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1.
Am J Hum Genet ; 111(3): 509-528, 2024 Mar 07.
Article in English | MEDLINE | ID: mdl-38412861

ABSTRACT

Neurodevelopmental disorders (NDDs) result from impaired development and functioning of the brain. Here, we identify loss-of-function (LoF) variation in ZFHX3 as a cause for syndromic intellectual disability (ID). ZFHX3 is a zinc-finger homeodomain transcription factor involved in various biological processes, including cell differentiation and tumorigenesis. We describe 42 individuals with protein-truncating variants (PTVs) or (partial) deletions of ZFHX3, exhibiting variable intellectual disability and autism spectrum disorder, recurrent facial features, relative short stature, brachydactyly, and, rarely, cleft palate. ZFHX3 LoF associates with a specific methylation profile in whole blood extracted DNA. Nuclear abundance of ZFHX3 increases during human brain development and neuronal differentiation. ZFHX3 was found to interact with the chromatin remodeling BRG1/Brm-associated factor complex and the cleavage and polyadenylation complex, suggesting a function in chromatin remodeling and mRNA processing. Furthermore, ChIP-seq for ZFHX3 revealed that it predominantly binds promoters of genes involved in nervous system development. We conclude that loss-of-function variants in ZFHX3 are a cause of syndromic ID associating with a specific DNA methylation profile.


Subject(s)
Autism Spectrum Disorder , Intellectual Disability , Neurodevelopmental Disorders , Humans , Intellectual Disability/genetics , Intellectual Disability/complications , Haploinsufficiency/genetics , Neurodevelopmental Disorders/genetics , Brain/metabolism , Homeodomain Proteins/genetics , Homeodomain Proteins/metabolism
2.
Am J Hum Genet ; 109(12): 2230-2252, 2022 12 01.
Article in English | MEDLINE | ID: mdl-36351433

ABSTRACT

EMILIN1 (elastin-microfibril-interface-located-protein-1) is a structural component of the elastic fiber network and localizes to the interface between the fibrillin microfibril scaffold and the elastin core. How EMILIN1 contributes to connective tissue integrity is not fully understood. Here, we report bi-allelic EMILIN1 loss-of-function variants causative for an entity combining cutis laxa, arterial tortuosity, aneurysm formation, and bone fragility, resembling autosomal-recessive cutis laxa type 1B, due to EFEMP2 (FBLN4) deficiency. In both humans and mice, absence of EMILIN1 impairs EFEMP2 extracellular matrix deposition and LOX activity resulting in impaired elastogenesis, reduced collagen crosslinking, and aberrant growth factor signaling. Collagen fiber ultrastructure and histopathology in EMILIN1- or EFEMP2-deficient skin and aorta corroborate these findings and murine Emilin1-/- femora show abnormal trabecular bone formation and strength. Altogether, EMILIN1 connects elastic fiber network with collagen fibril formation, relevant for both bone and vascular tissue homeostasis.


Subject(s)
Bone Diseases, Metabolic , Cutis Laxa , Animals , Humans , Mice , Collagen/genetics , Cutis Laxa/genetics , Elastin/metabolism , Extracellular Matrix Proteins/metabolism
3.
J Med Genet ; 61(2): 132-141, 2024 Jan 19.
Article in English | MEDLINE | ID: mdl-37580113

ABSTRACT

BACKGROUND: 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. METHODS: As a result of an international collaboration using GeneMatcher Phenome Central Repository and personal communications, here we describe the clinical and molecular genetic characteristics of 22 previously unreported individuals. RESULTS: The core clinical phenotype is characterised by developmental delay particularly in the domain of speech development, postnatal growth retardation, microcephaly and facial dysmorphism. Corpus callosum abnormalities appear less frequently than suggested by previous observations. The identified mutations concerned nonsense or frameshift variants that were mainly located in the last exon of the ZNF148 gene. Heterozygous deletion including the entire ZNF148 gene was found in only one case. Most mutations occurred de novo, but were inherited from an affected parent in two families. CONCLUSION: The GDACCF syndrome is clinically diverse, and a genotype-first approach, that is, exome sequencing is recommended for establishing a genetic diagnosis rather than a phenotype-first approach. However, the syndrome may be suspected based on some recurrent, recognisable features. Corpus callosum anomalies were not as constant as previously suggested, we therefore recommend to replace the term 'GDACCF syndrome' with 'ZNF148-related neurodevelopmental disorder'.


Subject(s)
Intellectual Disability , Leukoencephalopathies , Humans , Child , Corpus Callosum , Facies , Mutation/genetics , Phenotype , Genotype , Intellectual Disability/genetics , Intellectual Disability/diagnosis , Syndrome , Developmental Disabilities/pathology , DNA-Binding Proteins/genetics , Transcription Factors/genetics
4.
Am J Hum Genet ; 108(6): 1095-1114, 2021 06 03.
Article in English | MEDLINE | ID: mdl-33991472

ABSTRACT

Latent transforming growth factor ß (TGFß)-binding proteins (LTBPs) are microfibril-associated proteins essential for anchoring TGFß in the extracellular matrix (ECM) as well as for correct assembly of ECM components. Variants in LTBP2, LTBP3, and LTBP4 have been identified in several autosomal recessive Mendelian disorders with skeletal abnormalities with or without impaired development of elastin-rich tissues. Thus far, the human phenotype associated with LTBP1 deficiency has remained enigmatic. In this study, we report homozygous premature truncating LTBP1 variants in eight affected individuals from four unrelated consanguineous families. Affected individuals present with connective tissue features (cutis laxa and inguinal hernia), craniofacial dysmorphology, variable heart defects, and prominent skeletal features (craniosynostosis, short stature, brachydactyly, and syndactyly). In vitro studies on proband-derived dermal fibroblasts indicate distinct molecular mechanisms depending on the position of the variant in LTBP1. C-terminal variants lead to an altered LTBP1 loosely anchored in the microfibrillar network and cause increased ECM deposition in cultured fibroblasts associated with excessive TGFß growth factor activation and signaling. In contrast, N-terminal truncation results in a loss of LTBP1 that does not alter TGFß levels or ECM assembly. In vivo validation with two independent zebrafish lines carrying mutations in ltbp1 induce abnormal collagen fibrillogenesis in skin and intervertebral ligaments and ectopic bone formation on the vertebrae. In addition, one of the mutant zebrafish lines shows voluminous and hypo-mineralized vertebrae. Overall, our findings in humans and zebrafish show that LTBP1 function is crucial for skin and bone ECM assembly and homeostasis.


Subject(s)
Collagen/metabolism , Cutis Laxa/etiology , Genetic Variation , Latent TGF-beta Binding Proteins/genetics , Adolescent , Alleles , Animals , Cells, Cultured , Child , Child, Preschool , Cutis Laxa/pathology , Extracellular Matrix/metabolism , Female , Fibroblasts/metabolism , Fibroblasts/pathology , Humans , Infant , Male , Pedigree , Skin/metabolism , Skin/pathology , Zebrafish
5.
Genet Med ; 26(5): 101087, 2024 05.
Article in English | MEDLINE | ID: mdl-38288683

ABSTRACT

PURPOSE: Interneuronopathies are a group of neurodevelopmental disorders characterized by deficient migration and differentiation of gamma-aminobutyric acidergic interneurons resulting in a broad clinical spectrum, including autism spectrum disorders, early-onset epileptic encephalopathy, intellectual disability, and schizophrenic disorders. SP9 is a transcription factor belonging to the Krüppel-like factor and specificity protein family, the members of which harbor highly conserved DNA-binding domains. SP9 plays a central role in interneuron development and tangential migration, but it has not yet been implicated in a human neurodevelopmental disorder. METHODS: Cases with SP9 variants were collected through international data-sharing networks. To address the specific impact of SP9 variants, in silico and in vitro assays were carried out. RESULTS: De novo heterozygous variants in SP9 cause a novel form of interneuronopathy. SP9 missense variants affecting the glutamate 378 amino acid result in severe epileptic encephalopathy because of hypomorphic and neomorphic DNA-binding effects, whereas SP9 loss-of-function variants result in a milder phenotype with epilepsy, developmental delay, and autism spectrum disorder. CONCLUSION: De novo heterozygous SP9 variants are responsible for a neurodevelopmental disease. Interestingly, variants located in conserved DNA-binding domains of KLF/SP family transcription factors may lead to neomorphic DNA-binding functions resulting in a combination of loss- and gain-of-function effects.


Subject(s)
Autism Spectrum Disorder , Epilepsy , Intellectual Disability , Interneurons , Sp Transcription Factors , Transcription Factors , Adolescent , Child , Child, Preschool , Female , Humans , Male , Autism Spectrum Disorder/genetics , Autism Spectrum Disorder/pathology , Epilepsy/genetics , Epilepsy/pathology , Heterozygote , Intellectual Disability/genetics , Intellectual Disability/pathology , Interneurons/metabolism , Interneurons/pathology , Mutation, Missense/genetics , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/pathology , Phenotype , Transcription Factors/genetics , Transcription Factors/metabolism , Sp Transcription Factors/genetics
6.
Article in English | MEDLINE | ID: mdl-38852879

ABSTRACT

OBJECTIVE: Understanding the mechanisms of hip disease, such as osteoarthritis (OA), is crucial to advance their treatment. Such hip diseases often involve specific morphological changes. Genetic variations, called single nucleotide polymorphisms (SNPs), influence various hip morphological parameters. This study investigated the biological relevance of SNPs correlated to hip morphology in genome-wide association studies (GWAS). The SNP-associated genes were compared to genes associated with OA in other joints, aiming to see if the same genes play a role in both hip development and the risk of OA in other lower limb joints. METHODOLOGY: A systematic literature review was conducted to identify SNPs correlated with hip morphology, based on the Population, Intervention, Comparison, Outcome, and Study (PICOS) framework. Afterwards, Gene Ontology (GO) analysis was performed, using EnrichR, on the SNP-associated genes and compared with non-hip OA-associated genes, across different databases. RESULTS: Reviewing 49 GWAS identified 436 SNPs associated with hip joint morphology, encompassing variance in bone size, structure and shape. Among the SNP-associated genes, SOX9 plays a pivotal role in size, GDF5 impacts bone structure, and BMP7 affects shape. Overall, skeletal system development, regulation of cell differentiation, and chondrocyte differentiation emerged as crucial processes influencing hip morphology. Eighteen percent of GWAS-identified genes related to hip morphology were also associated with non-hip OA. CONCLUSION: Our findings indicate the existence of multiple shared genetic mechanisms across hip morphology and OA, highlighting the necessity for more extensive research in this area, as in contrast to the hip, the genetic background on knee or foot morphology remains largely understudied.

7.
Am J Med Genet A ; 194(4): e63486, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38041217

ABSTRACT

Aicardi-Goutières syndrome (AGS) is an autosomal recessive inflammatory syndrome that manifests as an early-onset encephalopathy with both neurologic and extraneurologic clinical findings. AGS has been associated with pathogenic variants in nine genes: TREX1, RNASEH2B, RNASEH2C, RNASEH2A, SAMHD1, ADAR, IFIH1, LSM11, and RNU7-1. Diagnosis is established by clinical findings (encephalopathy and acquired microcephaly, intellectual and physical impairments, dystonia, hepatosplenomegaly, sterile pyrexia, and/or chilblains), characteristic abnormalities on cranial CT (calcification of the basal ganglia and white matter) and MRI (leukodystrophic changes), or the identification of pathogenic/likely pathogenic variants in the known genes. One of the genes associated with AGS, SAMHD1, has also been associated with a spectrum of cerebrovascular diseases, including moyamoya disease (MMD). In this report, we describe a 31-year-old male referred to genetics for MMD since childhood who lacked the hallmark features of AGS patients but was found to have compound heterozygous SAMHD1 variants. He later developed mitral valve insufficiency due to recurrent chordal rupture and ultimately underwent a heart transplant at 37 years of age. Thus, these data suggest that SAMHD1 pathogenic variants can cause MMD without typical AGS symptoms and support that SAMHD1 should be assessed in MMD patients even in the absence of AGS features.


Subject(s)
Autoimmune Diseases of the Nervous System , Brain Diseases , Moyamoya Disease , Nervous System Malformations , Male , Humans , Child , Adult , SAM Domain and HD Domain-Containing Protein 1/genetics , Moyamoya Disease/complications , Mitral Valve/pathology , Mutation , Nervous System Malformations/diagnostic imaging , Nervous System Malformations/genetics , Autoimmune Diseases of the Nervous System/diagnosis , Autoimmune Diseases of the Nervous System/genetics , Autoimmune Diseases of the Nervous System/pathology , Brain Diseases/complications
8.
PLoS Genet ; 17(6): e1009603, 2021 06.
Article in English | MEDLINE | ID: mdl-34143769

ABSTRACT

The inability to maintain a strictly regulated endo(lyso)somal acidic pH through the proton-pumping action of the vacuolar-ATPases (v-ATPases) has been associated with various human diseases including heritable connective tissue disorders. Autosomal recessive (AR) cutis laxa (CL) type 2C syndrome is associated with genetic defects in the ATP6V1E1 gene and is characterized by skin wrinkles or loose redundant skin folds with pleiotropic systemic manifestations. The underlying pathological mechanisms leading to the clinical presentations remain largely unknown. Here, we show that loss of atp6v1e1b in zebrafish leads to early mortality, associated with craniofacial dysmorphisms, vascular anomalies, cardiac dysfunction, N-glycosylation defects, hypotonia, and epidermal structural defects. These features are reminiscent of the phenotypic manifestations in ARCL type 2C patients. Our data demonstrates that loss of atp6v1e1b alters endo(lyso)somal protein levels, and interferes with non-canonical v-ATPase pathways in vivo. In order to gain further insights into the processes affected by loss of atp6v1e1b, we performed an untargeted analysis of the transcriptome, metabolome, and lipidome in early atp6v1e1b-deficient larvae. We report multiple affected pathways including but not limited to oxidative phosphorylation, sphingolipid, fatty acid, and energy metabolism together with profound defects on mitochondrial respiration. Taken together, our results identify complex pathobiological effects due to loss of atp6v1e1b in vivo.


Subject(s)
Abnormalities, Multiple/genetics , Cutis Laxa/genetics , Epithelial Cells/metabolism , Skin/metabolism , Vacuolar Proton-Translocating ATPases/genetics , Zebrafish Proteins/genetics , Abnormalities, Multiple/metabolism , Abnormalities, Multiple/pathology , Animals , Cutis Laxa/metabolism , Cutis Laxa/pathology , Disease Models, Animal , Endosomes/metabolism , Endosomes/pathology , Epithelial Cells/pathology , Gene Expression Regulation , Humans , Larva/genetics , Larva/growth & development , Larva/metabolism , Lipidomics , Longevity/genetics , Lysosomes/metabolism , Lysosomes/pathology , Metabolome/genetics , Mitochondria/metabolism , Mitochondria/pathology , Oxidative Phosphorylation , Protein Isoforms/deficiency , Protein Isoforms/genetics , Skin/pathology , Syndrome , Transcriptome , Vacuolar Proton-Translocating ATPases/deficiency , Zebrafish/embryology , Zebrafish/genetics , Zebrafish/metabolism , Zebrafish Proteins/deficiency
9.
Clin Genet ; 103(6): 709-713, 2023 06.
Article in English | MEDLINE | ID: mdl-36896710

ABSTRACT

Epidermal nevus syndrome (ENS) comprises a heterogeneous group of neurocutaneous syndromes associated with the presence of epidermal nevi and variable extracutaneous manifestations. Postzygotic activating HRAS pathogenic variants were previously identified in nevus sebaceous (NS), keratinocytic epidermal nevus (KEN), and different ENS, including Schimmelpenning-Feuerstein-Mims and cutaneous-skeletal-hypophosphatasia syndrome (CSHS). Skeletal involvement in HRAS-related ENS ranges from localized bone dysplasia in association with KEN to fractures and limb deformities in CSHS. We describe the first association of HRAS-related ENS and auricular atresia, thereby expanding the disease spectrum with first branchial arch defects if affected by the mosaic variant. In addition, this report illustrates the first concurrent presence of verrucous EN, NS, and nevus comedonicus (NC), indicating the possibility of mosaic HRAS variation as an underlying cause of NC. Overall, this report extends the pleiotropy of conditions associated with mosaic pathogenic variants in HRAS affecting ectodermal and mesodermal progenitor cells.


Subject(s)
Nevus , Skin Neoplasms , Humans , Syndrome , Branchial Region/pathology , Nevus/pathology , Proto-Oncogene Proteins p21(ras)
10.
Am J Med Genet A ; 191(7): 1900-1910, 2023 07.
Article in English | MEDLINE | ID: mdl-37183572

ABSTRACT

Jansen-de Vries syndrome (JdVS) is a neurodevelopmental condition attributed to pathogenic variants in Exons 5 and 6 of PPM1D. As the full phenotypic spectrum and natural history remain to be defined, we describe a large cohort of children and adults with JdVS. This is a retrospective cohort study of 37 individuals from 34 families with disease-causing variants in PPM1D leading to JdVS. Clinical data were provided by treating physicians and/or families. Of the 37 individuals, 27 were male and 10 female, with median age 8.75 years (range 8 months to 62 years). Four families document autosomal dominant transmission, and 32/34 probands were diagnosed via exome sequencing. The facial gestalt, including a broad forehead and broad mouth with a thin and tented upper lip, was most recognizable between 18 and 48 months of age. Common manifestations included global developmental delay (35/36, 97%), hypotonia (25/34, 74%), short stature (14/33, 42%), constipation (22/31, 71%), and cyclic vomiting (6/35, 17%). Distinctive personality traits include a hypersocial affect (21/31, 68%) and moderate-to-severe anxiety (18/28, 64%). In conclusion, JdVS is a clinically recognizable neurodevelopmental syndrome with a characteristic personality and distinctive facial features. The association of pathogenic variants in PPM1D with cyclic vomiting bears not only medical attention but also further pathogenic and mechanistic evaluation.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Adult , Child , Female , Humans , Infant , Male , Developmental Disabilities/diagnosis , Developmental Disabilities/genetics , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Intellectual Disability/pathology , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/epidemiology , Neurodevelopmental Disorders/genetics , Phenotype , Protein Phosphatase 2C/genetics , Retrospective Studies , Vomiting , Child, Preschool , Adolescent , Young Adult , Middle Aged
11.
Brain ; 145(9): 3308-3327, 2022 09 14.
Article in English | MEDLINE | ID: mdl-35851598

ABSTRACT

Variants in RAC3, encoding a small GTPase RAC3 which is critical for the regulation of actin cytoskeleton and intracellular signal transduction, are associated with a rare neurodevelopmental disorder with structural brain anomalies and facial dysmorphism. We investigated a cohort of 10 unrelated participants presenting with global psychomotor delay, hypotonia, behavioural disturbances, stereotyped movements, dysmorphic features, seizures and musculoskeletal abnormalities. MRI of brain revealed a complex pattern of variable brain malformations, including callosal abnormalities, white matter thinning, grey matter heterotopia, polymicrogyria/dysgyria, brainstem anomalies and cerebellar dysplasia. These patients harboured eight distinct de novo RAC3 variants, including six novel variants (NM_005052.3): c.34G > C p.G12R, c.179G > A p.G60D, c.186_188delGGA p.E62del, c.187G > A p.D63N, c.191A > G p.Y64C and c.348G > C p.K116N. We then examined the pathophysiological significance of these novel and previously reported pathogenic variants p.P29L, p.P34R, p.A59G, p.Q61L and p.E62K. In vitro analyses revealed that all tested RAC3 variants were biochemically and biologically active to variable extent, and exhibited a spectrum of different affinities to downstream effectors including p21-activated kinase 1. We then focused on the four variants p.Q61L, p.E62del, p.D63N and p.Y64C in the Switch II region, which is essential for the biochemical activity of small GTPases and also a variation hot spot common to other Rho family genes, RAC1 and CDC42. Acute expression of the four variants in embryonic mouse brain using in utero electroporation caused defects in cortical neuron morphology and migration ending up with cluster formation during corticogenesis. Notably, defective migration by p.E62del, p.D63N and p.Y64C were rescued by a dominant negative version of p21-activated kinase 1. Our results indicate that RAC3 variants result in morphological and functional defects in cortical neurons during brain development through variant-specific mechanisms, eventually leading to heterogeneous neurodevelopmental phenotypes.


Subject(s)
Neurodevelopmental Disorders , rac GTP-Binding Proteins , Animals , Humans , Mice , Neurodevelopmental Disorders/genetics , Neurodevelopmental Disorders/metabolism , Neurons/metabolism , Phenotype , p21-Activated Kinases/genetics , rac GTP-Binding Proteins/genetics , rac GTP-Binding Proteins/metabolism
12.
Hum Mutat ; 43(5): 582-594, 2022 05.
Article in English | MEDLINE | ID: mdl-35170830

ABSTRACT

Auriculocondylar syndrome (ACS) is a rare craniofacial disorder characterized by mandibular hypoplasia and an auricular defect at the junction between the lobe and helix, known as a "Question Mark Ear" (QME). Several additional features, originating from the first and second branchial arches and other tissues, have also been reported. ACS is genetically heterogeneous with autosomal dominant and recessive modes of inheritance. The mutations identified to date are presumed to dysregulate the endothelin 1 signaling pathway. Here we describe 14 novel cases and reassess 25 published cases of ACS through a questionnaire for systematic data collection. All patients harbor mutation(s) in PLCB4, GNAI3, or EDN1. This series of patients contributes to the characterization of additional features occasionally associated with ACS such as respiratory, costal, neurodevelopmental, and genital anomalies, and provides management and monitoring recommendations.


Subject(s)
Ear Diseases , Ear/abnormalities , Ear Diseases/genetics , Humans , Pedigree , Phenotype
13.
Hum Mol Genet ; 29(9): 1476-1488, 2020 06 03.
Article in English | MEDLINE | ID: mdl-32307537

ABSTRACT

Arterial tortuosity syndrome (ATS) is a recessively inherited connective tissue disorder, mainly characterized by tortuosity and aneurysm formation of the major arteries. ATS is caused by loss-of-function mutations in SLC2A10, encoding the facilitative glucose transporter GLUT10. Former studies implicated GLUT10 in the transport of dehydroascorbic acid, the oxidized form of ascorbic acid (AA). Mouse models carrying homozygous Slc2a10 missense mutations did not recapitulate the human phenotype. Since mice, in contrast to humans, are able to intracellularly synthesize AA, we generated a novel ATS mouse model, deficient for Slc2a10 as well as Gulo, which encodes for L-gulonolactone oxidase, an enzyme catalyzing the final step in AA biosynthesis in mouse. Gulo;Slc2a10 double knock-out mice showed mild phenotypic anomalies, which were absent in single knock-out controls. While Gulo;Slc2a10 double knock-out mice did not fully phenocopy human ATS, histological and immunocytochemical analysis revealed compromised extracellular matrix formation. Transforming growth factor beta signaling remained unaltered, while mitochondrial function was compromised in smooth muscle cells derived from Gulo;Slc2a10 double knock-out mice. Altogether, our data add evidence that ATS is an ascorbate compartmentalization disorder, but additional factors underlying the observed phenotype in humans remain to be determined.


Subject(s)
Arteries/abnormalities , Ascorbic Acid Deficiency/genetics , Glucose Transport Proteins, Facilitative/genetics , Joint Instability/genetics , L-Gulonolactone Oxidase/genetics , Skin Diseases, Genetic/genetics , Vascular Malformations/genetics , Animals , Arteries/metabolism , Arteries/pathology , Ascorbic Acid/biosynthesis , Ascorbic Acid/genetics , Ascorbic Acid Deficiency/metabolism , Ascorbic Acid Deficiency/pathology , Disease Models, Animal , Homozygote , Humans , Joint Instability/metabolism , Joint Instability/pathology , Mice , Mice, Knockout , Mitochondria/genetics , Mitochondria/metabolism , Mitochondria/pathology , Respiration/genetics , Signal Transduction/genetics , Skin Diseases, Genetic/metabolism , Skin Diseases, Genetic/pathology , Vascular Malformations/metabolism , Vascular Malformations/pathology
14.
Hum Genet ; 141(1): 65-80, 2022 Jan.
Article in English | MEDLINE | ID: mdl-34748075

ABSTRACT

Pathogenic variants of the myelin transcription factor-1 like (MYT1L) gene include heterozygous missense, truncating variants and 2p25.3 microdeletions and cause a syndromic neurodevelopmental disorder (OMIM#616,521). Despite enrichment in de novo mutations in several developmental disorders and autism studies, the data on clinical characteristics and genotype-phenotype correlations are scarce, with only 22 patients with single nucleotide pathogenic variants reported. We aimed to further characterize this disorder at both the clinical and molecular levels by gathering a large series of patients with MYT1L-associated neurodevelopmental disorder. We collected genetic information on 40 unreported patients with likely pathogenic/pathogenic MYT1L variants and performed a comprehensive review of published data (total = 62 patients). We confirm that the main phenotypic features of the MYT1L-related disorder are developmental delay with language delay (95%), intellectual disability (ID, 70%), overweight or obesity (58%), behavioral disorders (98%) and epilepsy (23%). We highlight novel clinical characteristics, such as learning disabilities without ID (30%) and feeding difficulties during infancy (18%). We further describe the varied dysmorphic features (67%) and present the changes in weight over time of 27 patients. We show that patients harboring highly clustered missense variants in the 2-3-ZNF domains are not clinically distinguishable from patients with truncating variants. We provide an updated overview of clinical and genetic data of the MYT1L-associated neurodevelopmental disorder, hence improving diagnosis and clinical management of these patients.


Subject(s)
Genetic Variation , Nerve Tissue Proteins/genetics , Neurodevelopmental Disorders/genetics , Transcription Factors/genetics , Adolescent , Adult , Child , Child, Preschool , Epilepsy/genetics , Feeding and Eating Disorders/genetics , Female , Genetic Association Studies , Heterozygote , Humans , Infant , Language Development Disorders/genetics , Male , Obesity/genetics , Phenotype , Young Adult
15.
Am J Hum Genet ; 104(4): 758-766, 2019 04 04.
Article in English | MEDLINE | ID: mdl-30929739

ABSTRACT

By using exome sequencing and a gene matching approach, we identified de novo and inherited pathogenic variants in KDM3B in 14 unrelated individuals and three affected parents with varying degrees of intellectual disability (ID) or developmental delay (DD) and short stature. The individuals share additional phenotypic features that include feeding difficulties in infancy, joint hypermobility, and characteristic facial features such as a wide mouth, a pointed chin, long ears, and a low columella. Notably, two individuals developed cancer, acute myeloid leukemia and Hodgkin lymphoma, in childhood. KDM3B encodes for a histone demethylase and is involved in H3K9 demethylation, a crucial part of chromatin modification required for transcriptional regulation. We identified missense and truncating variants, suggesting that KDM3B haploinsufficiency is the underlying mechanism for this syndrome. By using a hybrid facial-recognition model, we show that individuals with a pathogenic variant in KDM3B have a facial gestalt, and that they show significant facial similarity compared to control individuals with ID. In conclusion, pathogenic variants in KDM3B cause a syndrome characterized by ID, short stature, and facial dysmorphism.


Subject(s)
Craniofacial Abnormalities/genetics , Developmental Disabilities/genetics , Dwarfism/genetics , Genetic Variation , Intellectual Disability/genetics , Jumonji Domain-Containing Histone Demethylases/genetics , Musculoskeletal Abnormalities/genetics , Body Height , Child , Exome , Face , Female , Genetic Association Studies , Germ-Line Mutation , Haploinsufficiency , Histones/chemistry , Humans , Male , Mutation, Missense , Phenotype
16.
Genet Med ; 24(2): 439-453, 2022 02.
Article in English | MEDLINE | ID: mdl-34906501

ABSTRACT

PURPOSE: This study aimed to describe a multisystemic disorder featuring cardiovascular, facial, musculoskeletal, and cutaneous anomalies caused by heterozygous loss-of-function variants in TAB2. METHODS: Affected individuals were analyzed by next-generation technologies and genomic array. The presumed loss-of-function effect of identified variants was assessed by luciferase assay in cells transiently expressing TAB2 deleterious alleles. In available patients' fibroblasts, variant pathogenicity was further explored by immunoblot and osteoblast differentiation assays. The transcriptomic profile of fibroblasts was investigated by RNA sequencing. RESULTS: A total of 11 individuals from 8 families were heterozygotes for a novel TAB2 variant. In total, 7 variants were predicted to be null alleles and 1 was a missense change. An additional subject was heterozygous for a 52 kb microdeletion involving TAB2 exons 1 to 3. Luciferase assay indicated a decreased transcriptional activation mediated by NF-κB signaling for all point variants. Immunoblot analysis showed a reduction of TAK1 phosphorylation while osteoblast differentiation was impaired. Transcriptomic analysis identified deregulation of multiple pleiotropic pathways, such as TGFß-, Ras-MAPK-, and Wnt-signaling networks. CONCLUSION: Our data defined a novel disorder associated with loss-of-function or, more rarely, hypomorphic alleles in a restricted linker region of TAB2. The pleiotropic manifestations in this disorder partly recapitulate the 6q25.1 (TAB2) microdeletion syndrome and deserve the definition of cardio-facial-cutaneous-articular syndrome.


Subject(s)
Adaptor Proteins, Signal Transducing , NF-kappa B , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Exons/genetics , Humans , NF-kappa B/genetics , NF-kappa B/metabolism , Phosphorylation , Signal Transduction
17.
Genet Med ; 24(6): 1261-1273, 2022 06.
Article in English | MEDLINE | ID: mdl-35341651

ABSTRACT

PURPOSE: This study aimed to undertake a multidisciplinary characterization of the phenotype associated with SOX11 variants. METHODS: Individuals with protein altering variants in SOX11 were identified through exome and genome sequencing and international data sharing. Deep clinical phenotyping was undertaken by referring clinicians. Blood DNA methylation was assessed using Infinium MethylationEPIC array. The expression pattern of SOX11 in developing human brain was defined using RNAscope. RESULTS: We reported 38 new patients with SOX11 variants. Idiopathic hypogonadotropic hypogonadism was confirmed as a feature of SOX11 syndrome. A distinctive pattern of blood DNA methylation was identified in SOX11 syndrome, separating SOX11 syndrome from other BAFopathies. CONCLUSION: SOX11 syndrome is a distinct clinical entity with characteristic clinical features and episignature differentiating it from BAFopathies.


Subject(s)
DNA Methylation , Hypogonadism , Klinefelter Syndrome , Neurodevelopmental Disorders , SOXC Transcription Factors , DNA Methylation/genetics , Humans , Hypogonadism/genetics , Klinefelter Syndrome/genetics , Neurodevelopmental Disorders/genetics , Phenotype , SOXC Transcription Factors/genetics , Exome Sequencing
18.
Clin Genet ; 102(2): 98-109, 2022 08.
Article in English | MEDLINE | ID: mdl-35616059

ABSTRACT

Biallelic variants of the gene encoding for the zinc-finger protein 142 (ZNF142) have recently been associated with intellectual disability (ID), speech impairment, seizures, and movement disorders in nine individuals from five families. In this study, we obtained phenotype and genotype information of 26 further individuals from 16 families. Among the 27 different ZNF142 variants identified in the total of 35 individuals only four were missense. Missense variants may give a milder phenotype by changing the local structure of ZF motifs as suggested by protein modeling; but this correlation should be validated in larger cohorts and pathogenicity of the missense variants should be investigated with functional studies. Clinical features of the 35 individuals suggest that biallelic ZNF142 variants lead to a syndromic neurodevelopmental disorder with mild to moderate ID, varying degrees of delay in language and gross motor development, early onset seizures, hypotonia, behavioral features, movement disorders, and facial dysmorphism. The differences in symptom frequencies observed in the unpublished individuals compared to those of published, and recognition of previously underemphasized facial features are likely to be due to the small sizes of the previous cohorts, which underlines the importance of larger cohorts for the phenotype descriptions of rare genetic disorders.


Subject(s)
Intellectual Disability , Movement Disorders , Neurodevelopmental Disorders , Transcription Factors , Humans , Intellectual Disability/diagnosis , Movement Disorders/complications , Neurodevelopmental Disorders/genetics , Phenotype , Seizures/complications , Seizures/genetics , Transcription Factors/genetics
19.
Am J Med Genet A ; 188(5): 1384-1395, 2022 05.
Article in English | MEDLINE | ID: mdl-35025139

ABSTRACT

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.


Subject(s)
Heart Defects, Congenital , Tetralogy of Fallot , Cryptorchidism , Facies , Growth Disorders , Hand Deformities, Congenital , Heart Defects, Congenital/complications , Humans , Intellectual Disability , Male , Neural Crest , Phenotype , Smad4 Protein/genetics , Tetralogy of Fallot/complications , Tetralogy of Fallot/genetics , Tetralogy of Fallot/surgery
20.
Int J Mol Sci ; 23(7)2022 Apr 06.
Article in English | MEDLINE | ID: mdl-35409398

ABSTRACT

Mosaic RASopathies are a molecularly heterogeneous group of (neuro)cutaneous syndromes with high phenotypical variability. Postzygotic variants in KRAS have been described in oculoectodermal syndrome (OES), encephalocraniocutaneous lipomatosis (ECCL) and epidermal nevus syndrome (ENS). This study confirms the continuum of mosaic neurocutaneous RASopathies showing codon 146 KRAS variants in an individual with OES and, for the first time, in an individual with (isolated) epidermal nevus. The presence of a nevus psiloliparus in individuals with OES indicates that this finding is not specific for ECCL and highlights the phenotypical overlap between ECCL and OES. The presence of the somatic KRAS variant in the nevus psiloliparus resolves the underlying molecular etiology of this fatty-tissue nevus. In addition, this finding refutes the theory of non-allelic twin-spotting as an underlying hypothesis to explain the concurrent presence of two different mosaicisms in one individual. The identification of codon 146 KRAS variants in isolated epidermal nevus introduces a new hot spot for this condition, which is useful for increasing molecular genetic testing using targeted gene sequencing panels.


Subject(s)
Hamartoma , Nevus , Codon/genetics , Dermoid Cyst , Ectodermal Dysplasia , Eye Diseases , Humans , Lipomatosis , Neurocutaneous Syndromes , Nevus/genetics , Proto-Oncogene Proteins p21(ras)/genetics
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