or nonsense-mediated decay. Two ZMYND11 variants located in the final exon-p.(Gln586*) (likely escaping nonsense-mediated decay) and p.(Cys574Arg)-are predicted to disrupt the MYND-type zinc-finger motif and likely interfere with binding to its interaction partners. Hence, the homogeneous phenotype likely results from a common mechanism of loss-of-function.

A maternally inherited frameshift CDKL5 variant in a male with global developmental delay and late-onset generalized epilepsy.

Fraser H; Goldman A; Wright R; ; Banka S

American journal of medical genetics. Part A 2019;179;3;507-511

Pathogenic CDKL5 variants cause an X-linked dominant infantile epileptic encephalopathy, predominantly in females. This condition is characterized by an early-onset severe mixed seizure disorder. We present a maternally inherited frameshift CDKL5 c.2809_2810insA p.(Cys937Ter) variant in a 13-year-old male with severe intellectual disability and late-onset generalized epilepsy. Interestingly, the variant segregation in the family is consistent with an X-linked recessive inheritance pattern, which has not previously been described with this gene. This variant is expected to result in truncation of some CDKL5 transcripts, which could potentially account for the later seizure onset and atypical inheritance pattern. Though the possibility of this variant not being causal cannot be completely excluded, this case adds to the variability of the documented phenotypic profile and to the debate around the role of C-terminus variants in CDKL5-related disease.

A novel NAA10 p.(R83H) variant with impaired acetyltransferase activity identified in two boys with ID and microcephaly.

Ree R; Geithus AS; Tørring PM; Sørensen KP; Damkjær M; ; Lynch SA; Arnesen T

BMC medical genetics 2019;20;1;101

N-terminal acetylation is a common protein modification in human cells and is catalysed by N-terminal acetyltransferases (NATs), mostly cotranslationally. The NAA10-NAA15 (NatA) protein complex is the major NAT, responsible for acetylating ~ 40% of human proteins. Recently, NAA10 germline variants were found in patients with the X-linked lethal Ogden syndrome, and in other familial or de novo cases with variable degrees of developmental delay, intellectual disability (ID) and cardiac anomalies.

A Syndromic Neurodevelopmental Disorder Caused by Mutations in SMARCD1, a Core SWI/SNF Subunit Needed for Context-Dependent Neuronal Gene Regulation in Flies.

Nixon KCJ; Rousseau J; Stone MH; Sarikahya M; Ehresmann S; Mizuno S; Matsumoto N; Miyake N; ; Baralle D; McKee S; Izumi K; Ritter AL; Heide S; Héron D; Depienne C; Titheradge H; Kramer JM; Campeau PM

American journal of human genetics 2019;104;4;596-610

Mutations in several genes encoding components of the SWI/SNF chromatin remodeling complex cause neurodevelopmental disorders (NDDs). Here, we report on five individuals with mutations in SMARCD1; the individuals present with developmental delay, intellectual disability, hypotonia, feeding difficulties, and small hands and feet. Trio exome sequencing proved the mutations to be de novo in four of the five individuals. Mutations in other SWI/SNF components cause Coffin-Siris syndrome, Nicolaides-Baraitser syndrome, or other syndromic and non-syndromic NDDs. Although the individuals presented here have dysmorphisms and some clinical overlap with these syndromes, they lack their typical facial dysmorphisms. To gain insight into the function of SMARCD1 in neurons, we investigated the Drosophila ortholog Bap60 in postmitotic memory-forming neurons of the adult Drosophila mushroom body (MB). Targeted knockdown of Bap60 in the MB of adult flies causes defects in long-term memory. Mushroom-body-specific transcriptome analysis revealed that Bap60 is required for context-dependent expression of genes involved in neuron function and development in juvenile flies when synaptic connections are actively being formed in response to experience. Taken together, we identify an NDD caused by SMARCD1 mutations and establish a role for the SMARCD1 ortholog Bap60 in the regulation of neurodevelopmental genes during a critical time window of juvenile adult brain development when neuronal circuits that are required for learning and memory are formed.

Bi-allelic Loss-of-Function CACNA1B Mutations in Progressive Epilepsy-Dyskinesia.

Gorman KM; Meyer E; Grozeva D; Spinelli E; McTague A; Sanchis-Juan A; Carss KJ; Bryant E; Reich A; Schneider AL; Pressler RM; Simpson MA; Debelle GD; Wassmer E; Morton J; Sieciechowicz D; Jan-Kamsteeg E; Paciorkowski AR; King MD; Cross JH; Poduri A; Mefford HC; Scheffer IE; Haack TB; McCullagh G; ; ; ; Millichap JJ; Carvill GL; Clayton-Smith J; Maher ER; Raymond FL; Kurian MA

American journal of human genetics 2019;104;5;948-956

The occurrence of non-epileptic hyperkinetic movements in the context of developmental epileptic encephalopathies is an increasingly recognized phenomenon. Identification of causative mutations provides an important insight into common pathogenic mechanisms that cause both seizures and abnormal motor control. We report bi-allelic loss-of-function CACNA1B variants in six children from three unrelated families whose affected members present with a complex and progressive neurological syndrome. All affected individuals presented with epileptic encephalopathy, severe neurodevelopmental delay (often with regression), and a hyperkinetic movement disorder. Additional neurological features included postnatal microcephaly and hypotonia. Five children died in childhood or adolescence (mean age of death: 9 years), mainly as a result of secondary respiratory complications. CACNA1B encodes the pore-forming subunit of the pre-synaptic neuronal voltage-gated calcium channel Cav2.2/N-type, crucial for SNARE-mediated neurotransmission, particularly in the early postnatal period. Bi-allelic loss-of-function variants in CACNA1B are predicted to cause disruption of Ca2+ influx, leading to impaired synaptic neurotransmission. The resultant effect on neuronal function is likely to be important in the development of involuntary movements and epilepsy. Overall, our findings provide further evidence for the key role of Cav2.2 in normal human neurodevelopment.

Biallelic human ITCH variants causing a multisystem disease with dysmorphic features: A second report.

Brittain HK; Feary J; Rosenthal M; Spoudeas H; ; Wilson LC

American journal of medical genetics. Part A 2019;179;7;1346-1350

We report a 23 year old female with biallelic truncating variants in the ITCH (Itchy E3 Ubiquitin protein ligase, mouse homolog of; OMIM60649) gene associated with marked short stature, severe early onset chronic lung disease resembling asthma, dysmorphic facial features, and symmetrical camptodactyly of the fingers but normal intellect. The condition has only been reported once previously (Lohr et al., American Journal of Human Genetics, 2010, 86, 447-453) in 10 children from an Old Order Amish family found to have a homozygous frameshift truncating variant in association with failure to thrive, chronic lung disease, motor and cognitive delay, and variable autoimmune diseases including autoimmune hepatitis, enteropathy, hypothyroidism, and diabetes. The condition is listed in OMIM as Autoimmune disease, Multisystem with Facial Dysmorphism (OMIM613385). The clinical course as well as the dysmorphic facial and limb features overlap closely with our patient. We believe the triad of marked syndromic short stature, chronic lung disease, and dysmorphism (with or without cognitive impairment and wider autoimmune involvement) is distinctive.

Cardiac disorders and structural brain abnormalities are commonly associated with hypospadias in children with neurodevelopmental disorders.

Gazdagh GE; Wang C; McGowan R; Tobias ES; Ahmed SF;

Clinical dysmorphology 2019;28;3;114-119

The objective of our study was to use an established cohort of boys to investigate common patterns of malformations in those with hypospadias. We performed a retrospective review of the phenotype of participants in the Deciphering Developmental Disorders Study with neurodevelopmental delay and an 'Abnormality of the genital system'. This group was divided into two subgroups: those with hypospadias and without hypospadias. Associated phenotypes of the two subgroups were compared and analysed. Of the 166 Deciphering Developmental Disorders participants with hypospadias and neurodevelopmental delay, 47 (28%) had cardiovascular and 40 (24%) had structural brain abnormalities. The rate of cardiovascular abnormalities in those with neurodevelopmental delay and genital abnormalities other than hypospadias (N = 645) was lower at 19% (P = 0.001). In addition, structural brain malformations were higher at 24% in the hypospadias group versus 15% in the group without hypospadias (P = 0.002). The constellation of these features occured at a higher rate in the hypospadias group versus the no hypospadias group (P = 0.038). In summary, this is the first study to indicate that cardiovascular and brain abnormalities are frequently encountered in association with hypospadias in children with neurodevelopmental disorders. Not only do these associations provide insight into the underlying aetiology but also they highlight the multisystem involvement in conditions with hypospadias.

Cerebrofaciothoracic dysplasia: Four new patients with a recurrent TMCO1 pathogenic variant.

Michael Yates T; Ng OH; Offiah AC; Willoughby J; Berg JN; ; Johnson DS

American journal of medical genetics. Part A 2019;179;1;43-49

Biallelic loss of function variants in the TMCO1 gene have been previously demonstrated to result in cerebrofaciothoracic dysplasia (CFTD; MIM #213980). The phenotype of this condition includes severe intellectual disability, as well as distinctive craniofacial features, including brachycephaly, synophrys, arched eyebrows, "cupid's bow" upper lip, and microdontia. In addition, nonspecific skeletal anomalies are common, including bifid ribs, scoliosis, and spinal fusion. Only 19 molecularly confirmed patients have been previously described. Here, we present four patients with CFTD, including three brothers from a Pakistani background and an additional unrelated white Scottish patient. All share the characteristic craniofacial appearance, with severe intellectual disability and skeletal abnormalities. We further define the phenotype with comparison to the published literature, and present images to define the dysmorphic features in a previously unreported ethnic group. All of our patient series are homozygous for the same c.292_293del (p.Ser98*) TMCO1 pathogenic variant, which has been previously reported only in an isolated Amish population. Thus we provide evidence that CFTD may be more common than previously thought. The patients presented here further delineate the phenotypic spectrum of CFTD and provide evidence for a recurrent pathogenic variant in TMCO1.

Clinical exome sequencing reveals locus heterogeneity and phenotypic variability of cohesinopathies.

Yuan B; Neira J; Pehlivan D; Santiago-Sim T; Song X; Rosenfeld J; Posey JE; Patel V; Jin W; Adam MP; Baple EL; Dean J; Fong CT; Hickey SE; Hudgins L; Leon E; Madan-Khetarpal S; Rawlins L; Rustad CF; Stray-Pedersen A; Tveten K; Wenger O; Diaz J; Jenkins L; Martin L; McGuire M; Pietryga M; Ramsdell L; Slattery L; ; Abid F; Bertuch AA; Grange D; Immken L; Schaaf CP; Van Esch H; Bi W; Cheung SW; Breman AM; Smith JL; Shaw C; Crosby AH; Eng C; Yang Y; Lupski JR; Xiao R; Liu P

Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;3;663-675

Defects in the cohesin pathway are associated with cohesinopathies, notably Cornelia de Lange syndrome (CdLS). We aimed to delineate pathogenic variants in known and candidate cohesinopathy genes from a clinical exome perspective.

Clinical Presentation of a Complex Neurodevelopmental Disorder Caused by Mutations in ADNP.

Van Dijck A; Vulto-van Silfhout AT; Cappuyns E; van der Werf IM; Mancini GM; Tzschach A; Bernier R; Gozes I; Eichler EE; Romano C; Lindstrand A; Nordgren A; ; Kvarnung M; Kleefstra T; de Vries BBA; Küry S; Rosenfeld JA; Meuwissen ME; Vandeweyer G; Kooy RF

Biological psychiatry 2019;85;4;287-297

In genome-wide screening studies for de novo mutations underlying autism and intellectual disability, mutations in the ADNP gene are consistently reported among the most frequent. ADNP mutations have been identified in children with autism spectrum disorder comorbid with intellectual disability, distinctive facial features, and deficits in multiple organ systems. However, a comprehensive clinical description of the Helsmoortel-Van der Aa syndrome is lacking.

Clinical spectrum of POLR3-related leukodystrophy caused by biallelic POLR1C pathogenic variants.

Gauquelin L; Cayami FK; Sztriha L; Yoon G; Tran LT; Guerrero K; Hocke F; van Spaendonk RML; Fung EL; D'Arrigo S; Vasco G; Thiffault I; Niyazov DM; Person R; Lewis KS; Wassmer E; Prescott T; Fallon P; McEntagart M; Rankin J; Webster R; Philippi H; van de Warrenburg B; Timmann D; Dixit A; Searle C; ; Thakur N; Kruer MC; Sharma S; Vanderver A; Tonduti D; van der Knaap MS; Bertini E; Goizet C; Fribourg S; Wolf NI; Bernard G

Neurology. Genetics 2019;5;6;e369

To determine the clinical, radiologic, and molecular characteristics of RNA polymerase III-related leukodystrophy (POLR3-HLD) caused by biallelic POLR1C pathogenic variants.

Clinically-relevant postzygotic mosaicism in parents and children with developmental disorders in trio exome sequencing data.

Wright CF; Prigmore E; Rajan D; Handsaker J; McRae J; Kaplanis J; Fitzgerald TW; FitzPatrick DR; Firth HV; Hurles ME

Nature Communications 2019;10;1;2985

Mosaic genetic variants can have major clinical impact. We systematically analyse trio exome sequence data from 4,293 probands from the DDD Study with severe developmental disorders for pathogenic postzygotic mosaicism (PZM) in the child or a clinically-unaffected parent, and use ultrahigh-depth sequencing to validate candidate mosaic variants. We observe that levels of mosaicism for small genetic variants are usually equivalent in both saliva and blood and ~3% of causative de novo mutations exhibit PZM; this is an important observation, as the sibling recurrence risk is extremely low. We identify parental PZM in 21 trios (0.5% of trios), resulting in a substantially increased sibling recurrence risk in future pregnancies. Together, these forms of mosaicism account for 40 (1%) diagnoses in our cohort. Likely child-PZM mutations occur equally on both parental haplotypes, and the penetrance of detectable mosaic pathogenic variants overall is likely to be less than half that of constitutive variants.

Contribution of retrotransposition to developmental disorders.

Gardner EJ; Prigmore E; Gallone G; Danecek P; Samocha KE; Handsaker J; Gerety SS; Ironfield H; Short PJ; Sifrim A; Singh T; Chandler KE; Clement E; Lachlan KL; Prescott K; Rosser E; FitzPatrick DR; Firth HV; Hurles ME

Nature Communications 2019;10;1;4630

Mobile genetic Elements (MEs) are segments of DNA which can copy themselves and other transcribed sequences through the process of retrotransposition (RT). In humans several disorders have been attributed to RT, but the role of RT in severe developmental disorders (DD) has not yet been explored. Here we identify RT-derived events in 9738 exome sequenced trios with DD-affected probands. We ascertain 9 de novo MEs, 4 of which are likely causative of the patient's symptoms (0.04%), as well as 2 de novo gene retroduplications. Beyond identifying likely diagnostic RT events, we estimate genome-wide germline ME mutation rate and selective constraint and demonstrate that coding RT events have signatures of purifying selection equivalent to those of truncating mutations. Overall, our analysis represents a comprehensive interrogation of the impact of retrotransposition on protein coding genes and a framework for future evolutionary and disease studies.

CTCF variants in 39 individuals with a variable neurodevelopmental disorder broaden the mutational and clinical spectrum.

Konrad EDH; Nardini N; Caliebe A; Nagel I; Young D; Horvath G; Santoro SL; Shuss C; Ziegler A; Bonneau D; Kempers M; Pfundt R; Legius E; Bouman A; Stuurman KE; Õunap K; Pajusalu S; Wojcik MH; Vasileiou G; Le Guyader G; Schnelle HM; Berland S; Zonneveld-Huijssoon E; Kersten S; Gupta A; Blackburn PR; Ellingson MS; Ferber MJ; Dhamija R; Klee EW; McEntagart M; Lichtenbelt KD; Kenney A; Vergano SA; Abou Jamra R; Platzer K; Ella Pierpont M; Khattar D; Hopkin RJ; Martin RJ; Jongmans MCJ; Chang VY; Martinez-Agosto JA; Kuismin O; Kurki MI; Pietiläinen O; Palotie A; Maarup TJ; Johnson DS; Venborg Pedersen K; Laulund LW; Lynch SA; Blyth M; Prescott K; Canham N; Ibitoye R; Brilstra EH; Shinawi M; Fassi E; ; Sticht H; Gregor A; Van Esch H; Zweier C

Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;12;2723-2733

Pathogenic variants in the chromatin organizer CTCF were previously reported in seven individuals with a neurodevelopmental disorder (NDD).

De novo and inherited TCF20 pathogenic variants are associated with intellectual disability, dysmorphic features, hypotonia, and neurological impairments with similarities to Smith-Magenis syndrome.

Vetrini F; McKee S; Rosenfeld JA; Suri M; Lewis AM; Nugent KM; Roeder E; Littlejohn RO; Holder S; Zhu W; Alaimo JT; Graham B; Harris JM; Gibson JB; Pastore M; McBride KL; Komara M; Al-Gazali L; Al Shamsi A; Fanning EA; Wierenga KJ; Scott DA; Ben-Neriah Z; Meiner V; Cassuto H; Elpeleg O; Holder JL; Burrage LC; Seaver LH; Van Maldergem L; Mahida S; Soul JS; Marlatt M; Matyakhina L; Vogt J; Gold JA; Park SM; Varghese V; Lampe AK; Kumar A; Lees M; Holder-Espinasse M; McConnell V; Bernhard B; Blair E; Harrison V; ; Muzny DM; Gibbs RA; Elsea SH; Posey JE; Bi W; Lalani S; Xia F; Yang Y; Eng CM; Lupski JR; Liu P

Genome medicine 2019;11;1;12

Neurodevelopmental disorders are genetically and phenotypically heterogeneous encompassing developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), structural brain abnormalities, and neurological manifestations with variants in a large number of genes (hundreds) associated. To date, a few de novo mutations potentially disrupting TCF20 function in patients with ID, ASD, and hypotonia have been reported. TCF20 encodes a transcriptional co-regulator structurally related to RAI1, the dosage-sensitive gene responsible for Smith-Magenis syndrome (deletion/haploinsufficiency) and Potocki-Lupski syndrome (duplication/triplosensitivity).

De novo DDX3X missense variants in males appear viable and contribute to syndromic intellectual disability.

Nicola P; Blackburn PR; Rasmussen KJ; Bertsch NL; Klee EW; Hasadsri L; Pichurin PN; Rankin J; Raymond FL; ; Clayton-Smith J

American journal of medical genetics. Part A 2019;179;4;570-578

DDX3X (Xp11.4) encodes a DEAD-box RNA helicase that escapes X chromosome inactivation. Pathogenic variants in DDX3X have been shown to cause X-linked intellectual disability (ID) (MRX102, MIM: 300958). The phenotypes associated with DDX3X variants are heterogeneous and include brain and behavioral abnormalities, microcephaly, hypotonia, and movement disorders and/or spasticity. The majority of DDX3X variants described are de novo mutations in females with ID. In contrast, most male DDX3X variants are inherited from an unaffected mother, with one documented exception being a recently identified de novo splice site variant. It has been suggested, therefore, that DDX3X exerts its effects through haploinsufficiency in females, and that affected males carry hypomorphic alleles that retain partial function. Given the lack of male de novo DDX3X variants, loss-of-function variants in this gene are suspected to be male lethal. Through whole-exome sequencing, we identified three unrelated males with hemizygous missense DDX3X variants and ID. All three variants were confirmed by Sanger sequencing, with two established as de novo. In silico analyses were supportive of pathogenicity. We report the male phenotypes and compare them to phenotypes observed in previously reported male and female patients. In conclusion, we propose that de novo DDX3X variants are not necessarily male lethal and should be considered as a cause of syndromic ID in both males and females.

De Novo Missense Substitutions in the Gene Encoding CDK8, a Regulator of the Mediator Complex, Cause a Syndromic Developmental Disorder.

Calpena E; Hervieu A; Kaserer T; Swagemakers SMA; Goos JAC; Popoola O; Ortiz-Ruiz MJ; Barbaro-Dieber T; Bownass L; Brilstra EH; Brimble E; Foulds N; Grebe TA; Harder AVE; Lees MM; Monaghan KG; Newbury-Ecob RA; Ong KR; Osio D; Reynoso Santos FJ; Ruzhnikov MRZ; Telegrafi A; van Binsbergen E; van Dooren MF; ; van der Spek PJ; Blagg J; Twigg SRF; Mathijssen IMJ; Clarke PA; Wilkie AOM

American journal of human genetics 2019;104;4;709-720

The Mediator is an evolutionarily conserved, multi-subunit complex that regulates multiple steps of transcription. Mediator activity is regulated by the reversible association of a four-subunit module comprising CDK8 or CDK19 kinases, together with cyclin C, MED12 or MED12L, and MED13 or MED13L. Mutations in MED12, MED13, and MED13L were previously identified in syndromic developmental disorders with overlapping phenotypes. Here, we report CDK8 mutations (located at 13q12.13) that cause a phenotypically related disorder. Using whole-exome or whole-genome sequencing, and by international collaboration, we identified eight different heterozygous missense CDK8 substitutions, including 10 shown to have arisen de novo, in 12 unrelated subjects; a recurrent mutation, c.185C>T (p.Ser62Leu), was present in five individuals. All predicted substitutions localize to the ATP-binding pocket of the kinase domain. Affected individuals have overlapping phenotypes characterized by hypotonia, mild to moderate intellectual disability, behavioral disorders, and variable facial dysmorphism. Congenital heart disease occurred in six subjects; additional features present in multiple individuals included agenesis of the corpus callosum, ano-rectal malformations, seizures, and hearing or visual impairments. To evaluate the functional impact of the mutations, we measured phosphorylation at STAT1-Ser727, a known CDK8 substrate, in a CDK8 and CDK19 CRISPR double-knockout cell line transfected with wild-type (WT) or mutant CDK8 constructs. These experiments demonstrated a reduction in STAT1 phosphorylation by all mutants, in most cases to a similar extent as in a kinase-dead control. We conclude that missense mutations in CDK8 cause a developmental disorder that has phenotypic similarity to syndromes associated with mutations in other subunits of the Mediator kinase module, indicating probable overlap in pathogenic mechanisms.

De Novo SOX4 Variants Cause a Neurodevelopmental Disease Associated with Mild Dysmorphism.

Zawerton A; Yao B; Yeager JP; Pippucci T; Haseeb A; Smith JD; Wischmann L; Kühl SJ; Dean JCS; Pilz DT; Holder SE; ; ; McNeill A; Graziano C; Lefebvre V

American journal of human genetics 2019;104;2;246-259

SOX4, together with SOX11 and SOX12, forms group C of SRY-related (SOX) transcription factors. They play key roles, often in redundancy, in multiple developmental pathways, including neurogenesis and skeletogenesis. De novo SOX11 heterozygous mutations have been shown to cause intellectual disability, growth deficiency, and dysmorphic features compatible with mild Coffin-Siris syndrome. Using trio-based exome sequencing, we here identify de novo SOX4 heterozygous missense variants in four children who share developmental delay, intellectual disability, and mild facial and digital morphological abnormalities. SOX4 is highly expressed in areas of active neurogenesis in human fetuses, and sox4 knockdown in Xenopus embryos diminishes brain and whole-body size. The SOX4 variants cluster in the highly conserved, SOX family-specific HMG domain, but each alters a different residue. In silico tools predict that each variant affects a distinct structural feature of this DNA-binding domain, and functional assays demonstrate that these SOX4 proteins carrying these variants are unable to bind DNA in vitro and transactivate SOX reporter genes in cultured cells. These variants are not found in the gnomAD database of individuals with presumably normal development, but 12 other SOX4 HMG-domain missense variants are recorded and all demonstrate partial to full activity in the reporter assay. Taken together, these findings point to specific SOX4 HMG-domain missense variants as the cause of a characteristic human neurodevelopmental disorder associated with mild facial and digital dysmorphism.

De novo variants in CNOT3 cause a variable neurodevelopmental disorder.

Martin R; Splitt M; Genevieve D; Aten E; Collins A; de Bie CI; Faivre L; Foulds N; Giltay J; Ibitoye R; Joss S; Kennedy J; Kerr B; Kivuva E; Koopmans M; Newbury-Ecob R; Jean-Marçais N; Peeters EAJ; Smithson S; Tomkins S; Tranmauthem F; Piton A; van Haeringen A

European journal of human genetics : EJHG 2019;27;11;1677-1682

As a result of exome-based sequencing work performed by the DDD study, de novo variants in CNOT3 have emerged as a newly recognised cause of a developmental disorder. This paper describes molecular and clinical details of 16 probands with developmental disorders and de novo CNOT3 variants. It is the first such description of the developmental phenotype associated with CNOT3 variants. Eight of these cases were discovered as part of the DDD study, while the other eight were found as a result of large-scale sequencing work performed by other groups. A highly specific phenotype was not recognised in these 16 cases. The most consistent phenotypic features seen in subjects with de novo variants in CNOT3 were hypotonia, relatively small stature, developmental delay, behavioural problems and intellectual disability. There is no easily recognisable facial phenotype, but some common dysmorphic features such as anteverted nares, thin upper lip and low set eyebrows were shared among some of the probands. Haploinsufficiency appears to be the most likely mechanism of action, with eight cases found to have protein-truncating variants. Of the other eight cases (all missense variants), three share an amino acid substitution at the same position which may therefore represent an important functional domain.

Deep phenotyping of 14 new patients with IQSEC2 variants, including monozygotic twins of discordant phenotype.

Radley JA; O'Sullivan RBG; Turton SE; Cox H; Vogt J; Morton J; Jones E; Smithson S; Lachlan K; Rankin J; Clayton-Smith J; Willoughby J; Elmslie FF; Sansbury FH; Cooper N; ; Balasubramanian M

Clinical genetics 2019;95;4;496-506

Whole-exome sequencing has established IQSEC2 as a neurodevelopmental disability gene. The IQSEC2 variant phenotype includes developmental delay, intellectual disability, epilepsy, hypotonia, autism, developmental regression, microcephaly and stereotypies but is yet to be fully described. Presented here are 14 new patients with IQSEC2 variants. In addition to the established features, we observed: gait ataxia in 7 of 9 (77.8%), drooling in 9 of 14 (64.2%), early feeding difficulties in 7 of 14 (50%), structural brain abnormalities in 6 of 13 (46.2%), brachycephaly in 5 of 14 (35.7%), and scoliosis and paroxysms of laughter each in 4 of 14 (28.6%). We suggest that these are features of the IQSEC2-related disorder. Gastrostomy requirement, plagiocephaly, strabismus and cortical blindness, each seen in 2 of 14 (14.3%), may also be associated. Shared facial features were noted in 8 of 14 patients, and shared hair patterning was identified in 5 of 14 patients. This study further delineates the IQSEC2 phenotypic spectrum and supports the notion of an emerging IQSEC2 syndrome. We draw parallels between the IQSEC2-related disorder and the Angelman-/Rett-/Pitt-Hopkins syndrome group of conditions and recommend the addition of IQSEC2 to epilepsy and developmental delay gene panels. We observed discordant phenotypes in monozygotic twins and apparent gonadal mosaicism, which has implications for recurrence risk counselling in the IQSEC2-related disorder.

Deleterious de novo variants of X-linked ZC4H2 in females cause a variable phenotype with neurogenic arthrogryposis multiplex congenita.

Frints SGM; Hennig F; Colombo R; Jacquemont S; Terhal P; Zimmerman HH; Hunt D; Mendelsohn BA; Kordaß U; Webster R; Sinnema M; Abdul-Rahman O; Suckow V; Fernández-Jaén A; van Roozendaal K; Stevens SJC; Macville MVE; Al-Nasiry S; van Gassen K; Utzig N; Koudijs SM; McGregor L; Maas SM; Baralle D; Dixit A; Wieacker P; Lee M; Lee AS; Engle EC; Houge G; Gradek GA; Douglas AGL; Longman C; Joss S; Velasco D; Hennekam RC; Hirata H; Kalscheuer VM

Human mutation 2019;40;12;2270-2285

Pathogenic variants in the X-linked gene ZC4H2, which encodes a zinc-finger protein, cause an infrequently described syndromic form of arthrogryposis multiplex congenita (AMC) with central and peripheral nervous system involvement. We present genetic and detailed phenotypic information on 23 newly identified families and simplex cases that include 19 affected females from 18 families and 14 affected males from nine families. Of note, the 15 females with deleterious de novo ZC4H2 variants presented with phenotypes ranging from mild to severe, and their clinical features overlapped with those seen in affected males. By contrast, of the nine carrier females with inherited ZC4H2 missense variants that were deleterious in affected male relatives, four were symptomatic. We also compared clinical phenotypes with previously published cases of both sexes and provide an overview on 48 males and 57 females from 42 families. The spectrum of ZC4H2 defects comprises novel and recurrent mostly inherited missense variants in affected males, and de novo splicing, frameshift, nonsense, and partial ZC4H2 deletions in affected females. Pathogenicity of two newly identified missense variants was further supported by studies in zebrafish. We propose ZC4H2 as a good candidate for early genetic testing of males and females with a clinical suspicion of fetal hypo-/akinesia and/or (neurogenic) AMC.

Delineation of dominant and recessive forms of LZTR1-associated Noonan syndrome.

Pagnamenta AT; Kaisaki PJ; Bennett F; Burkitt-Wright E; Martin HC; Ferla MP; Taylor JM; Gompertz L; Lahiri N; Tatton-Brown K; Newbury-Ecob R; Henderson A; Joss S; Weber A; Carmichael J; Turnpenny PD; McKee S; Forzano F; Ashraf T; Bradbury K; Shears D; Kini U; de Burca A; ; Blair E; Taylor JC; Stewart H

Clinical genetics 2019;95;6;693-703

Noonan syndrome (NS) is characterised by distinctive facial features, heart defects, variable degrees of intellectual disability and other phenotypic manifestations. Although the mode of inheritance is typically dominant, recent studies indicate LZTR1 may be associated with both dominant and recessive forms. Seeking to describe the phenotypic characteristics of LZTR1-associated NS, we searched for likely pathogenic variants using two approaches. First, scrutiny of exomes from 9624 patients recruited by the Deciphering Developmental Disorders (DDDs) study uncovered six dominantly-acting mutations (p.R97L; p.Y136C; p.Y136H, p.N145I, p.S244C; p.G248R) of which five arose de novo, and three patients with compound-heterozygous variants (p.R210*/p.V579M; p.R210*/p.D531N; c.1149+1G>T/p.R688C). One patient also had biallelic loss-of-function mutations in NEB, consistent with a composite phenotype. After removing this complex case, analysis of human phenotype ontology terms indicated significant phenotypic similarities (P = 0.0005), supporting a causal role for LZTR1. Second, targeted sequencing of eight unsolved NS-like cases identified biallelic LZTR1 variants in three further subjects (p.W469*/p.Y749C, p.W437*/c.-38T>A and p.A461D/p.I462T). Our study strengthens the association of LZTR1 with NS, with de novo mutations clustering around the KT1-4 domains. Although LZTR1 variants explain ~0.1% of cases across the DDD cohort, the gene is a relatively common cause of unsolved NS cases where recessive inheritance is suspected.

Dual diagnosis causing severe phenotype in a patient with Angelman syndrome.

Kanani F; Mordekar S; Parker MJ; Balasubramanian M;

Clinical dysmorphology 2019;28;3;160-163

ERF-related craniosynostosis: The phenotypic and developmental profile of a new craniosynostosis syndrome.

Glass GE; O'Hara J; Canham N; Cilliers D; Dunaway D; Fenwick AL; Jeelani NO; Johnson D; Lester T; Lord H; Morton JEV; Nishikawa H; Noons P; Schwiebert K; Shipster C; Taylor-Beadling A; Twigg SRF; Vasudevan P; Wall SA; Wilkie AOM; Wilson LC

American journal of medical genetics. Part A 2019;179;4;615-627

Mutations in the ERF gene, coding for ETS2 repressor factor, a member of the ETS family of transcription factors cause a recently recognized syndromic form of craniosynostosis (CRS4) with facial dysmorphism, Chiari-1 malformation, speech and language delay, and learning difficulties and/or behavioral problems. The overall prevalence of ERF mutations in patients with syndromic craniosynostosis is around 2%, and 0.7% in clinically nonsyndromic craniosynostosis. Here, we present findings from 16 unrelated probands with ERF-related craniosynostosis, with additional data from 20 family members sharing the mutations. Most of the probands exhibited multisutural (including pan-) synostosis but a pattern involving the sagittal and lambdoid sutures (Mercedes-Benz pattern) predominated. Importantly the craniosynostosis was often postnatal in onset, insidious and progressive with subtle effects on head morphology resulting in a median age at presentation of 42 months among the probands and, in some instances, permanent visual impairment due to unsuspected raised intracranial pressure (ICP). Facial dysmorphism (exhibited by all of the probands and many of the affected relatives) took the form of orbital hypertelorism, mild exorbitism and malar hypoplasia resembling Crouzon syndrome but, importantly, a Class I occlusal relationship. Speech delay, poor gross and/or fine motor control, hyperactivity and poor concentration were common. Cranial vault surgery for raised ICP and/or Chiari-1 malformation was expected when multisutural synostosis was observed. Variable expressivity and nonpenetrance among genetically affected relatives was encountered. These observations form the most complete phenotypic and developmental profile of this recently identified craniosynostosis syndrome yet described and have important implications for surgical intervention and follow-up.

Exome-wide assessment of the functional impact and pathogenicity of multinucleotide mutations.

Kaplanis J; Akawi N; Gallone G; McRae JF; Prigmore E; Wright CF; Fitzpatrick DR; Firth HV; Barrett JC; Hurles ME;

Genome research 2019;29;7;1047-1056

Approximately 2% of de novo single-nucleotide variants (SNVs) appear as part of clustered mutations that create multinucleotide variants (MNVs). MNVs are an important source of genomic variability as they are more likely to alter an encoded protein than a SNV, which has important implications in disease as well as evolution. Previous studies of MNVs have focused on their mutational origins and have not systematically evaluated their functional impact and contribution to disease. We identified 69,940 MNVs and 91 de novo MNVs in 6688 exome-sequenced parent-offspring trios from the Deciphering Developmental Disorders Study comprising families with severe developmental disorders. We replicated the previously described MNV mutational signatures associated with DNA polymerase zeta, an error-prone translesion polymerase, and the APOBEC family of DNA deaminases. We estimate the simultaneous MNV germline mutation rate to be 1.78 × 10-10 mutations per base pair per generation. We found that most MNVs within a single codon create a missense change that could not have been created by a SNV. MNV-induced missense changes were, on average, more physicochemically divergent, were more depleted in highly constrained genes (pLI ≥ 0.9), and were under stronger purifying selection compared with SNV-induced missense changes. We found that de novo MNVs were significantly enriched in genes previously associated with developmental disorders in affected children. This shows that MNVs can be more damaging than SNVs even when both induce missense changes, and are an important variant type to consider in relation to human disease.

Expanding the phenotype of the X-linked BCOR microphthalmia syndromes.

Ragge N; Isidor B; Bitoun P; Odent S; Giurgea I; Cogné B; Deb W; Vincent M; Le Gall J; Morton J; Lim D; ; Le Meur G; Zazo Seco C; Zafeiropoulou D; Bax D; Zwijnenburg P; Arteche A; Swafiri ST; Cleaver R; McEntagart M; Kini U; Newman W; Ayuso C; Corton M; Herenger Y; Jeanne M; Calvas P; Chassaing N

Human genetics 2019;138;8-9;1051-1069

Two distinct syndromes arise from pathogenic variants in the X-linked gene BCOR (BCL-6 corepressor): oculofaciocardiodental (OFCD) syndrome, which affects females, and a severe microphthalmia ('Lenz'-type) syndrome affecting males. OFCD is an X-linked dominant syndrome caused by a variety of BCOR null mutations. As it manifests only in females, it is presumed to be lethal in males. The severe male X-linked recessive microphthalmia syndrome ('Lenz') usually includes developmental delay in addition to the eye findings and is caused by hypomorphic BCOR variants, mainly by a specific missense variant c.254C > T, p.(Pro85Leu). Here, we detail 16 new cases (11 females with 4 additional, genetically confirmed, affected female relatives; 5 male cases each with unaffected carrier mothers). We describe new variants and broaden the phenotypic description for OFCD to include neuropathy, muscle hypotonia, pituitary underdevelopment, brain atrophy, lipoma and the first description of childhood lymphoma in an OFCD case. Our male X-linked recessive cases show significant new phenotypes: developmental delay (without eye anomalies) in two affected half-brothers with a novel BCOR variant, and one male with high myopia, megalophthalmos, posterior embryotoxon, developmental delay, and heart and bony anomalies with a previously undescribed BCOR splice site variant. Our female OFCD cases and their affected female relatives showed variable features, but consistently had early onset cataracts. We show that a mosaic carrier mother manifested early cataract and dental anomalies. All female carriers of the male X-linked recessive cases for whom genetic confirmation was available showed skewed X-inactivation and were unaffected. In view of the extended phenotype, we suggest a new term of X-linked BCOR-related syndrome.

Exploring the association between SRPX2 variants and neurodevelopment: How causal is it?

Schirwani S; McConnell V; Willoughby J; ; Balasubramanian M

Gene 2019;685;50-54

The SRPX2 gene (Sushi-repeat-containing protein, X-linked, 2, OMIM*300642), located on Xq22.1, encodes a secreted protein that is highly expressed in neurons of cerebral cortex. SRPX2 was first implicated in neurodevelopment, learning and rolandic seizure when two patients with potentially pathogenic variants, c.980A>G (p.Asn327Ser) and c.215A>C (p.Tyr72Ser), in SRPX2 gene were identified. Subsequent experimental studies demonstrated that SRPX2 is needed for vocalization and synapse formation in mice, and that both silencing SRPX2 and injecting (p.Asn327Ser) in mouse models results in alteration in neuronal migration in cerebral cortex and epilepsy. A number of studies demonstrated that SRPX2 interacts with FOXP2 (Foxhead box protein P2), a gene responsible for speech and language disorder, and that FoxP2 controls timing and level of expression of SRPX2. Despite the supportive evidence for the role of SRPX2 in speech and language development and disorders, there are questions over its definitive association with neurodevelopmental disorders and epilepsy. In this paper, the role of SRPX2 as one in a network of many genes involved in speech and language is discussed. The goal of this paper is to examine the role of SRPX2 variants through describing two patients with potentially pathogenic variants in SRPX2, c.751G>C (p.Ala251Pro) and c.762G>T (p.Lys254Asn) presenting with language and motor delay, intellectual disability as well as congenital anomalies. We explore the contribution of SRPX2 variants to clinical phenotype in our patients and conclude that these variants at least partially explain the phenotype. Further studies are necessary to establish and confirm the association between SRPX2 and neurodevelopment particularly speech and language development.

Extending the clinical and genetic spectrum of ARID2 related intellectual disability. A case series of 7 patients.

Gazdagh G; Blyth M; Scurr I; Turnpenny PD; Mehta SG; Armstrong R; McEntagart M; Newbury-Ecob R; Tobias ES; ; Joss S

European journal of medical genetics 2019;62;1;27-34

In the last 3 years de novo sequence variants in the ARID2 (AT-rich interaction domain 2) gene, a subunit of the SWI/SNF complex, have been linked to intellectual disabilities in 3 case reports including one which describes frameshift mutations in ARID2 in 2 patients with features resembling Coffin-Siris syndrome. Coffin-Siris syndrome (CSS) is a rare congenital syndrome characterized by intellectual deficit, coarse facial features and hypoplastic or absent fifth fingernails and/or toenails among other features. Mutations in a number of different genes encoding SWI/SNF chromatin remodelling complex proteins have been described but the underlying molecular cause remains unknown in approximately 40% of patients with CSS. Here we describe 7 unrelated individuals, 2 with deletions of the ARID2 region and 5 with de novo truncating mutations in the ARID2 gene. Similarities to CSS are evident. Although hypertrichosis and hypoplasia of the fifth finger nail and distal phalanx do not appear to be common in these patients, toenail hypoplasia and the presence of Wormian bones might support the involvement of ARID2.

Finding Diagnostically Useful Patterns in Quantitative Phenotypic Data.

Aitken S; Firth HV; McRae J; Halachev M; Kini U; Parker MJ; Lees MM; Lachlan K; Sarkar A; Joss S; Splitt M; McKee S; Németh AH; Scott RH; Wright CF; Marsh JA; Hurles ME; FitzPatrick DR;

American journal of human genetics 2019;105;5;933-946

Trio-based whole-exome sequence (WES) data have established confident genetic diagnoses in ∼40% of previously undiagnosed individuals recruited to the Deciphering Developmental Disorders (DDD) study. Here we aim to use the breadth of phenotypic information recorded in DDD to augment diagnosis and disease variant discovery in probands. Median Euclidean distances (mEuD) were employed as a simple measure of similarity of quantitative phenotypic data within sets of ≥10 individuals with plausibly causative de novo mutations (DNM) in 28 different developmental disorder genes. 13/28 (46.4%) showed significant similarity for growth or developmental milestone metrics, 10/28 (35.7%) showed similarity in HPO term usage, and 12/28 (43%) showed no phenotypic similarity. Pairwise comparisons of individuals with high-impact inherited variants to the 32 individuals with causative DNM in ANKRD11 using only growth z-scores highlighted 5 likely causative inherited variants and two unrecognized DNM resulting in an 18% diagnostic uplift for this gene. Using an independent approach, naive Bayes classification of growth and developmental data produced reasonably discriminative models for the 24 DNM genes with sufficiently complete data. An unsupervised naive Bayes classification of 6,993 probands with WES data and sufficient phenotypic information defined 23 in silico syndromes (ISSs) and was used to test a "phenotype first" approach to the discovery of causative genotypes using WES variants strictly filtered on allele frequency, mutation consequence, and evidence of constraint in humans. This highlighted heterozygous de novo nonsynonymous variants in SPTBN2 as causative in three DDD probands.

Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP.

Thormann A; Halachev M; McLaren W; Moore DJ; Svinti V; Campbell A; Kerr SM; Tischkowitz M; Hunt SE; Dunlop MG; Hurles ME; Wright CF; Firth HV; Cunningham F; FitzPatrick DR

Nature Communications 2019;10;1;2373

We aimed to develop an efficient, flexible and scalable approach to diagnostic genome-wide sequence analysis of genetically heterogeneous clinical presentations. Here we present G2P ( ) as an online system to establish, curate and distribute datasets for diagnostic variant filtering via association of allelic requirement and mutational consequence at a defined locus with phenotypic terms, confidence level and evidence links. An extension to Ensembl Variant Effect Predictor (VEP), VEP-G2P was used to filter both disease-associated and control whole exome sequence (WES) with Developmental Disorders G2P (G2PDD; 2044 entries). VEP-G2PDD shows a sensitivity/precision of 97.3%/33% for de novo and 81.6%/22.7% for inherited pathogenic genotypes respectively. Many of the missing genotypes are likely false-positive pathogenic assignments. The expected number and discriminative features of background genotypes are defined using control WES. Using only human genetic data VEP-G2P performs well compared to other freely-available diagnostic systems and future phenotypic matching capabilities should further enhance performance.

Heterozygous loss-of-function variants of MEIS2 cause a triad of palatal defects, congenital heart defects, and intellectual disability.

Verheije R; Kupchik GS; Isidor B; Kroes HY; Lynch SA; Hawkes L; Hempel M; Gelb BD; Ghoumid J; D'Amours G; Chandler K; Dubourg C; Loddo S; Tümer Z; Shaw-Smith C; Nizon M; Shevell M; Van Hoof E; Anyane-Yeboa K; Cerbone G; Clayton-Smith J; Cogné B; Corre P; Corveleyn A; De Borre M; Hjortshøj TD; Fradin M; Gewillig M; Goldmuntz E; Hens G; Lemyre E; Journel H; Kini U; Kortüm F; Le Caignec C; Novelli A; Odent S; Petit F; Revah-Politi A; Stong N; Strom TM; van Binsbergen E; ; Devriendt K; Breckpot J

European journal of human genetics : EJHG 2019;27;2;278-290

Deletions on chromosome 15q14 are a known chromosomal cause of cleft palate, typically co-occurring with intellectual disability, facial dysmorphism, and congenital heart defects. The identification of patients with loss-of-function variants in MEIS2, a gene within this deletion, suggests that these features are attributed to haploinsufficiency of MEIS2. To further delineate the phenotypic spectrum of the MEIS2-related syndrome, we collected 23 previously unreported patients with either a de novo sequence variant in MEIS2 (9 patients), or a 15q14 microdeletion affecting MEIS2 (14 patients). All but one de novo MEIS2 variant were identified by whole-exome sequencing. One variant was found by targeted sequencing of MEIS2 in a girl with a clinical suspicion of this syndrome. In addition to the triad of palatal defects, heart defects, and developmental delay, heterozygous loss of MEIS2 results in recurrent facial features, including thin and arched eyebrows, short alae nasi, and thin vermillion. Genotype-phenotype comparison between patients with 15q14 deletions and patients with sequence variants or intragenic deletions within MEIS2, showed a higher prevalence of moderate-to-severe intellectual disability in the former group, advocating for an independent locus for psychomotor development neighboring MEIS2.

Heterozygous Variants in KMT2E Cause a Spectrum of Neurodevelopmental Disorders and Epilepsy.

O'Donnell-Luria AH; Pais LS; Faundes V; Wood JC; Sveden A; Luria V; Abou Jamra R; Accogli A; Amburgey K; Anderlid BM; Azzarello-Burri S; Basinger AA; Bianchini C; Bird LM; Buchert R; Carre W; Ceulemans S; Charles P; Cox H; Culliton L; Currò A; ; Demurger F; Dowling JJ; Duban-Bedu B; Dubourg C; Eiset SE; Escobar LF; Ferrarini A; Haack TB; Hashim M; Heide S; Helbig KL; Helbig I; Heredia R; Héron D; Isidor B; Jonasson AR; Joset P; Keren B; Kok F; Kroes HY; Lavillaureix A; Lu X; Maas SM; Maegawa GHB; Marcelis CLM; Mark PR; Masruha MR; McLaughlin HM; McWalter K; Melchinger EU; Mercimek-Andrews S; Nava C; Pendziwiat M; Person R; Ramelli GP; Ramos LLP; Rauch A; Reavey C; Renieri A; Rieß A; Sanchez-Valle A; Sattar S; Saunders C; Schwarz N; Smol T; Srour M; Steindl K; Syrbe S; Taylor JC; Telegrafi A; Thiffault I; Trauner DA; van der Linden H; van Koningsbruggen S; Villard L; Vogel I; Vogt J; Weber YG; Wentzensen IM; Widjaja E; Zak J; Baxter S; Banka S; Rodan LH

American journal of human genetics 2019;104;6;1210-1222

We delineate a KMT2E-related neurodevelopmental disorder on the basis of 38 individuals in 36 families. This study includes 31 distinct heterozygous variants in KMT2E (28 ascertained from Matchmaker Exchange and three previously reported), and four individuals with chromosome 7q22.2-22.23 microdeletions encompassing KMT2E (one previously reported). Almost all variants occurred de novo, and most were truncating. Most affected individuals with protein-truncating variants presented with mild intellectual disability. One-quarter of individuals met criteria for autism. Additional common features include macrocephaly, hypotonia, functional gastrointestinal abnormalities, and a subtle facial gestalt. Epilepsy was present in about one-fifth of individuals with truncating variants and was responsive to treatment with anti-epileptic medications in almost all. More than 70% of the individuals were male, and expressivity was variable by sex; epilepsy was more common in females and autism more common in males. The four individuals with microdeletions encompassing KMT2E generally presented similarly to those with truncating variants, but the degree of developmental delay was greater. The group of four individuals with missense variants in KMT2E presented with the most severe developmental delays. Epilepsy was present in all individuals with missense variants, often manifesting as treatment-resistant infantile epileptic encephalopathy. Microcephaly was also common in this group. Haploinsufficiency versus gain-of-function or dominant-negative effects specific to these missense variants in KMT2E might explain this divergence in phenotype, but requires independent validation. Disruptive variants in KMT2E are an under-recognized cause of neurodevelopmental abnormalities.

HIST1H1E heterozygous protein-truncating variants cause a recognizable syndrome with intellectual disability and distinctive facial gestalt: A study to clarify the HIST1H1E syndrome phenotype in 30 individuals.

Burkardt DD; Zachariou A; Loveday C; Allen CL; Amor DJ; Ardissone A; Banka S; Bourgois A; Coubes C; Cytrynbaum C; Faivre L; Marion G; Horton R; Kotzot D; Lay-Son G; Lees M; Low K; Luk HM; Mark P; McConkie-Rosell A; McDonald M; Pappas J; Phillipe C; Shears D; Skotko B; Stewart F; Stewart H; Temple IK; Mau-Them FT; Verdugo RA; Weksberg R; Zarate YA; Graham JM; Tatton-Brown K

American journal of medical genetics. Part A 2019;179;10;2049-2055

Histone Gene Cluster 1 Member E, HIST1H1E, encodes Histone H1.4, is one of a family of epigenetic regulator genes, acts as a linker histone protein, and is responsible for higher order chromatin structure. HIST1H1E syndrome (also known as Rahman syndrome, OMIM #617537) is a recently described intellectual disability (ID) syndrome. Since the initial description of five unrelated individuals with three different heterozygous protein-truncating variants (PTVs) in the HIST1H1E gene in 2017, we have recruited 30 patients, all with HIST1H1E PTVs that result in the same shift in frame and that cluster to a 94-base pair region in the HIST1H1E carboxy terminal domain. The identification of 30 patients with HIST1H1E variants has allowed the clarification of the HIST1H1E syndrome phenotype. Major findings include an ID and a recognizable facial appearance. ID was reported in all patients and is most frequently of moderate severity. The facial gestalt consists of a high frontal hairline and full lower cheeks in early childhood and, in later childhood and adulthood, affected individuals have a strikingly high frontal hairline, frontal bossing, and deep-set eyes. Other associated clinical features include hypothyroidism, abnormal dentition, behavioral issues, cryptorchidism, skeletal anomalies, and cardiac anomalies. Brain magnetic resonance imaging (MRI) is frequently abnormal with a slender corpus callosum a frequent finding.

Homozygosity mapping provides supporting evidence of pathogenicity in recessive Mendelian disease.

Wakeling MN; Laver TW; Wright CF; De Franco E; Stals KL; Patch AM; Hattersley AT; Flanagan SE; Ellard S;

Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;4;982-986

One of the greatest challenges currently facing those studying Mendelian disease is identifying the pathogenic variant from the long list produced by a next-generation sequencing test. We investigate the predictive ability of homozygosity mapping for identifying the regions likely to contain the causative variant.

KAT6A Syndrome: genotype-phenotype correlation in 76 patients with pathogenic KAT6A variants.

Kennedy J; Goudie D; Blair E; Chandler K; Joss S; McKay V; Green A; Armstrong R; Lees M; Kamien B; Hopper B; Tan TY; Yap P; Stark Z; Okamoto N; Miyake N; Matsumoto N; Macnamara E; Murphy JL; McCormick E; Hakonarson H; Falk MJ; Li D; Blackburn P; Klee E; Babovic-Vuksanovic D; Schelley S; Hudgins L; Kant S; Isidor B; Cogne B; Bradbury K; Williams M; Patel C; Heussler H; Duff-Farrier C; Lakeman P; Scurr I; Kini U; Elting M; Reijnders M; Schuurs-Hoeijmakers J; Wafik M; Blomhoff A; Ruivenkamp CAL; Nibbeling E; Dingemans AJM; Douine ED; Nelson SF; ; Hempel M; Bierhals T; Lessel D; Johannsen J; Arboleda VA; Newbury-Ecob R

Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;4;850-860

Pathogenic variants in KAT6A have recently been identified as a cause of syndromic developmental delay. Within 2 years, the number of patients identified with pathogenic KAT6A variants has rapidly expanded and the full extent and variability of the clinical phenotype has not been reported.

Loss of function of NCOR1 and NCOR2 impairs memory through a novel GABAergic hypothalamus-CA3 projection.

Zhou W; He Y; Rehman AU; Kong Y; Hong S; Ding G; Yalamanchili HK; Wan YW; Paul B; Wang C; Gong Y; Zhou W; Liu H; Dean J; Scalais E; O'Driscoll M; Morton JEV; ; Hou X; Wu Q; Tong Q; Liu Z; Liu P; Xu Y; Sun Z

Nature Neuroscience 2019;22;2;205-217

Nuclear receptor corepressor 1 (NCOR1) and NCOR2 (also known as SMRT) regulate gene expression by activating histone deacetylase 3 through their deacetylase activation domain (DAD). We show that mice with DAD knock-in mutations have memory deficits, reduced anxiety levels, and reduced social interactions. Mice with NCOR1 and NORC2 depletion specifically in GABAergic neurons (NS-V mice) recapitulated the memory deficits and had reduced GABAA receptor subunit α2 (GABRA2) expression in lateral hypothalamus GABAergic (LHGABA) neurons. This was associated with LHGABA neuron hyperexcitability and impaired hippocampal long-term potentiation, through a monosynaptic LHGABA to CA3GABA projection. Optogenetic activation of this projection caused memory deficits, whereas targeted manipulation of LHGABA or CA3GABA neuron activity reversed memory deficits in NS-V mice. We describe de novo variants in NCOR1, NCOR2 or HDAC3 in patients with intellectual disability or neurodevelopmental disorders. These findings identify a hypothalamus-hippocampus projection that may link endocrine signals with synaptic plasticity through NCOR-mediated regulation of GABA signaling.

MAN1B-CDG: Novel variants with a distinct phenotype and review of literature.

Balasubramanian M; Johnson DS;

European journal of medical genetics 2019;62;2;109-114

Congenital disorders of glycosylation (CDG) are a group of rare metabolic diseases due to impaired lipid and protein glycosylation. It comprises a characteristic high frequency of intellectual disability (ID) and a wide range of clinical phenotypes.

Missense variants in TAF1 and developmental phenotypes: challenges of determining pathogenicity.

Cheng H; Capponi S; Wakeling E; Marchi E; Li Q; Zhao M; Weng C; Stefan PG; Ahlfors H; Kleyner R; Rope A; Lumaka A; Lukusa P; Devriendt K; Vermeesch J; Posey JE; Palmer EE; Murray L; Leon E; Diaz J; Worgan L; Mallawaarachchi A; Vogt J; de Munnik SA; Dreyer L; Baynam G; Ewans L; Stark Z; Lunke S; Gonçalves AR; Soares G; Oliveira J; Fassi E; Willing M; Waugh JL; Faivre L; Riviere JB; Moutton S; Mohammed S; Payne K; Walsh L; Begtrup A; Guillen Sacoto MJ; Douglas G; Alexander N; Buckley MF; Mark PR; Adès LC; Sandaradura SA; Lupski JR; Roscioli T; Agrawal PB; Kline AD; ; Wang K; Timmers HTM; Lyon GJ

Human mutation 2019

We recently described a new neurodevelopmental syndrome (TAF1/MRXS33 intellectual disability syndrome) (MIM# 300966) caused by pathogenic variants involving the X-linked gene TAF1, which participates in RNA polymerase II transcription. The initial study reported eleven families, and the syndrome was defined as presenting early in life with hypotonia, facial dysmorphia, and developmental delay that evolved into intellectual disability (ID) and/or autism spectrum disorder (ASD). We have now identified an additional 27 families through a genotype-first approach. Familial segregation analysis, clinical phenotyping, and bioinformatics were capitalized on to assess potential variant pathogenicity, and molecular modelling was performed for those variants falling within structurally characterized domains of TAF1. A novel phenotypic clustering approach was also applied, in which the phenotypes of affected individuals were classified using 51 standardized Human Phenotype Ontology (HPO) terms. Phenotypes associated with TAF1 variants show considerable pleiotropy and clinical variability, but prominent among previously unreported effects were brain morphological abnormalities, seizures, hearing loss, and heart malformations. Our allelic series broadens the phenotypic spectrum of TAF1/MRXS33 intellectual disability syndrome and the range of TAF1 molecular defects in humans. It also illustrates the challenges for determining the pathogenicity of inherited missense variants, particularly for genes mapping to chromosome X. This article is protected by copyright. All rights reserved.

Missense Variants in the Histone Acetyltransferase Complex Component Gene TRRAP Cause Autism and Syndromic Intellectual Disability.

Cogné B; Ehresmann S; Beauregard-Lacroix E; Rousseau J; Besnard T; Garcia T; Petrovski S; Avni S; McWalter K; Blackburn PR; Sanders SJ; Uguen K; Harris J; Cohen JS; Blyth M; Lehman A; Berg J; Li MH; Kini U; Joss S; von der Lippe C; Gordon CT; Humberson JB; Robak L; Scott DA; Sutton VR; Skraban CM; Johnston JJ; Poduri A; Nordenskjöld M; Shashi V; Gerkes EH; Bongers EMHF; Gilissen C; Zarate YA; Kvarnung M; Lally KP; Kulch PA; Daniels B; Hernandez-Garcia A; Stong N; McGaughran J; Retterer K; Tveten K; Sullivan J; Geisheker MR; Stray-Pedersen A; Tarpinian JM; Klee EW; Sapp JC; Zyskind J; Holla ØL; Bedoukian E; Filippini F; Guimier A; Picard A; Busk ØL; Punetha J; Pfundt R; Lindstrand A; Nordgren A; Kalb F; Desai M; Ebanks AH; Jhangiani SN; Dewan T; Coban Akdemir ZH; Telegrafi A; Zackai EH; Begtrup A; Song X; Toutain A; Wentzensen IM; Odent S; Bonneau D; Latypova X; Deb W; ; Redon S; Bilan F; Legendre M; Troyer C; Whitlock K; Caluseriu O; Murphree MI; Pichurin PN; Agre K; Gavrilova R; Rinne T; Park M; Shain C; Heinzen EL; Xiao R; Amiel J; Lyonnet S; Isidor B; Biesecker LG; Lowenstein D; Posey JE; Denommé-Pichon AS; ; Férec C; Yang XJ; Rosenfeld JA; Gilbert-Dussardier B; Audebert-Bellanger S; Redon R; Stessman HAF; Nellaker C; Yang Y; Lupski JR; Goldstein DB; Eichler EE; Bolduc F; Bézieau S; Küry S; Campeau PM

American journal of human genetics 2019;104;3;530-541

Acetylation of the lysine residues in histones and other DNA-binding proteins plays a major role in regulation of eukaryotic gene expression. This process is controlled by histone acetyltransferases (HATs/KATs) found in multiprotein complexes that are recruited to chromatin by the scaffolding subunit transformation/transcription domain-associated protein (TRRAP). TRRAP is evolutionarily conserved and is among the top five genes intolerant to missense variation. Through an international collaboration, 17 distinct de novo or apparently de novo variants were identified in TRRAP in 24 individuals. A strong genotype-phenotype correlation was observed with two distinct clinical spectra. The first is a complex, multi-systemic syndrome associated with various malformations of the brain, heart, kidneys, and genitourinary system and characterized by a wide range of intellectual functioning; a number of affected individuals have intellectual disability (ID) and markedly impaired basic life functions. Individuals with this phenotype had missense variants clustering around the c.3127G>A p.(Ala1043Thr) variant identified in five individuals. The second spectrum manifested with autism spectrum disorder (ASD) and/or ID and epilepsy. Facial dysmorphism was seen in both groups and included upslanted palpebral fissures, epicanthus, telecanthus, a wide nasal bridge and ridge, a broad and smooth philtrum, and a thin upper lip. RNA sequencing analysis of skin fibroblasts derived from affected individuals skin fibroblasts showed significant changes in the expression of several genes implicated in neuronal function and ion transport. Thus, we describe here the clinical spectrum associated with TRRAP pathogenic missense variants, and we suggest a genotype-phenotype correlation useful for clinical evaluation of the pathogenicity of the variants.

Mutations in MAGEL2 and L1CAM Are Associated With Congenital Hypopituitarism and Arthrogryposis.

Gregory LC; Shah P; Sanner JRF; Arancibia M; Hurst J; Jones WD; Spoudeas H; Le Quesne Stabej P; Williams HJ; Ocaka LA; Loureiro C; Martinez-Aguayo A; Dattani MT

The Journal of clinical endocrinology and metabolism 2019;104;12;5737-5750

Congenital hypopituitarism (CH) is rarely observed in combination with severe joint contractures (arthrogryposis). Schaaf-Yang syndrome (SHFYNG) phenotypically overlaps with Prader-Willi syndrome, with patients also manifesting arthrogryposis. L1 syndrome, a group of X-linked disorders that include hydrocephalus and lower limb spasticity, also rarely presents with arthrogryposis.

Mutations in PCYT2 disrupt etherlipid biosynthesis and cause a complex hereditary spastic paraplegia.

Vaz FM; McDermott JH; Alders M; Wortmann SB; Kölker S; Pras-Raves ML; Vervaart MAT; van Lenthe H; Luyf ACM; Elfrink HL; Metcalfe K; Cuvertino S; Clayton PE; Yarwood R; Lowe MP; Lovell S; Rogers RC; ; van Kampen AHC; Ruiter JPN; Wanders RJA; Ferdinandusse S; van Weeghel M; Engelen M; Banka S

Brain : a journal of neurology 2019;142;11;3382-3397

CTP:phosphoethanolamine cytidylyltransferase (ET), encoded by PCYT2, is the rate-limiting enzyme for phosphatidylethanolamine synthesis via the CDP-ethanolamine pathway. Phosphatidylethanolamine is one of the most abundant membrane lipids and is particularly enriched in the brain. We identified five individuals with biallelic PCYT2 variants clinically characterized by global developmental delay with regression, spastic para- or tetraparesis, epilepsy and progressive cerebral and cerebellar atrophy. Using patient fibroblasts we demonstrated that these variants are hypomorphic, result in altered but residual ET protein levels and concomitant reduced enzyme activity without affecting mRNA levels. The significantly better survival of hypomorphic CRISPR-Cas9 generated pcyt2 zebrafish knockout compared to a complete knockout, in conjunction with previously described data on the Pcyt2 mouse model, indicates that complete loss of ET function may be incompatible with life in vertebrates. Lipidomic analysis revealed profound lipid abnormalities in patient fibroblasts impacting both neutral etherlipid and etherphospholipid metabolism. Plasma lipidomics studies also identified changes in etherlipids that have the potential to be used as biomarkers for ET deficiency. In conclusion, our data establish PCYT2 as a disease gene for a new complex hereditary spastic paraplegia and confirm that etherlipid homeostasis is important for the development and function of the brain.

New GJA8 variants and phenotypes highlight its critical role in a broad spectrum of eye anomalies.

Ceroni F; Aguilera-Garcia D; Chassaing N; Bax DA; Blanco-Kelly F; Ramos P; Tarilonte M; Villaverde C; da Silva LRJ; Ballesta-Martínez MJ; Sanchez-Soler MJ; Holt RJ; Cooper-Charles L; Bruty J; Wallis Y; McMullan D; Hoffman J; Bunyan D; Stewart A; Stewart H; Lachlan K; ; Fryer A; McKay V; Roume J; Dureau P; Saggar A; Griffiths M; Calvas P; Ayuso C; Corton M; Ragge NK

Human genetics 2019;138;8-9;1027-1042

GJA8 encodes connexin 50 (Cx50), a transmembrane protein involved in the formation of lens gap junctions. GJA8 mutations have been linked to early onset cataracts in humans and animal models. In mice, missense mutations and homozygous Gja8 deletions lead to smaller lenses and microphthalmia in addition to cataract, suggesting that Gja8 may play a role in both lens development and ocular growth. Following screening of GJA8 in a cohort of 426 individuals with severe congenital eye anomalies, primarily anophthalmia, microphthalmia and coloboma, we identified four known [p.(Thr39Arg), p.(Trp45Leu), p.(Asp51Asn), and p.(Gly94Arg)] and two novel [p.(Phe70Leu) and p.(Val97Gly)] likely pathogenic variants in seven families. Five of these co-segregated with cataracts and microphthalmia, whereas the variant p.(Gly94Arg) was identified in an individual with congenital aphakia, sclerocornea, microphthalmia and coloboma. Four missense variants of unknown or unlikely clinical significance were also identified. Furthermore, the screening of GJA8 structural variants in a subgroup of 188 individuals identified heterozygous 1q21 microdeletions in five families with coloboma and other ocular and/or extraocular findings. However, the exact genotype-phenotype correlation of these structural variants remains to be established. Our data expand the spectrum of GJA8 variants and associated phenotypes, confirming the importance of this gene in early eye development.

Novel KAT6B proximal familial variant expands genotypic and phenotypic spectrum.

Yates TM; Langley CLM; ; Grozeva D; Raymond FL; Johnson DS

Clinical genetics 2019;95;2;334-335

Null variants and deletions in BRWD3 cause an X-linked syndrome of mild-moderate intellectual disability, macrocephaly, and obesity: A series of 17 patients.

Ostrowski PJ; Zachariou A; Loveday C; Baralle D; Blair E; Douzgou S; Field M; Foster A; Kyle C; Lachlan K; Mansour S; Naik S; Rea G; Smithson S; Sznajer Y; Thompson E; Cole T; Tatton-Brown K

American journal of medical genetics. Part C, Seminars in medical genetics 2019;181;4;638-643

BRWD3 has been described as a cause of X-linked intellectual disability, but relatively little is known about the specific phenotype. We report the largest BRWD3 patient series to date, comprising 17 males with 12 distinct null variants and 2 partial gene deletions. All patients presented with intellectual disability, which was classified as moderate (65%) or mild (35%). Behavioral issues were present in 75% of patients, including aggressive behavior, attention deficit/hyperactivity and/or autistic spectrum disorders. Mean head circumference was +2.8 SD (2.8 standard deviations above the mean), and mean BMI was +2.0 SD (in the context of a mean height of +1.3 SD), indicating a predominant macrocephaly/obesity phenotype. Shared facial features included a tall chin, prognathism, broad forehead, and prominent supraorbital ridge. Additional features, reported in a minority (<30%) of patients included cryptorchidism, neonatal hypotonia, and small joint hypermobility. This study delineates the clinical features associated with BRWD3 null variants and partial gene deletions, and suggests that BRWD3 should be included in the differential diagnosis of patients with an overgrowth-intellectual disability (OGID) phenotype, particularly in male patients with a mild or moderate intellectual disability associated with macrocephaly and/or obesity.

PAPSS2-related brachyolmia: Clinical and radiological phenotype in 18 new cases.

Bownass L; Abbs S; Armstrong R; Baujat G; Behzadi G; Berentsen RD; Burren C; Calder A; Cormier-Daire V; Newbury-Ecob R; Foulds N; Juliusson PB; Kant SG; Lefroy H; Mehta SG; Merckoll E; Michot C; Monsell F; Offiah AC; Richards A; Rosendahl K; Rustad CF; Shears D; Tveten K; Wellesley D; Wordsworth P; ; Smithson S

American journal of medical genetics. Part A 2019;179;9;1884-1894

Brachyolmia is a skeletal dysplasia characterized by short spine-short stature, platyspondyly, and minor long bone abnormalities. We describe 18 patients, from different ethnic backgrounds and ages ranging from infancy to 19 years, with the autosomal recessive form, associated with PAPSS2. The main clinical features include disproportionate short stature with short spine associated with variable symptoms of pain, stiffness, and spinal deformity. Eight patients presented prenatally with short femora, whereas later in childhood their short-spine phenotype emerged. We observed the same pattern of changing skeletal proportion in other patients. The radiological findings included platyspondyly, irregular end plates of the elongated vertebral bodies, narrow disc spaces and short over-faced pedicles. In the limbs, there was mild shortening of femoral necks and tibiae in some patients, whereas others had minor epiphyseal or metaphyseal changes. In all patients, exome and Sanger sequencing identified homozygous or compound heterozygous PAPSS2 variants, including c.809G>A, common to white European patients. Bi-parental inheritance was established where possible. Low serum DHEAS, but not overt androgen excess was identified. Our study indicates that autosomal recessive brachyolmia occurs across continents and may be under-recognized in infancy. This condition should be considered in the differential diagnosis of short femora presenting in the second trimester.

Pathogenicity and selective constraint on variation near splice sites.

Lord J; Gallone G; Short PJ; McRae JF; Ironfield H; Wynn EH; Gerety SS; He L; Kerr B; Johnson DS; McCann E; Kinning E; Flinter F; Temple IK; Clayton-Smith J; McEntagart M; Lynch SA; Joss S; Douzgou S; Dabir T; Clowes V; McConnell VPM; Lam W; Wright CF; FitzPatrick DR; Firth HV; Barrett JC; Hurles ME;

Genome research 2019;29;2;159-170

Mutations that perturb normal pre-mRNA splicing are significant contributors to human disease. We used exome sequencing data from 7833 probands with developmental disorders (DDs) and their unaffected parents, as well as more than 60,000 aggregated exomes from the Exome Aggregation Consortium, to investigate selection around the splice sites and quantify the contribution of splicing mutations to DDs. Patterns of purifying selection, a deficit of variants in highly constrained genes in healthy subjects, and excess de novo mutations in patients highlighted particular positions within and around the consensus splice site of greater functional relevance. By using mutational burden analyses in this large cohort of proband-parent trios, we could estimate in an unbiased manner the relative contributions of mutations at canonical dinucleotides (73%) and flanking noncanonical positions (27%), and calculate the positive predictive value of pathogenicity for different classes of mutations. We identified 18 patients with likely diagnostic de novo mutations in dominant DD-associated genes at noncanonical positions in splice sites. We estimate 35%-40% of pathogenic variants in noncanonical splice site positions are missing from public databases.

Phrank measures phenotype sets similarity to greatly improve Mendelian diagnostic disease prioritization.

Jagadeesh KA; Birgmeier J; Guturu H; Deisseroth CA; Wenger AM; Bernstein JA; Bejerano G

Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;2;464-470

Exome sequencing and diagnosis is beginning to spread across the medical establishment. The most time-consuming part of genome-based diagnosis is the manual step of matching the potentially long list of patient candidate genes to patient phenotypes to identify the causative disease.

PIGT-CDG, a disorder of the glycosylphosphatidylinositol anchor: description of 13 novel patients and expansion of the clinical characteristics.

Bayat A; Knaus A; Juul AW; Dukic D; Gardella E; Charzewska A; Clement E; Hjalgrim H; Hoffman-Zacharska D; Horn D; Horton R; Hurst JA; Josifova D; Larsen LHG; Lascelles K; Obersztyn E; Pagnamenta A; Pal DK; Pendziwiat M; Ryten M; Taylor J; Vogt J; Weber Y; Krawitz PM; Helbig I; Kini U; Møller RS;

Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;10;2216-2223

To provide a detailed electroclinical description and expand the phenotype of PIGT-CDG, to perform genotype-phenotype correlation, and to investigate the onset and severity of the epilepsy associated with the different genetic subtypes of this rare disorder. Furthermore, to use computer-assisted facial gestalt analysis in PIGT-CDG and to the compare findings with other glycosylphosphatidylinositol (GPI) anchor deficiencies.

Refining the Primrose syndrome phenotype: A study of five patients with ZBTB20 de novo variants and a review of the literature.

Cleaver R; Berg J; Craft E; Foster A; Gibbons RJ; Hobson E; Lachlan K; Naik S; Sampson JR; Sharif S; Smithson S; ; Parker MJ; Tatton-Brown K

American journal of medical genetics. Part A 2019;179;3;344-349

Primrose syndrome is a rare autosomal dominant condition caused by heterozygous missense variants within ZBTB20. Through an exome sequencing approach (as part of the Deciphering Developmental Disorders [DDD] study) we have identified five unrelated individuals with previously unreported, de novo ZBTB20 pathogenic missense variants. All five missense variants targeted the C2H2 zinc finger domains. This genotype-up approach has allowed further refinement of the Primrose syndrome phenotype. Major characteristics (>90% individuals) include an intellectual disability (most frequently in the moderate range), a recognizable facial appearance and brain MRI abnormalities, particularly abnormalities of the corpus callosum. Other frequent clinical associations (in 50-90% individuals) include sensorineural hearing loss (83%), hypotonia (78%), cryptorchidism in males (75%), macrocephaly (72%), behavioral issues (56%), and dysplastic/hypoplastic nails (57%). Based upon these clinical data we discuss our current management of patients with Primrose syndrome.

Spatially clustering de novo variants in CYFIP2, encoding the cytoplasmic FMRP interacting protein 2, cause intellectual disability and seizures.

Zweier M; Begemann A; McWalter K; Cho MT; Abela L; Banka S; Behring B; Berger A; Brown CW; Carneiro M; Chen J; Cooper GM; ; Finnila CR; Guillen Sacoto MJ; Henderson A; Hüffmeier U; Joset P; Kerr B; Lesca G; Leszinski GS; McDermott JH; Meltzer MR; Monaghan KG; Mostafavi R; Õunap K; Plecko B; Powis Z; Purcarin G; Reimand T; Riedhammer KM; Schreiber JM; Sirsi D; Wierenga KJ; Wojcik MH; Papuc SM; Steindl K; Sticht H; Rauch A

European journal of human genetics : EJHG 2019;27;5;747-759

CYFIP2, encoding the evolutionary highly conserved cytoplasmic FMRP interacting protein 2, has previously been proposed as a candidate gene for intellectual disability and autism because of its important role linking FMRP-dependent transcription regulation and actin polymerization via the WAVE regulatory complex (WRC). Recently, de novo variants affecting the amino acid p.Arg87 of CYFIP2 were reported in four individuals with epileptic encephalopathy. We here report 12 independent patients harboring a variety of de novo variants in CYFIP2 broadening the molecular and clinical spectrum of a novel CYFIP2-related neurodevelopmental disorder. Using trio whole-exome or -genome sequencing, we identified 12 independent patients carrying a total of eight distinct de novo variants in CYFIP2 with a shared phenotype of intellectual disability, seizures, and muscular hypotonia. We detected seven different missense variants, of which two occurred recurrently (p.(Arg87Cys) and p.(Ile664Met)), and a splice donor variant in the last intron for which we showed exon skipping in the transcript. The latter is expected to escape nonsense-mediated mRNA decay resulting in a truncated protein. Despite the large spacing in the primary structure, the variants spatially cluster in the tertiary structure and are all predicted to weaken the interaction with WAVE1 or NCKAP1 of the actin polymerization regulating WRC-complex. Preliminary genotype-phenotype correlation indicates a profound phenotype in p.Arg87 substitutions and a more variable phenotype in other alterations. This study evidenced a variety of de novo variants in CYFIP2 as a novel cause of mostly severe intellectual disability with seizures and muscular hypotonia.

STXBP1-associated neurodevelopmental disorder: a comparative study of behavioural characteristics.

O'Brien S; Ng-Cordell E; ; Astle DE; Scerif G; Baker K

Journal of neurodevelopmental disorders 2019;11;1;17

De novo loss of function mutations in STXBP1 are a relatively common cause of epilepsy and intellectual disability (ID). However, little is known about the types and severities of behavioural features associated with this genetic diagnosis.

The CHD8 overgrowth syndrome: A detailed evaluation of an emerging overgrowth phenotype in 27 patients.

Ostrowski PJ; Zachariou A; Loveday C; Beleza-Meireles A; Bertoli M; Dean J; Douglas AGL; Ellis I; Foster A; Graham JM; Hague J; Hilhorst-Hofstee Y; Hoffer M; Johnson D; Josifova D; Kant SG; Kini U; Lachlan K; Lam W; Lees M; Lynch S; Maitz S; McKee S; Metcalfe K; Nathanson K; Ockeloen CW; Parker MJ; Pierson TM; Rahikkala E; Sanchez-Lara PA; Spano A; Van Maldergem L; Cole T; Douzgou S; Tatton-Brown K

American journal of medical genetics. Part C, Seminars in medical genetics 2019;181;4;557-564

CHD8 has been reported as an autism susceptibility/intellectual disability gene but emerging evidence suggests that it additionally causes an overgrowth phenotype. This study reports 27 unrelated patients with pathogenic or likely pathogenic CHD8 variants (25 null variants, two missense variants) and a male:female ratio of 21:6 (3.5:1, p < .01). All patients presented with intellectual disability, with 85% in the mild or moderate range, and 85% had a height and/or head circumference ≥2 standard deviations above the mean, meeting our clinical criteria for overgrowth. Behavioral problems were reported in the majority of patients (78%), with over half (56%) either formally diagnosed with an autistic spectrum disorder or described as having autistic traits. Additional clinical features included neonatal hypotonia (33%), and less frequently seizures, pes planus, scoliosis, fifth finger clinodactyly, umbilical hernia, and glabellar hemangioma (≤15% each). These results suggest that, in addition to its established link with autism and intellectual disability, CHD8 causes an overgrowth phenotype, and should be considered in the differential diagnosis of patients presenting with increased height and/or head circumference in association with intellectual disability.

The clinical presentation caused by truncating CHD8 variants.

Douzgou S; Liang HW; Metcalfe K; Somarathi S; Tischkowitz M; Mohamed W; Kini U; McKee S; Yates L; Bertoli M; Lynch SA; Holder S; ; Banka S

Clinical genetics 2019;96;1;72-84

Variants in the chromodomain helicase DNA-binding protein 8 (CHD8) have been associated with intellectual disability (ID), autism spectrum disorders (ASDs) and overgrowth and CHD8 is one of the causative genes for OGID (overgrowth and ID). We investigated 25 individuals with CHD8 protein truncating variants (PTVs), including 10 previously unreported patients and found a male to female ratio of 2.7:1 (19:7) and a pattern of common features: macrocephaly (62.5%), tall stature (47%), developmental delay and/or intellectual disability (81%), ASDs (84%), sleep difficulties (50%), gastrointestinal problems (40%), and distinct facial features. Most of the individuals in this cohort had moderate-to-severe ID, some had regression of speech (37%), seizures (27%) and hypotonia (27%) and two individuals were non-ambulant. Our study shows that haploinsufficiency of CHD8 is associated with a distinctive OGID syndrome with pronounced autistic traits and supports a sex-dependent penetrance of CHD8 PTVs in humans.

The clinical spectrum of the congenital myasthenic syndrome resulting from COL13A1 mutations.

Rodríguez Cruz PM; Cossins J; Estephan EP; Munell F; Selby K; Hirano M; Maroofin R; Mehrjardi MYV; Chow G; Carr A; Manzur A; Robb S; Munot P; Wei Liu W; Banka S; Fraser H; De Goede C; Zanoteli E; Conti Reed U; Sage A; Gratacos M; Macaya A; Dusl M; Senderek J; Töpf A; Hofer M; Knight R; Ramdas S; Jayawant S; Lochmüller H; Palace J; Beeson D

Brain : a journal of neurology 2019;142;6;1547-1560

Next generation sequencing techniques were recently used to show mutations in COL13A1 cause synaptic basal lamina-associated congenital myasthenic syndrome type 19. Animal studies showed COL13A1, a synaptic extracellular-matrix protein, is involved in the formation and maintenance of the neuromuscular synapse that appears independent of the Agrin-LRP4-MuSK-DOK7 acetylcholine receptor clustering pathway. Here, we report the phenotypic spectrum of 16 patients from 11 kinships harbouring homozygous or heteroallelic mutations in COL13A1. Clinical presentation was mostly at birth with hypotonia and breathing and feeding difficulties often requiring ventilation and artificial feeding. Respiratory crisis related to recurrent apnoeas, sometimes triggered by chest infections, were common early in life but resolved over time. The predominant pattern of muscle weakness included bilateral ptosis (non-fatigable in adulthood), myopathic facies and marked axial weakness, especially of neck flexion, while limb muscles were less involved. Other features included facial dysmorphism, skeletal abnormalities and mild learning difficulties. All patients tested had results consistent with abnormal neuromuscular transmission. Muscle biopsies were within normal limits or showed non-specific changes. Muscle MRI and serum creatine kinase levels were normal. In keeping with COL13A1 mutations affecting both synaptic structure and presynaptic function, treatment with 3,4-diaminopyridine and salbutamol resulted in motor and respiratory function improvement. In non-treated cases, disease severity and muscle strength improved gradually over time and several adults recovered normal muscle strength in the limbs. In summary, patients with COL13A1 mutations present mostly with severe early-onset myasthenic syndrome with feeding and breathing difficulties. Axial weakness is greater than limb weakness. Disease course improves gradually over time, which could be consistent with the less prominent role of COL13A1 once the neuromuscular junction is mature. This report emphasizes the role of collagens at the human muscle endplate and should facilitate the recognition of this disorder, which can benefit from pharmacological treatment.

The phenotypic spectrum of WWOX-related disorders: 20 additional cases of WOREE syndrome and review of the literature.

Piard J; Hawkes L; Milh M; Villard L; Borgatti R; Romaniello R; Fradin M; Capri Y; Héron D; Nougues MC; Nava C; Arsene OT; Shears D; Taylor J; Pagnamenta A; Taylor JC; Sogawa Y; Johnson D; Firth H; Vasudevan P; Jones G; Nguyen-Morel MA; Busa T; Roubertie A; van den Born M; Brischoux-Boucher E; Koenig M; Mignot C; ; Kini U; Philippe C

Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;6;1308-1318

Germline WWOX pathogenic variants have been associated with disorder of sex differentiation (DSD), spinocerebellar ataxia (SCA), and WWOX-related epileptic encephalopathy (WOREE syndrome). We review clinical and molecular data on WWOX-related disorders, further describing WOREE syndrome and phenotype/genotype correlations.

The preferences of potential stakeholders in psychiatric genomic research regarding consent procedures and information delivery.

Sundby A; Boolsen MW; Burgdorf KS; Ullum H; Hansen TF; Middleton A; Mors O

European psychiatry : the journal of the Association of European Psychiatrists 2019;55;29-35

Genomic sequencing plays an increasing role in genetic research, also in psychiatry. This raises challenges concerning the validity and type of the informed consent and the return of incidental findings. However, no solution currently exists on the best way to obtain the informed consent and deliver findings to research subjects.

When genomic medicine reveals misattributed genetic relationships-the debate about disclosure revisited.

Wright CF; Parker M; Lucassen AM

Genetics in medicine : official journal of the American College of Medical Genetics 2019;21;1;97-101

Accidental discovery of misattributed parentage is an age-old problem in clinical medicine, but the ability to detect it routinely has increased recently as a result of high-throughput DNA sequencing technologies coupled with family sequencing studies. Problems arise at the clinical-research boundary, where policies and consent forms guaranteeing nondisclosure may conflict with standard clinical care.

ZMIZ1 Variants Cause a Syndromic Neurodevelopmental Disorder.

Carapito R; Ivanova EL; Morlon A; Meng L; Molitor A; Erdmann E; Kieffer B; Pichot A; Naegely L; Kolmer A; Paul N; Hanauer A; Tran Mau-Them F; Jean-Marçais N; Hiatt SM; Cooper GM; Tvrdik T; Muir AM; Dimartino C; Chopra M; Amiel J; Gordon CT; Dutreux F; Garde A; Thauvin-Robinet C; Wang X; Leduc MS; Phillips M; Crawford HP; Kukolich MK; Hunt D; Harrison V; Kharbanda M; ; ; Smigiel R; Gold N; Hung CY; Viskochil DH; Dugan SL; Bayrak-Toydemir P; Joly-Helas G; Guerrot AM; Schluth-Bolard C; Rio M; Wentzensen IM; McWalter K; Schnur RE; Lewis AM; Lalani SR; Mensah-Bonsu N; Céraline J; Sun Z; Ploski R; Bacino CA; Mefford HC; Faivre L; Bodamer O; Chelly J; Isidor B; Bahram S

American journal of human genetics 2019;104;2;319-330

ZMIZ1 is a coactivator of several transcription factors, including p53, the androgen receptor, and NOTCH1. Here, we report 19 subjects with intellectual disability and developmental delay carrying variants in ZMIZ1. The associated features include growth failure, feeding difficulties, microcephaly, facial dysmorphism, and various other congenital malformations. Of these 19, 14 unrelated subjects carried de novo heterozygous single-nucleotide variants (SNVs) or single-base insertions/deletions, 3 siblings harbored a heterozygous single-base insertion, and 2 subjects had a balanced translocation disrupting ZMIZ1 or involving a regulatory region of ZMIZ1. In total, we identified 13 point mutations that affect key protein regions, including a SUMO acceptor site, a central disordered alanine-rich motif, a proline-rich domain, and a transactivation domain. All identified variants were absent from all available exome and genome databases. In vitro, ZMIZ1 showed impaired coactivation of the androgen receptor. In vivo, overexpression of ZMIZ1 mutant alleles in developing mouse brains using in utero electroporation resulted in abnormal pyramidal neuron morphology, polarization, and positioning, underscoring the importance of ZMIZ1 in neural development and supporting mutations in ZMIZ1 as the cause of a rare neurodevelopmental syndrome.

A homozygous variant disrupting the PIGH start-codon is associated with developmental delay, epilepsy, and microcephaly.

Pagnamenta AT; Murakami Y; Anzilotti C; Titheradge H; Oates AJ; Morton J; ; Kinoshita T; Kini U; Taylor JC

Human mutation 2018;39;6;822-826

Defective glycosylphosphatidylinositol (GPI)-anchor biogenesis can cause a spectrum of predominantly neurological problems. For eight genes critical to this biological process, disease associations are not yet reported. Scanning exomes from 7,833 parent-child trios and 1,792 singletons from the DDD study for biallelic variants in this gene-set uncovered a rare PIGH variant in a boy with epilepsy, microcephaly, and behavioral difficulties. Although only 2/2 reads harbored this c.1A > T transversion, the presence of ∼25 Mb autozygosity at this locus implied homozygosity, which was confirmed using Sanger sequencing. A similarly-affected sister was also homozygous. FACS analysis of PIGH-deficient CHO cells indicated that cDNAs with c.1A > T could not efficiently restore expression of GPI-APs. Truncation of PIGH protein was consistent with the utilization of an in-frame start-site at codon 63. In summary, we describe siblings harboring a homozygous c.1A > T variant resulting in defective GPI-anchor biogenesis and highlight the importance of exploring low-coverage variants within autozygous regions.

A novel PIGA variant associated with severe X-linked epilepsy and profound developmental delay.

Low KJ; James M; Sharples PM; Eaton M; Jenkinson S; Study DDD; Smithson SF

Seizure 2018;56;1-3

A Recurrent De Novo PACS2 Heterozygous Missense Variant Causes Neonatal-Onset Developmental Epileptic Encephalopathy, Facial Dysmorphism, and Cerebellar Dysgenesis.

Olson HE; Jean-Marçais N; Yang E; Heron D; Tatton-Brown K; van der Zwaag PA; Bijlsma EK; Krock BL; Backer E; Kamsteeg EJ; Sinnema M; Reijnders MRF; Bearden D; Begtrup A; Telegrafi A; Lunsing RJ; Burglen L; Lesca G; Cho MT; Smith LA; Sheidley BR; Moufawad El Achkar C; Pearl PL; Poduri A; Skraban CM; Tarpinian J; Nesbitt AI; Fransen van de Putte DE; Ruivenkamp CAL; Rump P; Chatron N; Sabatier I; De Bellescize J; Guibaud L; Sweetser DA; Waxler JL; Wierenga KJ; ; Donadieu J; Narayanan V; Ramsey KM; ; Nava C; Rivière JB; Vitobello A; Tran Mau-Them F; Philippe C; Bruel AL; Duffourd Y; Thomas L; Lelieveld SH; Schuurs-Hoeijmakers J; Brunner HG; Keren B; Thevenon J; Faivre L; Thomas G; Thauvin-Robinet C

American journal of human genetics 2018;102;5;995-1007

Developmental and epileptic encephalopathies (DEEs) represent a large clinical and genetic heterogeneous group of neurodevelopmental diseases. The identification of pathogenic genetic variants in DEEs remains crucial for deciphering this complex group and for accurately caring for affected individuals (clinical diagnosis, genetic counseling, impacting medical, precision therapy, clinical trials, etc.). Whole-exome sequencing and intensive data sharing identified a recurrent de novo PACS2 heterozygous missense variant in 14 unrelated individuals. Their phenotype was characterized by epilepsy, global developmental delay with or without autism, common cerebellar dysgenesis, and facial dysmorphism. Mixed focal and generalized epilepsy occurred in the neonatal period, controlled with difficulty in the first year, but many improved in early childhood. PACS2 is an important PACS1 paralog and encodes a multifunctional sorting protein involved in nuclear gene expression and pathway traffic regulation. Both proteins harbor cargo(furin)-binding regions (FBRs) that bind cargo proteins, sorting adaptors, and cellular kinase. Compared to the defined PACS1 recurrent variant series, individuals with PACS2 variant have more consistently neonatal/early-infantile-onset epilepsy that can be challenging to control. Cerebellar abnormalities may be similar but PACS2 individuals exhibit a pattern of clear dysgenesis ranging from mild to severe. Functional studies demonstrated that the PACS2 recurrent variant reduces the ability of the predicted autoregulatory domain to modulate the interaction between the PACS2 FBR and client proteins, which may disturb cellular function. These findings support the causality of this recurrent de novo PACS2 heterozygous missense in DEEs with facial dysmorphim and cerebellar dysgenesis.

BRD4 interacts with NIPBL and BRD4 is mutated in a Cornelia de Lange-like syndrome.

Olley G; Ansari M; Bengani H; Grimes GR; Rhodes J; von Kriegsheim A; Blatnik A; Stewart FJ; Wakeling E; Carroll N; Ross A; Park SM; ; Bickmore WA; Pradeepa MM; FitzPatrick DR

Nature Genetics 2018;50;3;329-332

We found that the clinical phenotype associated with BRD4 haploinsufficiency overlapped with that of Cornelia de Lange syndrome (CdLS), which is most often caused by mutation of NIPBL. More typical CdLS was observed with a de novo BRD4 missense variant, which retained the ability to coimmunoprecipitate with NIPBL, but bound poorly to acetylated histones. BRD4 and NIPBL displayed correlated binding at super-enhancers and appeared to co-regulate developmental gene expression.

CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language.

Snijders Blok L; Rousseau J; Twist J; Ehresmann S; Takaku M; Venselaar H; Rodan LH; Nowak CB; Douglas J; Swoboda KJ; Steeves MA; Sahai I; Stumpel CTRM; Stegmann APA; Wheeler P; Willing M; Fiala E; Kochhar A; Gibson WT; Cohen ASA; Agbahovbe R; Innes AM; Au PYB; Rankin J; Anderson IJ; Skinner SA; Louie RJ; Warren HE; Afenjar A; Keren B; Nava C; Buratti J; Isapof A; Rodriguez D; Lewandowski R; Propst J; van Essen T; Choi M; Lee S; Chae JH; Price S; Schnur RE; Douglas G; Wentzensen IM; Zweier C; Reis A; Bialer MG; Moore C; Koopmans M; Brilstra EH; Monroe GR; van Gassen KLI; van Binsbergen E; Newbury-Ecob R; Bownass L; Bader I; Mayr JA; Wortmann SB; Jakielski KJ; Strand EA; Kloth K; Bierhals T; ; Roberts JD; Petrovich RM; Machida S; Kurumizaka H; Lelieveld S; Pfundt R; Jansen S; Deriziotis P; Faivre L; Thevenon J; Assoum M; Shriberg L; Kleefstra T; Brunner HG; Wade PA; Fisher SE; Campeau PM

Nature Communications 2018;9;1;4619

Chromatin remodeling is of crucial importance during brain development. Pathogenic alterations of several chromatin remodeling ATPases have been implicated in neurodevelopmental disorders. We describe an index case with a de novo missense mutation in CHD3, identified during whole genome sequencing of a cohort of children with rare speech disorders. To gain a comprehensive view of features associated with disruption of this gene, we use a genotype-driven approach, collecting and characterizing 35 individuals with de novo CHD3 mutations and overlapping phenotypes. Most mutations cluster within the ATPase/helicase domain of the encoded protein. Modeling their impact on the three-dimensional structure demonstrates disturbance of critical binding and interaction motifs. Experimental assays with six of the identified mutations show that a subset directly affects ATPase activity, and all but one yield alterations in chromatin remodeling. We implicate de novo CHD3 mutations in a syndrome characterized by intellectual disability, macrocephaly, and impaired speech and language.

Common genetic variants contribute to risk of rare severe neurodevelopmental disorders.

Niemi MEK; Martin HC; Rice DL; Gallone G; Gordon S; Kelemen M; McAloney K; McRae J; Radford EJ; Yu S; Gecz J; Martin NG; Wright CF; Fitzpatrick DR; Firth HV; Hurles ME; Barrett JC

Nature 2018;562;7726;268-271

There are thousands of rare human disorders that are caused by single deleterious, protein-coding genetic variants1. However, patients with the same genetic defect can have different clinical presentations2-4, and some individuals who carry known disease-causing variants can appear unaffected5. Here, to understand what explains these differences, we study a cohort of 6,987 children assessed by clinical geneticists to have severe neurodevelopmental disorders such as global developmental delay and autism, often in combination with abnormalities of other organ systems. Although the genetic causes of these neurodevelopmental disorders are expected to be almost entirely monogenic, we show that 7.7% of variance in risk is attributable to inherited common genetic variation. We replicated this genome-wide common variant burden by showing, in an independent sample of 728 trios (comprising a child plus both parents) from the same cohort, that this burden is over-transmitted from parents to children with neurodevelopmental disorders. Our common-variant signal is significantly positively correlated with genetic predisposition to lower educational attainment, decreased intelligence and risk of schizophrenia. We found that common-variant risk was not significantly different between individuals with and without a known protein-coding diagnostic variant, which suggests that common-variant risk affects patients both with and without a monogenic diagnosis. In addition, previously published common-variant scores for autism, height, birth weight and intracranial volume were all correlated with these traits within our cohort, which suggests that phenotypic expression in individuals with monogenic disorders is affected by the same variants as in the general population. Our results demonstrate that common genetic variation affects both overall risk and clinical presentation in neurodevelopmental disorders that are typically considered to be monogenic.

De Novo and Inherited Loss-of-Function Variants in TLK2: Clinical and Genotype-Phenotype Evaluation of a Distinct Neurodevelopmental Disorder.

Reijnders MRF; Miller KA; Alvi M; Goos JAC; Lees MM; de Burca A; Henderson A; Kraus A; Mikat B; de Vries BBA; Isidor B; Kerr B; Marcelis C; Schluth-Bolard C; Deshpande C; Ruivenkamp CAL; Wieczorek D; ; Baralle D; Blair EM; Engels H; Lüdecke HJ; Eason J; Santen GWE; Clayton-Smith J; Chandler K; Tatton-Brown K; Payne K; Helbig K; Radtke K; Nugent KM; Cremer K; Strom TM; Bird LM; Sinnema M; Bitner-Glindzicz M; van Dooren MF; Alders M; Koopmans M; Brick L; Kozenko M; Harline ML; Klaassens M; Steinraths M; Cooper NS; Edery P; Yap P; Terhal PA; van der Spek PJ; Lakeman P; Taylor RL; Littlejohn RO; Pfundt R; Mercimek-Andrews S; Stegmann APA; Kant SG; McLean S; Joss S; Swagemakers SMA; Douzgou S; Wall SA; Küry S; Calpena E; Koelling N; McGowan SJ; Twigg SRF; Mathijssen IMJ; Nellaker C; Brunner HG; Wilkie AOM

American journal of human genetics 2018;102;6;1195-1203

Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.

De novo and inherited mutations in the X-linked gene CLCN4 are associated with syndromic intellectual disability and behavior and seizure disorders in males and females.

Palmer EE; Stuhlmann T; Weinert S; Haan E; Van Esch H; Holvoet M; Boyle J; Leffler M; Raynaud M; Moraine C; van Bokhoven H; Kleefstra T; Kahrizi K; Najmabadi H; Ropers HH; Delgado MR; Sirsi D; Golla S; Sommer A; Pietryga MP; Chung WK; Wynn J; Rohena L; Bernardo E; Hamlin D; Faux BM; Grange DK; Manwaring L; Tolmie J; Joss S; ; Cobben JM; Duijkers FAM; Goehringer JM; Challman TD; Hennig F; Fischer U; Grimme A; Suckow V; Musante L; Nicholl J; Shaw M; Lodh SP; Niu Z; Rosenfeld JA; Stankiewicz P; Jentsch TJ; Gecz J; Field M; Kalscheuer VM

Molecular psychiatry 2018;23;2;222-230

Variants in CLCN4, which encodes the chloride/hydrogen ion exchanger CIC-4 prominently expressed in brain, were recently described to cause X-linked intellectual disability and epilepsy. We present detailed phenotypic information on 52 individuals from 16 families with CLCN4-related disorder: 5 affected females and 2 affected males with a de novo variant in CLCN4 (6 individuals previously unreported) and 27 affected males, 3 affected females and 15 asymptomatic female carriers from 9 families with inherited CLCN4 variants (4 families previously unreported). Intellectual disability ranged from borderline to profound. Behavioral and psychiatric disorders were common in both child- and adulthood, and included autistic features, mood disorders, obsessive-compulsive behaviors and hetero- and autoaggression. Epilepsy was common, with severity ranging from epileptic encephalopathy to well-controlled seizures. Several affected individuals showed white matter changes on cerebral neuroimaging and progressive neurological symptoms, including movement disorders and spasticity. Heterozygous females can be as severely affected as males. The variability of symptoms in females is not correlated with the X inactivation pattern studied in their blood. The mutation spectrum includes frameshift, missense and splice site variants and one single-exon deletion. All missense variants were predicted to affect CLCN4's function based on in silico tools and either segregated with the phenotype in the family or were de novo. Pathogenicity of all previously unreported missense variants was further supported by electrophysiological studies in Xenopus laevis oocytes. We compare CLCN4-related disorder with conditions related to dysfunction of other members of the CLC family.

De novo mutations in MED13, a component of the Mediator complex, are associated with a novel neurodevelopmental disorder.

Snijders Blok L; Hiatt SM; Bowling KM; Prokop JW; Engel KL; Cochran JN; Bebin EM; Bijlsma EK; Ruivenkamp CAL; Terhal P; Simon MEH; Smith R; Hurst JA; ; McLaughlin H; Person R; Crunk A; Wangler MF; Streff H; Symonds JD; Zuberi SM; Elliott KS; Sanders VR; Masunga A; Hopkin RJ; Dubbs HA; Ortiz-Gonzalez XR; Pfundt R; Brunner HG; Fisher SE; Kleefstra T; Cooper GM

Human genetics 2018;137;5;375-388

Many genetic causes of developmental delay and/or intellectual disability (DD/ID) are extremely rare, and robust discovery of these requires both large-scale DNA sequencing and data sharing. Here we describe a GeneMatcher collaboration which led to a cohort of 13 affected individuals harboring protein-altering variants, 11 of which are de novo, in MED13; the only inherited variant was transmitted to an affected child from an affected mother. All patients had intellectual disability and/or developmental delays, including speech delays or disorders. Other features that were reported in two or more patients include autism spectrum disorder, attention deficit hyperactivity disorder, optic nerve abnormalities, Duane anomaly, hypotonia, mild congenital heart abnormalities, and dysmorphisms. Six affected individuals had mutations that are predicted to truncate the MED13 protein, six had missense mutations, and one had an in-frame-deletion of one amino acid. Out of the seven non-truncating mutations, six clustered in two specific locations of the MED13 protein: an N-terminal and C-terminal region. The four N-terminal clustering mutations affect two adjacent amino acids that are known to be involved in MED13 ubiquitination and degradation, p.Thr326 and p.Pro327. MED13 is a component of the CDK8-kinase module that can reversibly bind Mediator, a multi-protein complex that is required for Polymerase II transcription initiation. Mutations in several other genes encoding subunits of Mediator have been previously shown to associate with DD/ID, including MED13L, a paralog of MED13. Thus, our findings add MED13 to the group of CDK8-kinase module-associated disease genes.

De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation.

Basilicata MF; Bruel AL; Semplicio G; Valsecchi CIK; Aktaş T; Duffourd Y; Rumpf T; Morton J; Bache I; Szymanski WG; Gilissen C; Vanakker O; Õunap K; Mittler G; van der Burgt I; El Chehadeh S; Cho MT; Pfundt R; Tan TY; Kirchhoff M; Menten B; Vergult S; Lindstrom K; Reis A; Johnson DS; Fryer A; McKay V; ; Fisher RB; Thauvin-Robinet C; Francis D; Roscioli T; Pajusalu S; Radtke K; Ganesh J; Brunner HG; Wilson M; Faivre L; Kalscheuer VM; Thevenon J; Akhtar A

Nature Genetics 2018;50;10;1442-1451

The etiological spectrum of ultra-rare developmental disorders remains to be fully defined. Chromatin regulatory mechanisms maintain cellular identity and function, where misregulation may lead to developmental defects. Here, we report pathogenic variations in MSL3, which encodes a member of the chromatin-associated male-specific lethal (MSL) complex responsible for bulk histone H4 lysine 16 acetylation (H4K16ac) in flies and mammals. These variants cause an X-linked syndrome affecting both sexes. Clinical features of the syndrome include global developmental delay, progressive gait disturbance, and recognizable facial dysmorphism. MSL3 mutations affect MSL complex assembly and activity, accompanied by a pronounced loss of H4K16ac levels in vivo. Patient-derived cells display global transcriptome alterations of pathways involved in morphogenesis and cell migration. Finally, we use histone deacetylase inhibitors to rebalance acetylation levels, alleviating some of the molecular and cellular phenotypes of patient cells. Taken together, we characterize a syndrome that allowed us to decipher the developmental importance of MSL3 in humans.

De novo mutations in regulatory elements in neurodevelopmental disorders.

Short PJ; McRae JF; Gallone G; Sifrim A; Won H; Geschwind DH; Wright CF; Firth HV; FitzPatrick DR; Barrett JC; Hurles ME

Nature 2018;555;7698;611-616

We previously estimated that 42% of patients with severe developmental disorders carry pathogenic de novo mutations in coding sequences. The role of de novo mutations in regulatory elements affecting genes associated with developmental disorders, or other genes, has been essentially unexplored. We identified de novo mutations in three classes of putative regulatory elements in almost 8,000 patients with developmental disorders. Here we show that de novo mutations in highly evolutionarily conserved fetal brain-active elements are significantly and specifically enriched in neurodevelopmental disorders. We identified a significant twofold enrichment of recurrently mutated elements. We estimate that, genome-wide, 1-3% of patients without a diagnostic coding variant carry pathogenic de novo mutations in fetal brain-active regulatory elements and that only 0.15% of all possible mutations within highly conserved fetal brain-active elements cause neurodevelopmental disorders with a dominant mechanism. Our findings represent a robust estimate of the contribution of de novo mutations in regulatory elements to this genetically heterogeneous set of disorders, and emphasize the importance of combining functional and evolutionary evidence to identify regulatory causes of genetic disorders.

De Novo Pathogenic Variants in CACNA1E Cause Developmental and Epileptic Encephalopathy with Contractures, Macrocephaly, and Dyskinesias.

Helbig KL; Lauerer RJ; Bahr JC; Souza IA; Myers CT; Uysal B; Schwarz N; Gandini MA; Huang S; Keren B; Mignot C; Afenjar A; Billette de Villemeur T; Héron D; Nava C; Valence S; Buratti J; Fagerberg CR; Soerensen KP; Kibaek M; Kamsteeg EJ; Koolen DA; Gunning B; Schelhaas HJ; Kruer MC; Fox J; Bakhtiari S; Jarrar R; Padilla-Lopez S; Lindstrom K; Jin SC; Zeng X; Bilguvar K; Papavasileiou A; Xing Q; Zhu C; Boysen K; Vairo F; Lanpher BC; Klee EW; Tillema JM; Payne ET; Cousin MA; Kruisselbrink TM; Wick MJ; Baker J; Haan E; Smith N; Sadeghpour A; Davis EE; Katsanis N; ; Corbett MA; MacLennan AH; Gecz J; Biskup S; Goldmann E; Rodan LH; Kichula E; Segal E; Jackson KE; Asamoah A; Dimmock D; McCarrier J; Botto LD; Filloux F; Tvrdik T; Cascino GD; Klingerman S; Neumann C; Wang R; Jacobsen JC; Nolan MA; Snell RG; Lehnert K; Sadleir LG; Anderlid BM; Kvarnung M; Guerrini R; Friez MJ; Lyons MJ; Leonhard J; Kringlen G; Casas K; El Achkar CM; Smith LA; Rotenberg A; Poduri A; Sanchis-Juan A; Carss KJ; Rankin J; Zeman A; Raymond FL; Blyth M; Kerr B; Ruiz K; Urquhart J; Hughes I; Banka S; ; Hedrich UBS; Scheffer IE; Helbig I; Zamponi GW; Lerche H; Mefford HC

American journal of human genetics 2018;103;5;666-678

Developmental and epileptic encephalopathies (DEEs) are severe neurodevelopmental disorders often beginning in infancy or early childhood that are characterized by intractable seizures, abundant epileptiform activity on EEG, and developmental impairment or regression. CACNA1E is highly expressed in the central nervous system and encodes the α1-subunit of the voltage-gated CaV2.3 channel, which conducts high voltage-activated R-type calcium currents that initiate synaptic transmission. Using next-generation sequencing techniques, we identified de novo CACNA1E variants in 30 individuals with DEE, characterized by refractory infantile-onset seizures, severe hypotonia, and profound developmental impairment, often with congenital contractures, macrocephaly, hyperkinetic movement disorders, and early death. Most of the 14, partially recurring, variants cluster within the cytoplasmic ends of all four S6 segments, which form the presumed CaV2.3 channel activation gate. Functional analysis of several S6 variants revealed consistent gain-of-function effects comprising facilitated voltage-dependent activation and slowed inactivation. Another variant located in the domain II S4-S5 linker results in facilitated activation and increased current density. Five participants achieved seizure freedom on the anti-epileptic drug topiramate, which blocks R-type calcium channels. We establish pathogenic variants in CACNA1E as a cause of DEEs and suggest facilitated R-type calcium currents as a disease mechanism for human epilepsy and developmental disorders.

De Novo Variants in the F-Box Protein FBXO11 in 20 Individuals with a Variable Neurodevelopmental Disorder.

Gregor A; Sadleir LG; Asadollahi R; Azzarello-Burri S; Battaglia A; Ousager LB; Boonsawat P; Bruel AL; Buchert R; Calpena E; Cogné B; Dallapiccola B; Distelmaier F; Elmslie F; Faivre L; Haack TB; Harrison V; Henderson A; Hunt D; Isidor B; Joset P; Kumada S; Lachmeijer AMA; Lees M; Lynch SA; Martinez F; Matsumoto N; McDougall C; Mefford HC; Miyake N; Myers CT; Moutton S; Nesbitt A; Novelli A; Orellana C; Rauch A; Rosello M; Saida K; Santani AB; Sarkar A; Scheffer IE; Shinawi M; Steindl K; Symonds JD; Zackai EH; ; ; Reis A; Sticht H; Zweier C

American journal of human genetics 2018;103;2;305-316

Next-generation sequencing combined with international data sharing has enormously facilitated identification of new disease-associated genes and mutations. This is particularly true for genetically extremely heterogeneous entities such as neurodevelopmental disorders (NDDs). Through exome sequencing and world-wide collaborations, we identified and assembled 20 individuals with de novo variants in FBXO11. They present with mild to severe developmental delay associated with a range of features including short (4/20) or tall (2/20) stature, obesity (5/20), microcephaly (4/19) or macrocephaly (2/19), behavioral problems (17/20), seizures (5/20), cleft lip or palate or bifid uvula (3/20), and minor skeletal anomalies. FBXO11 encodes a member of the F-Box protein family, constituting a subunit of an E3-ubiquitin ligase complex. This complex is involved in ubiquitination and proteasomal degradation and thus in controlling critical biological processes by regulating protein turnover. The identified de novo aberrations comprise two large deletions, ten likely gene disrupting variants, and eight missense variants distributed throughout FBXO11. Structural modeling for missense variants located in the CASH or the Zinc-finger UBR domains suggests destabilization of the protein. This, in combination with the observed spectrum and localization of identified variants and the lack of apparent genotype-phenotype correlations, is compatible with loss of function or haploinsufficiency as an underlying mechanism. We implicate de novo missense and likely gene disrupting variants in FBXO11 in a neurodevelopmental disorder with variable intellectual disability and various other features.

Expanding the molecular basis and phenotypic spectrum of ZDHHC9-associated X-linked intellectual disability.

Schirwani S; Wakeling E; Smith K; ; Balasubramanian M

American journal of medical genetics. Part A 2018;176;5;1238-1244

Pathogenic variants in Zinc Finger DHHC-Type Containing 9 (ZDHHC9) gene have been identified as the cause of X-linked intellectual disability (XLID) in a small number of families. There are a total of 11 reported pathogenic variants in ZDHHC9 in the literature. The majority of reported variants are familial point mutations. There is one report of XLID associated with a de novo mutation in ZDHHC9, and one family with intragenic deletion within ZDHHC9 detected by array CGH. Although initial reports of families with ZDHHC9 pathogenic variants suggested a nonsyndromic XLID, more recent reports suggest a syndromic phenotype with facial dysmorphism. Here we report four patients with pathogenic variants in ZDHHC9, a family with two siblings and their maternal uncle who presented with XLID due to intragenic deletion of ZDHHC9 detected by array CGH and an 11-year-old boy with a de novo pathogenic missense variant in ZDHHC9, which is the first recurrent ZDHHC9 mutation. Our patients had some distinctive facial features in common, including elongated and down-slanting palpebral fissures and high hairline. Marfanoid habitus and seizures that have been previously reported in association with pathogenic variants in ZDHHC9 were absent in our cohort. Clinical information on patients with ZDHHC9-associated XLID is very scarce. New reports of families with detailed clinical description will add to the existing knowledge and help understand the condition better.

Extending the phenotype associated with the CSNK2A1-related Okur-Chung syndrome-A clinical study of 11 individuals.

Owen CI; Bowden R; Parker MJ; Patterson J; Patterson J; Price S; Sarkar A; Castle B; Deshpande C; Splitt M; Ghali N; Dean J; Green AJ; Crosby C; ; Tatton-Brown K

American journal of medical genetics. Part A 2018;176;5;1108-1114

Variants in the Protein Kinase CK2 alpha subunit, encoding the CSNK2A1 gene, have previously been reported in children with an intellectual disability and dysmorphic facial features syndrome: now termed the Okur-Chung neurodevelopmental syndrome. More recently, through trio-based exome sequencing undertaken by the Deciphering Developmental Disorders Study (DDD study), a further 11 children with de novo CSNK2A1 variants have been identified. We have undertaken detailed phenotyping of these patients. Consistent with previously reported patients, patients in this series had apparent intellectual disability, swallowing difficulties, and hypotonia. While there are some shared facial characteristics, the gestalt is neither consistent nor readily recognized. Congenital heart abnormalities were identified in nearly 30% of the patients, representing a newly recognized CSNK2A1 clinical association. Based upon the clinical findings from this study and the previously reported patients, we suggest an initial approach to the management of patients with this recently described intellectual disability syndrome.

Functional mRNA analysis reveals aberrant splicing caused by novel intronic mutation in WDR45 in NBIA patient.

Willoughby J; Duff-Farrier C; Desurkar A; Kurian M; Raghavan A; ; Balasubramanian M

American journal of medical genetics. Part A 2018;176;5;1049-1054

WDR45 gene-associated neurodegeneration with brain iron accumulation (NBIA), referred to as beta-propeller protein-associated neurodegeneration (BPAN), is a rare disorder that presents with a very nonspecific clinical phenotype in children constituting global developmental delay. This case report illustrates the power of a combination of trio exome sequencing, in silico splicing analysis, and mRNA analysis to provide sufficient evidence for pathogenicity of a relatively intronic variant in WDR45, and in so doing, find a genetic diagnosis for a 6-year-old patient with developmental delay and seizures, a diagnosis which may otherwise have only been found once the characteristic MRI patterns of the disease became more obvious in young adulthood.

Further delineation of an entity caused by CREBBP and EP300 mutations but not resembling Rubinstein-Taybi syndrome.

Menke LA; ; Gardeitchik T; Hammond P; Heimdal KR; Houge G; Hufnagel SB; Ji J; Johansson S; Kant SG; Kinning E; Leon EL; Newbury-Ecob R; Paolacci S; Pfundt R; Ragge NK; Rinne T; Ruivenkamp C; Saitta SC; Sun Y; Tartaglia M; Terhal PA; van Essen AJ; Vigeland MD; Xiao B; Hennekam RC

American journal of medical genetics. Part A 2018;176;4;862-876

In 2016, we described that missense variants in parts of exons 30 and 31 of CREBBP can cause a phenotype that differs from Rubinstein-Taybi syndrome (RSTS). Here we report on another 11 patients with variants in this region of CREBBP (between bp 5,128 and 5,614) and two with variants in the homologous region of EP300. None of the patients show characteristics typical for RSTS. The variants were detected by exome sequencing using a panel for intellectual disability in all but one individual, in whom Sanger sequencing was performed upon clinical recognition of the entity. The main characteristics of the patients are developmental delay (90%), autistic behavior (65%), short stature (42%), and microcephaly (43%). Medical problems include feeding problems (75%), vision (50%), and hearing (54%) impairments, recurrent upper airway infections (42%), and epilepsy (21%). Major malformations are less common except for cryptorchidism (46% of males), and cerebral anomalies (70%). Individuals with variants between bp 5,595 and 5,614 of CREBBP show a specific phenotype (ptosis, telecanthi, short and upslanted palpebral fissures, depressed nasal ridge, short nose, anteverted nares, short columella, and long philtrum). 3D face shape demonstrated resemblance to individuals with a duplication of 16p13.3 (the region that includes CREBBP), possibly indicating a gain of function. The other affected individuals show a less specific phenotype. We conclude that there is now more firm evidence that variants in these specific regions of CREBBP and EP300 result in a phenotype that differs from RSTS, and that this phenotype may be heterogeneous.

Heterozygous mutations affecting the protein kinase domain of CDK13 cause a syndromic form of developmental delay and intellectual disability.

Hamilton MJ; Caswell RC; Canham N; Cole T; Firth HV; Foulds N; Heimdal K; Hobson E; Houge G; Joss S; Kumar D; Lampe AK; Maystadt I; McKay V; Metcalfe K; Newbury-Ecob R; Park SM; Robert L; Rustad CF; Wakeling E; Wilkie AOM; Study TDDD; Twigg SRF; Suri M

Journal of medical genetics 2018;55;1;28-38

Recent evidence has emerged linking mutations in CDK13 to syndromic congenital heart disease. We present here genetic and phenotypic data pertaining to 16 individuals with CDK13 mutations.

Histone Lysine Methylases and Demethylases in the Landscape of Human Developmental Disorders.

Faundes V; Newman WG; Bernardini L; Canham N; Clayton-Smith J; Dallapiccola B; Davies SJ; Demos MK; Goldman A; Gill H; Horton R; Kerr B; Kumar D; Lehman A; McKee S; Morton J; Parker MJ; Rankin J; Robertson L; Temple IK; ; ; Banka S

American journal of human genetics 2018;102;1;175-187

Histone lysine methyltransferases (KMTs) and demethylases (KDMs) underpin gene regulation. Here we demonstrate that variants causing haploinsufficiency of KMTs and KDMs are frequently encountered in individuals with developmental disorders. Using a combination of human variation databases and existing animal models, we determine 22 KMTs and KDMs as additional candidates for dominantly inherited developmental disorders. We show that KMTs and KDMs that are associated with, or are candidates for, dominant developmental disorders tend to have a higher level of transcription, longer canonical transcripts, more interactors, and a higher number and more types of post-translational modifications than other KMT and KDMs. We provide evidence to firmly associate KMT2C, ASH1L, and KMT5B haploinsufficiency with dominant developmental disorders. Whereas KMT2C or ASH1L haploinsufficiency results in a predominantly neurodevelopmental phenotype with occasional physical anomalies, KMT5B mutations cause an overgrowth syndrome with intellectual disability. We further expand the phenotypic spectrum of KMT2B-related disorders and show that some individuals can have severe developmental delay without dystonia at least until mid-childhood. Additionally, we describe a recessive histone lysine-methylation defect caused by homozygous or compound heterozygous KDM5B variants and resulting in a recognizable syndrome with developmental delay, facial dysmorphism, and camptodactyly. Collectively, these results emphasize the significance of histone lysine methylation in normal human development and the importance of this process in human developmental disorders. Our results demonstrate that systematic clinically oriented pathway-based analysis of genomic data can accelerate the discovery of rare genetic disorders.

HUWE1 variants cause dominant X-linked intellectual disability: a clinical study of 21 patients.

Moortgat S; Berland S; Aukrust I; Maystadt I; Baker L; Benoit V; Caro-Llopis A; Cooper NS; Debray FG; Faivre L; Gardeitchik T; Haukanes BI; Houge G; Kivuva E; Martinez F; Mehta SG; Nassogne MC; Powell-Hamilton N; Pfundt R; Rosello M; Prescott T; Vasudevan P; van Loon B; Verellen-Dumoulin C; Verloes A; Lippe CV; Wakeling E; Wilkie AOM; Wilson L; Yuen A; Study D; Low KJ; Newbury-Ecob RA

European journal of human genetics : EJHG 2018;26;1;64-74

Whole-gene duplications and missense variants in the HUWE1 gene (NM_031407.6) have been reported in association with intellectual disability (ID). Increased gene dosage has been observed in males with non-syndromic mild to moderate ID with speech delay. Missense variants reported previously appear to be associated with severe ID in males and mild or no ID in obligate carrier females. Here, we report the largest cohort of patients with HUWE1 variants, consisting of 14 females and 7 males, with 15 different missense variants and one splice site variant. Clinical assessment identified common clinical features consisting of moderate to profound ID, delayed or absent speech, short stature with small hands and feet and facial dysmorphism consisting of a broad nasal tip, deep set eyes, epicanthic folds, short palpebral fissures, and a short philtrum. We describe for the first time that females can be severely affected, despite preferential inactivation of the affected X chromosome. Three females with the c.329 G  >  A p.Arg110Gln variant, present with a phenotype of mild ID, specific facial features, scoliosis and craniosynostosis, as reported previously in a single patient. In these females, the X inactivation pattern appeared skewed in favour of the affected transcript. In summary, HUWE1 missense variants may cause syndromic ID in both males and females.

KIAA1109 Variants Are Associated with a Severe Disorder of Brain Development and Arthrogryposis.

Gueneau L; Fish RJ; Shamseldin HE; Voisin N; Tran Mau-Them F; Preiksaitiene E; Monroe GR; Lai A; Putoux A; Allias F; Ambusaidi Q; Ambrozaityte L; Cimbalistienė L; Delafontaine J; Guex N; Hashem M; Kurdi W; Jamuar SS; Ying LJ; Bonnard C; Pippucci T; Pradervand S; Roechert B; van Hasselt PM; Wiederkehr M; Wright CF; ; Xenarios I; van Haaften G; Shaw-Smith C; Schindewolf EM; Neerman-Arbez M; Sanlaville D; Lesca G; Guibaud L; Reversade B; Chelly J; Kučinskas V; Alkuraya FS; Reymond A

American journal of human genetics 2018;102;1;116-132

Whole-exome and targeted sequencing of 13 individuals from 10 unrelated families with overlapping clinical manifestations identified loss-of-function and missense variants in KIAA1109 allowing delineation of an autosomal-recessive multi-system syndrome, which we suggest to name Alkuraya-Kučinskas syndrome (MIM 617822). Shared phenotypic features representing the cardinal characteristics of this syndrome combine brain atrophy with clubfoot and arthrogryposis. Affected individuals present with cerebral parenchymal underdevelopment, ranging from major cerebral parenchymal thinning with lissencephalic aspect to moderate parenchymal rarefaction, severe to mild ventriculomegaly, cerebellar hypoplasia with brainstem dysgenesis, and cardiac and ophthalmologic anomalies, such as microphthalmia and cataract. Severe loss-of-function cases were incompatible with life, whereas those individuals with milder missense variants presented with severe global developmental delay, syndactyly of 2nd and 3rd toes, and severe muscle hypotonia resulting in incapacity to stand without support. Consistent with a causative role for KIAA1109 loss-of-function/hypomorphic variants in this syndrome, knockdowns of the zebrafish orthologous gene resulted in embryos with hydrocephaly and abnormally curved notochords and overall body shape, whereas published knockouts of the fruit fly and mouse orthologous genes resulted in lethality or severe neurological defects reminiscent of the probands' features.

Making new genetic diagnoses with old data: iterative reanalysis and reporting from genome-wide data in 1,133 families with developmental disorders.

Wright CF; McRae JF; Clayton S; Gallone G; Aitken S; FitzGerald TW; Jones P; Prigmore E; Rajan D; Lord J; Sifrim A; Kelsell R; Parker MJ; Barrett JC; Hurles ME; FitzPatrick DR; Firth HV;

Genetics in medicine : official journal of the American College of Medical Genetics 2018;20;10;1216-1223

Given the rapid pace of discovery in rare disease genomics, it is likely that improvements in diagnostic yield can be made by systematically reanalyzing previously generated genomic sequence data in light of new knowledge.

Missense Mutations of the Pro65 Residue of PCGF2 Cause a Recognizable Syndrome Associated with Craniofacial, Neurological, Cardiovascular, and Skeletal Features.

Turnpenny PD; Wright MJ; Sloman M; Caswell R; van Essen AJ; Gerkes E; Pfundt R; White SM; Shaul-Lotan N; Carpenter L; Schaefer GB; Fryer A; Innes AM; Forbes KP; Chung WK; McLaughlin H; Henderson LB; Roberts AE; Heath KE; Paumard-Hernández B; Gener B; ; Fawcett KA; Gjergja-Juraški R; Pilz DT; Fry AE

American journal of human genetics 2018;103;5;786-793

PCGF2 encodes the polycomb group ring finger 2 protein, a transcriptional repressor involved in cell proliferation, differentiation, and embryogenesis. PCGF2 is a component of the polycomb repressive complex 1 (PRC1), a multiprotein complex which controls gene silencing through histone modification and chromatin remodelling. We report the phenotypic characterization of 13 patients (11 unrelated individuals and a pair of monozygotic twins) with missense mutations in PCGF2. All the mutations affected the same highly conserved proline in PCGF2 and were de novo, excepting maternal mosaicism in one. The patients demonstrated a recognizable facial gestalt, intellectual disability, feeding problems, impaired growth, and a range of brain, cardiovascular, and skeletal abnormalities. Computer structural modeling suggests the substitutions alter an N-terminal loop of PCGF2 critical for histone biding. Mutant PCGF2 may have dominant-negative effects, sequestering PRC1 components into complexes that lack the ability to interact efficiently with histones. These findings demonstrate the important role of PCGF2 in human development and confirm that heterozygous substitutions of the Pro65 residue of PCGF2 cause a recognizable syndrome characterized by distinctive craniofacial, neurological, cardiovascular, and skeletal features.

Missense Variants in RHOBTB2 Cause a Developmental and Epileptic Encephalopathy in Humans, and Altered Levels Cause Neurological Defects in Drosophila.

Straub J; Konrad EDH; Grüner J; Toutain A; Bok LA; Cho MT; Crawford HP; Dubbs H; Douglas G; Jobling R; Johnson D; Krock B; Mikati MA; Nesbitt A; Nicolai J; Phillips M; Poduri A; Ortiz-Gonzalez XR; Powis Z; Santani A; Smith L; Stegmann APA; Stumpel C; Vreeburg M; ; Fliedner A; Gregor A; Sticht H; Zweier C

American journal of human genetics 2018;102;1;44-57

Although the role of typical Rho GTPases and other Rho-linked proteins in synaptic plasticity and cognitive function and dysfunction is widely acknowledged, the role of atypical Rho GTPases (such as RHOBTB2) in neurodevelopment has barely been characterized. We have now identified de novo missense variants clustering in the BTB-domain-encoding region of RHOBTB2 in ten individuals with a similar phenotype, including early-onset epilepsy, severe intellectual disability, postnatal microcephaly, and movement disorders. Three of the variants were recurrent. Upon transfection of HEK293 cells, we found that mutant RHOBTB2 was more abundant than the wild-type, most likely because of impaired degradation in the proteasome. Similarly, elevated amounts of the Drosophila ortholog RhoBTB in vivo were associated with seizure susceptibility and severe locomotor defects. Knockdown of RhoBTB in the Drosophila dendritic arborization neurons resulted in a decreased number of dendrites, thus suggesting a role of RhoBTB in dendritic development. We have established missense variants in the BTB-domain-encoding region of RHOBTB2 as causative for a developmental and epileptic encephalopathy and have elucidated the role of atypical Rho GTPase RhoBTB in Drosophila neurological function and possibly dendrite development.

Mutations in the BAF-Complex Subunit DPF2 Are Associated with Coffin-Siris Syndrome.

Vasileiou G; Vergarajauregui S; Endele S; Popp B; Büttner C; Ekici AB; Gerard M; Bramswig NC; Albrecht B; Clayton-Smith J; Morton J; Tomkins S; Low K; Weber A; Wenzel M; Altmüller J; Li Y; Wollnik B; Hoganson G; Plona MR; Cho MT; ; Thiel CT; Lüdecke HJ; Strom TM; Calpena E; Wilkie AOM; Wieczorek D; Engel FB; Reis A

American journal of human genetics 2018;102;3;468-479

Variants affecting the function of different subunits of the BAF chromatin-remodelling complex lead to various neurodevelopmental syndromes, including Coffin-Siris syndrome. Furthermore, variants in proteins containing PHD fingers, motifs recognizing specific histone tail modifications, have been associated with several neurological and developmental-delay disorders. Here, we report eight heterozygous de novo variants (one frameshift, two splice site, and five missense) in the gene encoding the BAF complex subunit double plant homeodomain finger 2 (DPF2). Affected individuals share common clinical features described in individuals with Coffin-Siris syndrome, including coarse facial features, global developmental delay, intellectual disability, speech impairment, and hypoplasia of fingernails and toenails. All variants occur within the highly conserved PHD1 and PHD2 motifs. Moreover, missense variants are situated close to zinc binding sites and are predicted to disrupt these sites. Pull-down assays of recombinant proteins and histone peptides revealed that a subset of the identified missense variants abolish or impaire DPF2 binding to unmodified and modified H3 histone tails. These results suggest an impairment of PHD finger structural integrity and cohesion and most likely an aberrant recognition of histone modifications. Furthermore, the overexpression of these variants in HEK293 and COS7 cell lines was associated with the formation of nuclear aggregates and the recruitment of both wild-type DPF2 and BRG1 to these aggregates. Expression analysis of truncating variants found in the affected individuals indicated that the aberrant transcripts escape nonsense-mediated decay. Altogether, we provide compelling evidence that de novo variants in DPF2 cause Coffin-Siris syndrome and propose a dominant-negative mechanism of pathogenicity.

NALCN Dysfunction as a Cause of Disordered Respiratory Rhythm With Central Apnea.

Campbell J; FitzPatrick DR; Azam T; Gibson NA; Somerville L; Joss SK; ; Urquhart DS

Pediatrics 2018;141;Suppl 5;S485-S490

The sodium leak channel nonselective protein (NALCN) is a regulator of the pacemaker neurons that are responsible for rhythmic behavior (including respiration), maintaining the resting membrane potential, and are required for action potential production. NALCN-null mice show early death associated with disrupted respiratory rhythms, characterized by frequent and profound apneas. We report 3 children (2 siblings) with compound heterozygous mutations in NALCN associated with developmental impairment, hypotonia, and central sleep-disordered breathing causing apneas. Supplemental oxygen normalized the respiratory rhythm. NALCN mutations have been previously reported to cause severe hypotonia, speech impairment, and cognitive delay as well as infantile neuroaxonal dystrophy and facial dysmorphism. Nonsynonymous changes in the 2 affected extracellular loops may be responsible for the deleterious effect on the stability of the respiratory rhythm. Although oxygen is known to be a stabilizer of respiratory rhythm in central apnea in children, its role in NALCN dysfunction requires further investigation.

Neurologic phenotypes associated with COL4A1/2 mutations: Expanding the spectrum of disease.

Zagaglia S; Selch C; Nisevic JR; Mei D; Michalak Z; Hernandez-Hernandez L; Krithika S; Vezyroglou K; Varadkar SM; Pepler A; Biskup S; Leão M; Gärtner J; Merkenschlager A; Jaksch M; Møller RS; Gardella E; Kristiansen BS; Hansen LK; Vari MS; Helbig KL; Desai S; Smith-Hicks CL; Hino-Fukuyo N; Talvik T; Laugesaar R; Ilves P; Õunap K; Körber I; Hartlieb T; Kudernatsch M; Winkler P; Schimmel M; Hasse A; Knuf M; Heinemeyer J; Makowski C; Ghedia S; Subramanian GM; Striano P; Thomas RH; Micallef C; Thom M; Werring DJ; Kluger GJ; Cross JH; Guerrini R; Balestrini S; Sisodiya SM

Neurology 2018;91;22;e2078-e2088

To characterize the neurologic phenotypes associated with COL4A1/2 mutations and to seek genotype-phenotype correlation.

Observation of Cleft Palate in an Individual with SOX11 Mutation: Indication of a Role for SOX11 in Human Palatogenesis.

Khan U; Study D; Baker E; Clayton-Smith J

The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association 2018;55;3;456-461

Point mutations and deletions within the SOX11 gene have recently been described in individuals with a rare variant of Coffin-Siris syndrome, OMIM 615866, an intellectual disability syndrome with associated features of nail hypoplasia, microcephaly, and characteristic facial features including a wide mouth and prominent lips.

Paediatric genomics: diagnosing rare disease in children.

Wright CF; FitzPatrick DR; Firth HV

Nature Reviews. Genetics 2018;19;5;253-268

The majority of rare diseases affect children, most of whom have an underlying genetic cause for their condition. However, making a molecular diagnosis with current technologies and knowledge is often still a challenge. Paediatric genomics is an immature but rapidly evolving field that tackles this issue by incorporating next-generation sequencing technologies, especially whole-exome sequencing and whole-genome sequencing, into research and clinical workflows. This complex multidisciplinary approach, coupled with the increasing availability of population genetic variation data, has already resulted in an increased discovery rate of causative genes and in improved diagnosis of rare paediatric disease. Importantly, for affected families, a better understanding of the genetic basis of rare disease translates to more accurate prognosis, management, surveillance and genetic advice; stimulates research into new therapies; and enables provision of better support.

Phenotype of CNTNAP1: a study of patients demonstrating a specific severe congenital hypomyelinating neuropathy with survival beyond infancy.

Low KJ; Stals K; Caswell R; Wakeling M; Clayton-Smith J; Donaldson A; Foulds N; Norman A; Splitt M; Urankar K; Vijayakumar K; Majumdar A; Study D; Ellard S; Smithson SF

European journal of human genetics : EJHG 2018;26;6;796-807

CHN is genetically heterogeneous and its genetic basis is difficult to determine on features alone. CNTNAP1 encodes CASPR, integral in the paranodal junction high molecular mass complex. Nineteen individuals with biallelic variants have been described in association with severe congenital hypomyelinating neuropathy, respiratory compromise, profound intellectual disability and death within the first year. We report 7 additional patients ascertained through exome sequencing. We identified 9 novel CNTNAP1 variants in 6 families: three missense variants, four nonsense variants, one frameshift variant and one splice site variant. Significant polyhydramnios occurred in 6/7 pregnancies. Severe respiratory compromise was seen in 6/7 (tracheostomy in 5). A complex neurological phenotype was seen in all patients who had marked brain hypomyelination/demyelination and profound developmental delay. Additional neurological findings included cranial nerve compromise: orobulbar dysfunction in 5/7, facial nerve weakness in 4/7 and vocal cord paresis in 5/7. Dystonia occurred in 2/7 patients and limb contractures in 5/7. All had severe gastroesophageal reflux, and a gastrostomy was required in 5/7. In contrast to most previous reports, only one patient died in the first year of life. Protein modelling was performed for all detected CNTNAP1 variants. We propose a genotype-phenotype correlation, whereby hypomorphic missense variants partially ameliorate the phenotype, prolonging survival. This study suggests that biallelic variants in CNTNAP1 cause a distinct recognisable syndrome, which is not caused by other genes associated with CHN. Neonates presenting with this phenotype will benefit from early genetic definition to inform clinical management and enable essential genetic counselling for their families.

Phenotypic spectrum associated with de novo mutations in QRICH1 gene.

Ververi A; Splitt M; Dean JCS; ; Brady AF

Clinical genetics 2018;93;2;286-292

Rare de novo mutations represent a significant cause of idiopathic developmental delay (DD). The use of next-generation sequencing (NGS) has boosted the identification of de novo mutations in an increasing number of novel genes. Here we present 3 unrelated children with de novo loss-of-function (LoF) mutations in QRICH1, diagnosed through trio-based exome sequencing. QRICH1 encodes the glutamine-rich protein 1, which contains 1 caspase activation recruitment domain and is likely to be involved in apoptosis and inflammation. All 3 children had speech delay, learning difficulties, a prominent nose and a thin upper lip. In addition, 2 of them had mildly raised creatine kinase (CK) and 1 of them had autism. Despite their small number, the patients had a relatively consistent pattern of clinical features suggesting the presence of a QRICH1-associated phenotype. LoF mutations in QRICH1 are suggested as a novel cause of DD.

PURA syndrome: clinical delineation and genotype-phenotype study in 32 individuals with review of published literature.

Reijnders MRF; Janowski R; Alvi M; Self JE; van Essen TJ; Vreeburg M; Rouhl RPW; Stevens SJC; Stegmann APA; Schieving J; Pfundt R; van Dijk K; Smeets E; Stumpel CTRM; Bok LA; Cobben JM; Engelen M; Mansour S; Whiteford M; Chandler KE; Douzgou S; Cooper NS; Tan EC; Foo R; Lai AHM; Rankin J; Green A; Lönnqvist T; Isohanni P; Williams S; Ruhoy I; Carvalho KS; Dowling JJ; Lev DL; Sterbova K; Lassuthova P; Neupauerová J; Waugh JL; Keros S; Clayton-Smith J; Smithson SF; Brunner HG; van Hoeckel C; Anderson M; Clowes VE; Siu VM; Ddd Study T; Selber P; Leventer RJ; Nellaker C; Niessing D; Hunt D; Baralle D

Journal of medical genetics 2018;55;2;104-113

De novo mutations in PURA have recently been described to cause PURA syndrome, a neurodevelopmental disorder characterised by severe intellectual disability (ID), epilepsy, feeding difficulties and neonatal hypotonia.

Quantifying the contribution of recessive coding variation to developmental disorders.

Martin HC; Jones WD; McIntyre R; Sanchez-Andrade G; Sanderson M; Stephenson JD; Jones CP; Handsaker J; Gallone G; Bruntraeger M; McRae JF; Prigmore E; Short P; Niemi M; Kaplanis J; Radford EJ; Akawi N; Balasubramanian M; Dean J; Horton R; Hulbert A; Johnson DS; Johnson K; Kumar D; Lynch SA; Mehta SG; Morton J; Parker MJ; Splitt M; Turnpenny PD; Vasudevan PC; Wright M; Bassett A; Gerety SS; Wright CF; FitzPatrick DR; Firth HV; Hurles ME; Barrett JC;

Science 2018;362;6419;1161-1164

We estimated the genome-wide contribution of recessive coding variation in 6040 families from the Deciphering Developmental Disorders study. The proportion of cases attributable to recessive coding variants was 3.6% in patients of European ancestry, compared with 50% explained by de novo coding mutations. It was higher (31%) in patients with Pakistani ancestry, owing to elevated autozygosity. Half of this recessive burden is attributable to known genes. We identified two genes not previously associated with recessive developmental disorders, KDM5B and EIF3F, and functionally validated them with mouse and cellular models. Our results suggest that recessive coding variants account for a small fraction of currently undiagnosed nonconsanguineous individuals, and that the role of noncoding variants, incomplete penetrance, and polygenic mechanisms need further exploration.

Refining the phenotype associated with GNB1 mutations: Clinical data on 18 newly identified patients and review of the literature.

Hemati P; Revah-Politi A; Bassan H; Petrovski S; Bilancia CG; Ramsey K; Griffin NG; Bier L; Cho MT; Rosello M; Lynch SA; Colombo S; Weber A; Haug M; Heinzen EL; Sands TT; Narayanan V; Primiano M; Aggarwal VS; Millan F; Sattler-Holtrop SG; Caro-Llopis A; Pillar N; Baker J; Freedman R; Kroes HY; Sacharow S; Stong N; Lapunzina P; Schneider MC; Mendelsohn NJ; Singleton A; Loik Ramey V; Wou K; Kuzminsky A; Monfort S; Weiss M; Doyle S; Iglesias A; Martinez F; Mckenzie F; Orellana C; van Gassen KLI; Palomares M; Bazak L; Lee A; Bircher A; Basel-Vanagaite L; Hafström M; Houge G; ; ; Goldstein DB; Anyane-Yeboa K

American journal of medical genetics. Part A 2018;176;11;2259-2275

De novo germline mutations in GNB1 have been associated with a neurodevelopmental phenotype. To date, 28 patients with variants classified as pathogenic have been reported. We add 18 patients with de novo mutations to this cohort, including a patient with mosaicism for a GNB1 mutation who presented with a milder phenotype. Consistent with previous reports, developmental delay in these patients was moderate to severe, and more than half of the patients were non-ambulatory and nonverbal. The most observed substitution affects the p.Ile80 residue encoded in exon 6, with 28% of patients carrying a variant at this residue. Dystonia and growth delay were observed more frequently in patients carrying variants in this residue, suggesting a potential genotype-phenotype correlation. In the new cohort of 18 patients, 50% of males had genitourinary anomalies and 61% of patients had gastrointestinal anomalies, suggesting a possible association of these findings with variants in GNB1. In addition, cutaneous mastocytosis, reported once before in a patient with a GNB1 variant, was observed in three additional patients, providing further evidence for an association to GNB1. We will review clinical and molecular data of these new cases and all previously reported cases to further define the phenotype and establish possible genotype-phenotype correlations.

SET de novo frameshift variants associated with developmental delay and intellectual disabilities.

Richardson R; Splitt M; Newbury-Ecob R; Hulbert A; Kennedy J; Weber A;

European journal of human genetics : EJHG 2018;26;9;1306-1311

Trio based whole exome sequencing via the Deciphering Developmental Disorders (DDD) study has identified three individuals with de novo frameshift variants in the Suppressor of Variegation, Enhancer of Zeste, and Trithorax (SET) gene. Variants in the SET gene have not previously been recognised to be associated with human developmental disorders. Here we report detailed phenotypic information and propose that SET is a new Intellectual Disability/Developmental Delay (ID/DD) gene.

SHANK3 variant as a cause of nonsyndromal autism in an 11-year-old boy and a review of published literature.

Kanani F; Study D; Balasubramanian M

Clinical dysmorphology 2018;27;4;113-115

Autism spectrum disorder (ASD) encompasses a spectrum of pervasive neuropsychiatric disorders characterized by deficits in social interaction, communication, unusual and repetitive behaviours. The aetiology of ASD is believed to involve complex interactions between genetic and environmental factors; it can be further classified as syndromic or nonsyndromic, according to whether it is the primary diagnosis or secondary to an existing condition where both common and rare genetic variants contribute to the development of ASD or are clearly causal. The prevalence of ASD in children is increasing with higher rates of diagnosis and an estimated one in 100 affected in the UK. Given that heritability is a major contributing factor, we aim to discuss research findings to-date in the context of a high-risk autism candidate gene, SHANK3 (SH3 and multiple ankyrin repeat domain 3), with its loss resulting in synaptic function disruption. We present a 10-year-old patient with a pathogenic de novo heterozygous c.1231delC, p.Arg411Val frameshift variant in SHANK3. He presented with severe autism, attention deficit hyperactivity disorder and pathological demand avoidance, on a background of developmental impairment and language regression. The number of genes associated with autism is ever increasing. It is a heterogeneous group of disorders with no single gene conferring pathogenesis in the majority of cases. Genetic abnormalities can be detected in ~15% of ASD and these range from copy number variants in 16p11.2 and 15q13.2q13.3 to several well-known genetic disorders including tuberous sclerosis and fragile X syndrome. Further, high confidence autism genes include but are not limited to NRXN, NLGN3, NLGN4, SHANK2 and SHANK3.

The Tatton-Brown-Rahman Syndrome: A clinical study of 55 individuals with de novo constitutive DNMT3A variants.

Tatton-Brown K; Zachariou A; Loveday C; Renwick A; Mahamdallie S; Aksglaede L; Baralle D; Barge-Schaapveld D; Blyth M; Bouma M; Breckpot J; Crabb B; Dabir T; Cormier-Daire V; Fauth C; Fisher R; Gener B; Goudie D; Homfray T; Hunter M; Jorgensen A; Kant SG; Kirally-Borri C; Koolen D; Kumar A; Labilloy A; Lees M; Marcelis C; Mercer C; Mignot C; Miller K; Neas K; Newbury-Ecob R; Pilz DT; Posmyk R; Prada C; Ramsey K; Randolph LM; Selicorni A; Shears D; Suri M; Temple IK; Turnpenny P; Val Maldergem L; Varghese V; Veenstra-Knol HE; Yachelevich N; Yates L; ; ; Rahman N

Wellcome open research 2018;3;46

Tatton-Brown-Rahman syndrome (TBRS; OMIM 615879), also known as the DNMT3A-overgrowth syndrome, is an overgrowth intellectual disability syndrome first described in 2014 with a report of 13 individuals with constitutive heterozygous DNMT3A variants. Here we have undertaken a detailed clinical study of 55 individuals with de novoDNMT3A variants, including the 13 previously reported individuals. An intellectual disability and overgrowth were reported in >80% of individuals with TBRS and were designated major clinical associations. Additional frequent clinical associations (reported in 20-80% individuals) included an evolving facial appearance with low-set, heavy, horizontal eyebrows and prominent upper central incisors; joint hypermobility (74%); obesity (weight ³2SD, 67%); hypotonia (54%); behavioural/psychiatric issues (most frequently autistic spectrum disorder, 51%); kyphoscoliosis (33%) and afebrile seizures (22%). One individual was diagnosed with acute myeloid leukaemia in teenage years. Based upon the results from this study, we present our current management for individuals with TBRS.

The TBR1-related autistic-spectrum-disorder phenotype and its clinical spectrum.

McDermott JH; Study DDD; Clayton-Smith J; Briggs TA

European journal of medical genetics 2018;61;5;253-256

A diverse range of genetic aberrations can lead to Autistic Spectrum Disorder (ASD) and many of these have been identified via Next Generation Sequencing (NGS) as part of large scale consortium studies. ASD is a phenotypically variable disorder and detailed clinical descriptions are essential to appreciate genotype-phenotype relationships. In this report, we provide a comprehensive clinical description of a child with ASD in whom a TBR1 variant was identified. We review this case in the context of the current TBR1 literature and highlight the variable spectrum of disease associated with this gene. The phenotypic information outlined within the literature is incomplete, exemplifying the limitations of massively-parallel sequencing studies with regards to clinical annotation. We suggest that future reporting of ASD variants should include standardised phenotypic descriptions. This would develop a more thorough understanding of genotype-phenotype relationship, so allowing us to better counsel and support our patients.

A 7q21.11 microdeletion presenting with apparent intellectual disability without epilepsy.

Siddique A; Willoughby J; ; McNeill A

American journal of medical genetics. Part A 2017;173;4;1128-1130

A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations.

Palmer EE; Kumar R; Gordon CT; Shaw M; Hubert L; Carroll R; Rio M; Murray L; Leffler M; Dudding-Byth T; Oufadem M; Lalani SR; Lewis AM; Xia F; Tam A; Webster R; Brammah S; Filippini F; Pollard J; Spies J; Minoche AE; Cowley MJ; Risen S; Powell-Hamilton NN; Tusi JE; Immken L; Nagakura H; Bole-Feysot C; Nitschké P; Garrigue A; de Saint Basile G; Kivuva E; ; Scott RH; Rendon A; Munnich A; Newman W; Kerr B; Besmond C; Rosenfeld JA; Amiel J; Field M; Gecz J

American journal of human genetics 2017;101;6;995-1005

A recurrent de novo missense variant within the C-terminal Sin3-like domain of ZSWIM6 was previously reported to cause acromelic frontonasal dysostosis (AFND), an autosomal-dominant severe frontonasal and limb malformation syndrome, associated with neurocognitive and motor delay, via a proposed gain-of-function effect. We present detailed phenotypic information on seven unrelated individuals with a recurrent de novo nonsense variant (c.2737C>T [p.Arg913Ter]) in the penultimate exon of ZSWIM6 who have severe-profound intellectual disability and additional central and peripheral nervous system symptoms but an absence of frontonasal or limb malformations. We show that the c.2737C>T variant does not trigger nonsense-mediated decay of the ZSWIM6 mRNA in affected individual-derived cells. This finding supports the existence of a truncated ZSWIM6 protein lacking the Sin3-like domain, which could have a dominant-negative effect. This study builds support for a key role for ZSWIM6 in neuronal development and function, in addition to its putative roles in limb and craniofacial development, and provides a striking example of different variants in the same gene leading to distinct phenotypes.

ACTB Loss-of-Function Mutations Result in a Pleiotropic Developmental Disorder.

Cuvertino S; Stuart HM; Chandler KE; Roberts NA; Armstrong R; Bernardini L; Bhaskar S; Callewaert B; Clayton-Smith J; Davalillo CH; Deshpande C; Devriendt K; Digilio MC; Dixit A; Edwards M; Friedman JM; Gonzalez-Meneses A; Joss S; Kerr B; Lampe AK; Langlois S; Lennon R; Loget P; Ma DYT; McGowan R; Des Medt M; O'Sullivan J; Odent S; Parker MJ; Pebrel-Richard C; Petit F; Stark Z; Stockler-Ipsiroglu S; Tinschert S; Vasudevan P; Villa O; White SM; Zahir FR; ; Woolf AS; Banka S

American journal of human genetics 2017;101;6;1021-1033

ACTB encodes β-actin, an abundant cytoskeletal housekeeping protein. In humans, postulated gain-of-function missense mutations cause Baraitser-Winter syndrome (BRWS), characterized by intellectual disability, cortical malformations, coloboma, sensorineural deafness, and typical facial features. To date, the consequences of loss-of-function ACTB mutations have not been proven conclusively. We describe heterozygous ACTB deletions and nonsense and frameshift mutations in 33 individuals with developmental delay, apparent intellectual disability, increased frequency of internal organ malformations (including those of the heart and the renal tract), growth retardation, and a recognizable facial gestalt (interrupted wavy eyebrows, dense eyelashes, wide nose, wide mouth, and a prominent chin) that is distinct from characteristics of individuals with BRWS. Strikingly, this spectrum overlaps with that of several chromatin-remodeling developmental disorders. In wild-type mouse embryos, β-actin expression was prominent in the kidney, heart, and brain. ACTB mRNA expression levels in lymphoblastic lines and fibroblasts derived from affected individuals were decreased in comparison to those in control cells. Fibroblasts derived from an affected individual and ACTB siRNA knockdown in wild-type fibroblasts showed altered cell shape and migration, consistent with known roles of cytoplasmic β-actin. We also demonstrate that ACTB haploinsufficiency leads to reduced cell proliferation, altered expression of cell-cycle genes, and decreased amounts of nuclear, but not cytoplasmic, β-actin. In conclusion, we show that heterozygous loss-of-function ACTB mutations cause a distinct pleiotropic malformation syndrome with intellectual disability. Our biological studies suggest that a critically reduced amount of this protein alters cell shape, migration, proliferation, and gene expression to the detriment of brain, heart, and kidney development.

Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders.

Pagnamenta AT; Murakami Y; Taylor JM; Anzilotti C; Howard MF; Miller V; Johnson DS; Tadros S; Mansour S; Temple IK; Firth R; Rosser E; Harrison RE; Kerr B; Popitsch N; ; Kinoshita T; Taylor JC; Kini U

European journal of human genetics : EJHG 2017;25;6;669-679

Over 150 different proteins attach to the plasma membrane using glycosylphosphatidylinositol (GPI) anchors. Mutations in 18 genes that encode components of GPI-anchor biogenesis result in a phenotypic spectrum that includes learning disability, epilepsy, microcephaly, congenital malformations and mild dysmorphic features. To determine the incidence of GPI-anchor defects, we analysed the exome data from 4293 parent-child trios recruited to the Deciphering Developmental Disorders (DDD) study. All probands recruited had a neurodevelopmental disorder. We searched for variants in 31 genes linked to GPI-anchor biogenesis and detected rare biallelic variants in PGAP3, PIGN, PIGT (n=2), PIGO and PIGL, providing a likely diagnosis for six families. In five families, the variants were in a compound heterozygous configuration while in a consanguineous Afghani kindred, a homozygous c.709G>C; p.(E237Q) variant in PIGT was identified within 10-12 Mb of autozygosity. Validation and segregation analysis was performed using Sanger sequencing. Across the six families, five siblings were available for testing and in all cases variants co-segregated consistent with them being causative. In four families, abnormal alkaline phosphatase results were observed in the direction expected. FACS analysis of knockout HEK293 cells that had been transfected with wild-type or mutant cDNA constructs demonstrated that the variants in PIGN, PIGT and PIGO all led to reduced activity. Splicing assays, performed using leucocyte RNA, showed that a c.336-2A>G variant in PIGL resulted in exon skipping and p.D113fs*2. Our results strengthen recently reported disease associations, suggest that defective GPI-anchor biogenesis may explain ~0.15% of individuals with developmental disorders and highlight the benefits of data sharing.

Chitayat syndrome: hyperphalangism, characteristic facies, hallux valgus and bronchomalacia results from a recurrent c.266A>G p.(Tyr89Cys) variant in the ERF gene.

Balasubramanian M; Lord H; Levesque S; Guturu H; Thuriot F; Sillon G; Wenger AM; Sureka DL; Lester T; Johnson DS; Bowen J; Calhoun AR; Viskochil DH; ; Bejerano G; Bernstein JA; Chitayat D

Journal of medical genetics 2017;54;3;157-165

In 1993, Chitayat et al., reported a newborn with hyperphalangism, facial anomalies, and bronchomalacia. We identified three additional families with similar findings. Features include bilateral accessory phalanx resulting in shortened index fingers; hallux valgus; distinctive face; respiratory compromise.

Clinical and molecular consequences of disease-associated de novo mutations in SATB2.

Bengani H; Handley M; Alvi M; Ibitoye R; Lees M; Lynch SA; Lam W; Fannemel M; Nordgren A; Malmgren H; Kvarnung M; Mehta S; McKee S; Whiteford M; Stewart F; Connell F; Clayton-Smith J; Mansour S; Mohammed S; Fryer A; Morton J; ; Grozeva D; Asam T; Moore D; Sifrim A; McRae J; Hurles ME; Firth HV; Raymond FL; Kini U; Nellåker C; Ddd Study ; FitzPatrick DR

Genetics in medicine : official journal of the American College of Medical Genetics 2017;19;8;900-908

To characterize features associated with de novo mutations affecting SATB2 function in individuals ascertained on the basis of intellectual disability.

Clinical features associated with CTNNB1 de novo loss of function mutations in ten individuals.

Kharbanda M; Pilz DT; Tomkins S; Chandler K; Saggar A; Fryer A; McKay V; Louro P; Smith JC; Burn J; Kini U; De Burca A; FitzPatrick DR; Kinning E;

European journal of medical genetics 2017;60;2;130-135

Loss of function mutations in CTNNB1 have been reported in individuals with intellectual disability [MIM #615075] associated with peripheral spasticity, microcephaly and central hypotonia, suggesting a recognisable phenotype associated with haploinsufficiency for this gene. Trio based whole exome sequencing via the Deciphering Developmental Disorders (DDD) study has identified eleven further individuals with de novo loss of function mutations in CTNNB1. Here we report detailed phenotypic information on ten of these. We confirm the features that have been previously described and further delineate the skin and hair findings, including fair skin and fair and sparse hair with unusual patterning.

Compound heterozygous variants in NBAS as a cause of atypical osteogenesis imperfecta.

Balasubramanian M; Hurst J; Brown S; Bishop NJ; Arundel P; DeVile C; Pollitt RC; Crooks L; Longman D; Caceres JF; Shackley F; Connolly S; Payne JH; Offiah AC; Hughes D; ; Parker MJ; Hide W; Skerry TM

Bone 2017;94;65-74

Osteogenesis imperfecta (OI), the commonest inherited bone fragility disorder, affects 1 in 15,000 live births resulting in frequent fractures and reduced mobility, with significant impact on quality of life. Early diagnosis is important, as therapeutic advances can lead to improved clinical outcome and patient benefit.