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1.
Am J Hum Genet ; 110(8): 1414-1435, 2023 08 03.
Article in English | MEDLINE | ID: mdl-37541189

ABSTRACT

Heterogeneous nuclear ribonucleoprotein C (HNRNPC) is an essential, ubiquitously abundant protein involved in mRNA processing. Genetic variants in other members of the HNRNP family have been associated with neurodevelopmental disorders. Here, we describe 13 individuals with global developmental delay, intellectual disability, behavioral abnormalities, and subtle facial dysmorphology with heterozygous HNRNPC germline variants. Five of them bear an identical in-frame deletion of nine amino acids in the extreme C terminus. To study the effect of this recurrent variant as well as HNRNPC haploinsufficiency, we used induced pluripotent stem cells (iPSCs) and fibroblasts obtained from affected individuals. While protein localization and oligomerization were unaffected by the recurrent C-terminal deletion variant, total HNRNPC levels were decreased. Previously, reduced HNRNPC levels have been associated with changes in alternative splicing. Therefore, we performed a meta-analysis on published RNA-seq datasets of three different cell lines to identify a ubiquitous HNRNPC-dependent signature of alternative spliced exons. The identified signature was not only confirmed in fibroblasts obtained from an affected individual but also showed a significant enrichment for genes associated with intellectual disability. Hence, we assessed the effect of decreased and increased levels of HNRNPC on neuronal arborization and neuronal migration and found that either condition affects neuronal function. Taken together, our data indicate that HNRNPC haploinsufficiency affects alternative splicing of multiple intellectual disability-associated genes and that the developing brain is sensitive to aberrant levels of HNRNPC. Hence, our data strongly support the inclusion of HNRNPC to the family of HNRNP-related neurodevelopmental disorders.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Humans , Intellectual Disability/genetics , Alternative Splicing/genetics , Heterogeneous-Nuclear Ribonucleoprotein Group C/genetics , Haploinsufficiency/genetics , Neurodevelopmental Disorders/genetics , Heterogeneous-Nuclear Ribonucleoproteins/genetics
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.
Am J Hum Genet ; 108(6): 1083-1094, 2021 06 03.
Article in English | MEDLINE | ID: mdl-34022131

ABSTRACT

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.


Subject(s)
5' Untranslated Regions , Developmental Disabilities/etiology , Genetic Predisposition to Disease , Loss of Function Mutation , Child , Cohort Studies , DNA Copy Number Variations , Developmental Disabilities/pathology , Humans , MEF2 Transcription Factors/genetics , Exome Sequencing
4.
Clin Genet ; 105(5): 470-487, 2024 05.
Article in English | MEDLINE | ID: mdl-38420660

ABSTRACT

ASXL3-related disorder, sometimes referred to as Bainbridge-Ropers syndrome, was first identified as a distinct neurodevelopmental disorder by Bainbridge et al. in 2013. Since then, there have been a number of case series and single case reports published worldwide. A comprehensive review of the literature was carried out. Abstracts were screened, relevant literature was analysed, and descriptions of common phenotypic features were quantified. ASXL3 variants were collated and categorised. Common phenotypic features comprised global developmental delay or intellectual disability (97%), feeding problems (76%), hypotonia (88%) and characteristic facial features (93%). The majority of genetic variants were de novo truncating variants in exon 11 or 12 of the ASXL3 gene. Several gaps in our knowledge of this disorder were identified, namely, underlying pathophysiology and disease mechanism, disease contribution of missense variants, relevance of variant location, prevalence and penetrance data. Clinical information is currently limited by patient numbers and lack of longitudinal data, which this review aims to address.


Subject(s)
Abnormalities, Multiple , Developmental Disabilities , Facies , Intellectual Disability , Neurodevelopmental Disorders , Child , Humans , Developmental Disabilities/genetics , Transcription Factors/genetics , Phenotype , Syndrome , Intellectual Disability/genetics , Repressor Proteins/genetics
5.
Epilepsia ; 65(5): 1439-1450, 2024 May.
Article in English | MEDLINE | ID: mdl-38491959

ABSTRACT

OBJECTIVE: YWHAG variant alleles have been associated with a rare disease trait whose clinical synopsis includes an early onset epileptic encephalopathy with predominantly myoclonic seizures, developmental delay/intellectual disability, and facial dysmorphisms. Through description of a large cohort, which doubles the number of reported patients, we further delineate the spectrum of YWHAG-related epilepsy. METHODS: We included in this study 24 patients, 21 new and three previously described, with pathogenic/likely pathogenic variants in YWHAG. We extended the analysis of clinical, electroencephalographic, brain magnetic resonance imaging, and molecular genetic information to 24 previously published patients. RESULTS: The phenotypic spectrum of YWHAG-related disorders ranges from mild developmental delay to developmental and epileptic encephalopathy (DEE). Epilepsy onset is in the first 2 years of life. Seizure freedom can be achieved in half of the patients (13/24, 54%). Intellectual disability (23/24, 96%), behavioral disorders (18/24, 75%), neurological signs (13/24, 54%), and dysmorphisms (6/24, 25%) are common. A genotype-phenotype correlation emerged, as DEE is more represented in patients with missense variants located in the ligand-binding domain than in those with truncating or missense variants in other domains (90% vs. 19%, p < .001). SIGNIFICANCE: This study suggests that pathogenic YWHAG variants cause a wide range of clinical presentations with variable severity, ranging from mild developmental delay to DEE. In this allelic series, a genotype-phenotype correlation begins to emerge, potentially providing prognostic information for clinical management and genetic counseling.


Subject(s)
Epilepsy , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Infant , Male , Young Adult , Cohort Studies , Developmental Disabilities/genetics , Electroencephalography , Epilepsy/diagnostic imaging , Epilepsy/genetics , Epilepsy/pathology , Genetic Association Studies , Intellectual Disability/genetics , Magnetic Resonance Imaging , Phenotype
6.
Am J Med Genet A ; 191(1): 29-36, 2023 Jan.
Article in English | MEDLINE | ID: mdl-36177608

ABSTRACT

De novo truncating and splicing pathogenic variants in the Additional Sex Combs-Like 3 (ASXL3) gene are known to cause neurodevelopmental delay, intellectual disability, behavioral difficulties, hypotonia, feeding problems and characteristic facial features. We previously reported 45 patients with ASXL3-related disorder including three individuals with a familial variant. Here we report the detailed clinical and molecular characteristics of these three families with inherited ASXL3-related disorder. First, a father and son with c.2791_2792del p.Gln931fs pathogenic variant. The second, a mother, daughter and son with c.4534C > T, p.Gln1512Ter pathogenic variant. The third, a mother and her daughter with c.4441dup, p.Leu1481fs maternally inherited pathogenic variant. This report demonstrates intrafamilial phenotypic heterogeneity and confirms heritability of ASXL3-related disorder.


Subject(s)
Abnormalities, Multiple , Developmental Disabilities , Intellectual Disability , Child , Female , Humans , Developmental Disabilities/genetics , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Phenotype , Syndrome , Transcription Factors/genetics
7.
J Med Genet ; 59(8): 810-816, 2022 08.
Article in English | MEDLINE | ID: mdl-34462290

ABSTRACT

BACKGROUND: Secreted protein, acidic, cysteine rich (SPARC)-related osteogenesis imperfecta (OI), also referred to as OI type XVII, was first described in 2015, since then there has been only one further report of this form of OI. SPARC is located on chromosome 5 between bands q31 and q33. The encoded protein is necessary for calcification of the collagen in bone, synthesis of extracellular matrix and the promotion of changes to cell shape. METHODS: We describe a further two patients with previously unreported homozygous SPARC variants with OI: one splice site; one nonsense pathogenic variant. We present detailed information on the clinical and radiological phenotype and correlate this with their genotype. There are only two previous reports by Mendozo-Londono et al and Hayat et al with clinical descriptions of patients with SPARC variants. RESULTS: From the data we have obtained, common clinical features in individuals with OI type XVII caused by SPARC variants include scoliosis (5/5), vertebral compression fractures (5/5), multiple long bone fractures (5/5) and delayed motor development (3/3). Interestingly, 2/4 patients also had abnormal brain MRI, including high subcortical white matter changes, abnormal fluid-attenuated inversion in the para-atrial white matter and a large spinal canal from T10 to L1. Of significance, both patients reported here presented with significant neuromuscular weakness prompting early workup. CONCLUSION: Common phenotypic expressions include delayed motor development with neuromuscular weakness, scoliosis and multiple fractures. The data presented here broaden the phenotypic spectrum establishing similar patterns of neuromuscular presentation with a presumed diagnosis of 'myopathy'.


Subject(s)
Fractures, Compression , Osteogenesis Imperfecta , Scoliosis , Spinal Fractures , Collagen Type I/genetics , Humans , Mutation , Osteogenesis Imperfecta/genetics , Osteogenesis Imperfecta/pathology , Osteonectin/genetics , Phenotype
8.
Am J Med Genet A ; 188(3): 931-940, 2022 03.
Article in English | MEDLINE | ID: mdl-34821460

ABSTRACT

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.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Child , Developmental Disabilities/genetics , Developmental Disabilities/pathology , Genetic Association Studies , Heterozygote , Humans , Intellectual Disability/genetics , Neurodevelopmental Disorders/genetics , Phenotype , Exome Sequencing
9.
Am J Med Genet A ; 188(5): 1497-1514, 2022 05.
Article in English | MEDLINE | ID: mdl-35138025

ABSTRACT

Pathogenic variants in heterogeneous nuclear ribonucleoprotein U (HNRNPU) results in a novel neurodevelopmental disorder recently delineated. Here, we report on 17 previously unpublished patients carrying HNRNPU pathogenic variants. All patients were found to harbor de novo loss-of-function variants except for one individual where the inheritance could not be determined, as a parent was unavailable for testing. All patients had seizures which started in early childhood, global developmental delay, intellectual disability, and dysmorphic features. In addition, hypotonia, behavioral abnormalities (such as autistic features, aggression, anxiety, and obsessive-compulsive behaviors), and cardiac (septal defects) and/or brain abnormalities (ventriculomegaly and corpus callosum thinning/agenesis) were frequently observed. We have noted four recurrent variants in the literature (c.1089G>A p.(Trp363*), c.706_707del p.(Glu236Thrfs*6), c.847_857del p.(Phe283Serfs*5), and c.1681dels p.(Gln561Serfs*45)).


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Agenesis of Corpus Callosum/genetics , Child , Child, Preschool , Developmental Disabilities/genetics , Heterogeneous-Nuclear Ribonucleoprotein U/genetics , Humans , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Neurodevelopmental Disorders/genetics , Phenotype , Seizures/genetics
10.
Am J Med Genet A ; 188(11): 3331-3342, 2022 11.
Article in English | MEDLINE | ID: mdl-35971781

ABSTRACT

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.


Subject(s)
Heart Defects, Congenital , Intellectual Disability , Adaptor Proteins, Signal Transducing/genetics , Child , Developmental Disabilities/genetics , Genetic Association Studies , Heart Defects, Congenital/genetics , Humans , Intellectual Disability/genetics , Phenotype , Exome Sequencing
11.
Am J Med Genet A ; 188(3): 867-877, 2022 03.
Article in English | MEDLINE | ID: mdl-34894057

ABSTRACT

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.


Subject(s)
Autism Spectrum Disorder , Intellectual Disability , Autism Spectrum Disorder/genetics , Child , Female , Humans , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Male , NAV1.2 Voltage-Gated Sodium Channel/genetics , Phenotype , Seizures/genetics
12.
Am J Hum Genet ; 102(1): 69-87, 2018 01 04.
Article in English | MEDLINE | ID: mdl-29290338

ABSTRACT

Neurofibromatosis type 1 (NF1), a common genetic disorder with a birth incidence of 1:2,000-3,000, is characterized by a highly variable clinical presentation. To date, only two clinically relevant intragenic genotype-phenotype correlations have been reported for NF1 missense mutations affecting p.Arg1809 and a single amino acid deletion p.Met922del. Both variants predispose to a distinct mild NF1 phenotype with neither externally visible cutaneous/plexiform neurofibromas nor other tumors. Here, we report 162 individuals (129 unrelated probands and 33 affected relatives) heterozygous for a constitutional missense mutation affecting one of five neighboring NF1 codons-Leu844, Cys845, Ala846, Leu847, and Gly848-located in the cysteine-serine-rich domain (CSRD). Collectively, these recurrent missense mutations affect ∼0.8% of unrelated NF1 mutation-positive probands in the University of Alabama at Birmingham (UAB) cohort. Major superficial plexiform neurofibromas and symptomatic spinal neurofibromas were more prevalent in these individuals compared with classic NF1-affected cohorts (both p < 0.0001). Nearly half of the individuals had symptomatic or asymptomatic optic pathway gliomas and/or skeletal abnormalities. Additionally, variants in this region seem to confer a high predisposition to develop malignancies compared with the general NF1-affected population (p = 0.0061). Our results demonstrate that these NF1 missense mutations, although located outside the GAP-related domain, may be an important risk factor for a severe presentation. A genotype-phenotype correlation at the NF1 region 844-848 exists and will be valuable in the management and genetic counseling of a significant number of individuals.


Subject(s)
Codon/genetics , Genetic Association Studies , Mutation, Missense/genetics , Neurofibromatosis 1/genetics , Neurofibromin 1/genetics , Adolescent , Amino Acid Sequence , Child , Cohort Studies , Computer Simulation , Demography , Female , Heterozygote , Humans , Male , Neurofibromin 1/chemistry , Phenotype , Young Adult
13.
J Clin Immunol ; 41(8): 1781-1793, 2021 11.
Article in English | MEDLINE | ID: mdl-34386911

ABSTRACT

PURPOSE: Biallelic pathogenic NBAS variants manifest as a multisystem disorder with heterogeneous clinical phenotypes such as recurrent acute liver failure, growth retardation, and susceptibility to infections. This study explores how NBAS-associated disease affects cells of the innate and adaptive immune system. METHODS: Clinical and laboratory parameters were combined with functional multi-parametric immunophenotyping methods in fifteen NBAS-deficient patients to discover possible alterations in their immune system. RESULTS: Our study revealed reduced absolute numbers of mature CD56dim natural killer (NK) cells. Notably, the residual NK cell population in NBAS-deficient patients exerted a lower potential for activation and degranulation in response to K562 target cells, suggesting an NK cell-intrinsic role for NBAS in the release of cytotoxic granules. NBAS-deficient NK cell activation and degranulation was normalized upon pre-activation by IL-2 in vitro, suggesting that functional impairment was reversible. In addition, we observed a reduced number of naïve B cells in the peripheral blood associated with hypogammaglobulinemia. CONCLUSION: In summary, we demonstrate that pathogenic biallelic variants in NBAS are associated with dysfunctional NK cells as well as impaired adaptive humoral immunity.


Subject(s)
B-Lymphocytes/immunology , Immunologic Deficiency Syndromes/genetics , Immunologic Deficiency Syndromes/immunology , Killer Cells, Natural/immunology , Neoplasm Proteins/genetics , Adolescent , Adult , Child , Child, Preschool , Cytokines/immunology , Gene Expression , Genotype , Humans , Infant , Leukocyte Count , Neoplasm Proteins/deficiency , Phenotype , Young Adult
14.
Clin Genet ; 99(4): 547-557, 2021 04.
Article in English | MEDLINE | ID: mdl-33381861

ABSTRACT

SATB2-Associated syndrome (SAS) is an autosomal dominant, multisystemic, neurodevelopmental disorder due to alterations in SATB2 at 2q33.1. A limited number of individuals with 2q33.1 contiguous deletions encompassing SATB2 (ΔSAS) have been described in the literature. We describe 17 additional individuals with ΔSAS, review the phenotype of 33 previously published individuals with 2q33.1 deletions (n = 50, mean age = 8.5 ± 7.8 years), and provide a comprehensive comparison to individuals with other molecular mechanisms that result in SAS (non-ΔSAS). Individuals in the ΔSAS group were often underweight for age (20/41 = 49%) with a progressive decline in weight (95% CI = -2.3 to -1.1, p < 0.0001) and height (95% CI = -2.3 to -1.0, p < 0.0001) Z-score means from birth to last available measurement. ΔSAS individuals were often noted to have a broad spectrum of facial dysmorphism. A composite image of ΔSAS individuals generated by automated image analysis was distinct as compared to matched controls and non-ΔSAS individuals. We also present additional genotype-phenotype correlations for individuals in the ΔSAS group such as an increased risk for aortic root/ascending aorta dilation and primary pulmonary hypertension for those individuals with contiguous gene deletions that include COL3A1/COL5A2 and BMPR2, respectively. Based on these findings, we provide additional care recommendations for individuals with ΔSAS variants.


Subject(s)
Chromosome Deletion , Chromosomes, Human, Pair 2/genetics , Matrix Attachment Region Binding Proteins/deficiency , Transcription Factors/deficiency , Adult , Child , Child, Preschool , Chromosomes, Human, Pair 2/ultrastructure , Collagen Type III/deficiency , Collagen Type III/genetics , Collagen Type V/deficiency , Collagen Type V/genetics , Dwarfism/genetics , Face/abnormalities , Female , Genetic Association Studies , Gestational Age , Humans , Hypertension, Pulmonary/genetics , Infant , Male , Matrix Attachment Region Binding Proteins/genetics , Microcephaly/genetics , Phenotype , Thinness/genetics , Transcription Factors/genetics
15.
Clin Genet ; 100(4): 412-429, 2021 10.
Article in English | MEDLINE | ID: mdl-34216016

ABSTRACT

ZMYND11 is the critical gene in chromosome 10p15.3 microdeletion syndrome, a syndromic cause of intellectual disability. The phenotype of ZMYND11 variants has recently been extended to autism and seizures. We expand on the epilepsy phenotype of 20 individuals with pathogenic variants in ZMYND11. We obtained clinical descriptions of 16 new and nine published individuals, plus detailed case history of two children. New individuals were identified through GeneMatcher, ClinVar and the European Network for Therapies in Rare Epilepsy (NETRE). Genetic evaluation was performed using gene panels or exome sequencing; variants were classified using American College of Medical Genetics (ACMG) criteria. Individuals with ZMYND11 associated epilepsy fell into three groups: (i) atypical benign partial epilepsy or idiopathic focal epilepsy (n = 8); (ii) generalised epilepsies/infantile epileptic encephalopathy (n = 4); (iii) unclassified (n = 8). Seizure prognosis ranged from spontaneous remission to drug resistant. Neurodevelopmental deficits were invariable. Dysmorphic features were variable. Variants were distributed across the gene and mostly de novo with no precise genotype-phenotype correlation. ZMYND11 is one of a small group of chromatin reader genes associated in the pathogenesis of epilepsy, and specifically ABPE. More detailed epilepsy descriptions of larger cohorts and functional studies might reveal genotype-phenotype correlation. The epileptogenic mechanism may be linked to interaction with histone H3.3.


Subject(s)
Cell Cycle Proteins/genetics , Co-Repressor Proteins/genetics , DNA-Binding Proteins/genetics , Epilepsy/diagnosis , Epilepsy/genetics , Genetic Variation , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/genetics , Phenotype , Adolescent , Adult , Alleles , Amino Acid Substitution , Child , Child, Preschool , Databases, Factual , Electroencephalography , Epilepsy/therapy , Epilepsy, Generalized/diagnosis , Epilepsy, Generalized/genetics , Female , Genetic Association Studies , Genetic Predisposition to Disease , Genetic Testing , Genotype , Humans , Male , Middle Aged , Mutation , Young Adult
16.
Ultrastruct Pathol ; 45(6): 414-420, 2021 Nov 02.
Article in English | MEDLINE | ID: mdl-34538206

ABSTRACT

Vascular Ehlers-Danlos Syndrome (vEDS) and Osteogenesis Imperfecta (OI) are two forms of connective tissue disorders. Previously, transmission electron microscopy of skin biopsies was routinely performed on all patients who were clinically suspected to have vEDS. At present, molecular genetics using genomic DNA extracted from a blood sample is the first line investigation for these patients. However, when variants of uncertain clinical significance are identified on genetic testing and individuals do not have the classical features of OI or vEDS, additional phenotypic information obtained from a skin biopsy can be valuable for contributing to the evidence for re-classifying pathogenicity of variants.We present a cohort of six patients with molecularly confirmed vEDS and one patient with a severe form of OI, who each had expanded (or dilated), protein-filled, rough endoplasmic reticulum identified on transmission electron microscopy. The patients were identified through retrospective screening of medical records, and biopsies were taken between 1999-2016. We discuss the potential role for assessing rough endoplasmic reticulum expansion as a useful tool to allow further phenotyping of these individuals.


Subject(s)
Ehlers-Danlos Syndrome , Osteogenesis Imperfecta , Collagen Type III , Ehlers-Danlos Syndrome/diagnosis , Ehlers-Danlos Syndrome/genetics , Endoplasmic Reticulum, Rough , Humans , Osteogenesis Imperfecta/diagnosis , Osteogenesis Imperfecta/genetics , Retrospective Studies
17.
Hum Mutat ; 41(5): 1042-1050, 2020 05.
Article in English | MEDLINE | ID: mdl-32097528

ABSTRACT

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.


Subject(s)
Cell Cycle Proteins/genetics , Co-Repressor Proteins/genetics , DNA-Binding Proteins/genetics , Genetic Association Studies , Genetic Predisposition to Disease , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Alleles , Child , Child, Preschool , Facies , Female , Genetic Association Studies/methods , Genotype , Haploinsufficiency , Humans , Male , Mutation , Nonsense Mediated mRNA Decay , Phenotype , Syndrome , Zinc Fingers
18.
Hum Genet ; 139(5): 575-592, 2020 May.
Article in English | MEDLINE | ID: mdl-32193685

ABSTRACT

RAD21 encodes a key component of the cohesin complex, and variants in RAD21 have been associated with Cornelia de Lange Syndrome (CdLS). Limited information on phenotypes attributable to RAD21 variants and genotype-phenotype relationships is currently published. We gathered a series of 49 individuals from 33 families with RAD21 alterations [24 different intragenic sequence variants (2 recurrent), 7 unique microdeletions], including 24 hitherto unpublished cases. We evaluated consequences of 12 intragenic variants by protein modelling and molecular dynamic studies. Full clinical information was available for 29 individuals. Their phenotype is an attenuated CdLS phenotype compared to that caused by variants in NIPBL or SMC1A for facial morphology, limb anomalies, and especially for cognition and behavior. In the 20 individuals with limited clinical information, additional phenotypes include Mungan syndrome (in patients with biallelic variants) and holoprosencephaly, with or without CdLS characteristics. We describe several additional cases with phenotypes including sclerocornea, in which involvement of the RAD21 variant is uncertain. Variants were frequently familial, and genotype-phenotype analyses demonstrated striking interfamilial and intrafamilial variability. Careful phenotyping is essential in interpreting consequences of RAD21 variants, and protein modeling and dynamics can be helpful in determining pathogenicity. The current study should be helpful when counseling families with a RAD21 variation.


Subject(s)
Cell Cycle Proteins/genetics , Cell Cycle Proteins/metabolism , Chromosome Deletion , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , De Lange Syndrome/genetics , De Lange Syndrome/pathology , Mutation , Adolescent , Adult , Cell Cycle Proteins/chemistry , Child , Child, Preschool , DNA-Binding Proteins/chemistry , Female , Genetic Association Studies , Genotype , Humans , Infant , Infant, Newborn , Male , Middle Aged , Molecular Dynamics Simulation , Phenotype , Protein Conformation , Young Adult
20.
Genet Med ; 22(9): 1498-1506, 2020 09.
Article in English | MEDLINE | ID: mdl-32499606

ABSTRACT

PURPOSE: Enrichment of heterozygous missense and truncating SMAD6 variants was previously reported in nonsyndromic sagittal and metopic synostosis, and interaction of SMAD6 variants with a common polymorphism nearBMP2 (rs1884302) was proposed to contribute to inconsistent penetrance. We determined the occurrence of SMAD6 variants in all types of craniosynostosis, evaluated the impact of different missense variants on SMAD6 function, and tested independently whether rs1884302 genotype significantly modifies the phenotype. METHODS: We performed resequencing of SMAD6 in 795 unsolved patients with any type of craniosynostosis and genotyped rs1884302 in SMAD6-positive individuals and relatives. We examined the inhibitory activity and stability of SMAD6 missense variants. RESULTS: We found 18 (2.3%) different rare damaging SMAD6 variants, with the highest prevalence in metopic synostosis (5.8%) and an 18.3-fold enrichment of loss-of-function variants comparedwith gnomAD data (P < 10-7). Combined with eight additional variants, ≥20/26 were transmitted from an unaffected parent but rs1884302 genotype did not predict phenotype. CONCLUSION: Pathogenic SMAD6 variants substantially increase the risk of both nonsyndromic and syndromic presentations of craniosynostosis, especially metopic synostosis. Functional analysis is important to evaluate missense variants. Genotyping of rs1884302 is not clinically useful. Mechanisms to explain the remarkable diversity of phenotypes associated with SMAD6 variants remain obscure.


Subject(s)
Craniosynostoses , Craniosynostoses/genetics , Genotype , Humans , Mutation, Missense/genetics , Penetrance , Phenotype , Smad6 Protein/genetics
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