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1.
Am J Hum Genet ; 111(4): 729-741, 2024 04 04.
Article in English | MEDLINE | ID: mdl-38579670

ABSTRACT

Glutamine synthetase (GS), encoded by GLUL, catalyzes the conversion of glutamate to glutamine. GS is pivotal for the generation of the neurotransmitters glutamate and gamma-aminobutyric acid and is the primary mechanism of ammonia detoxification in the brain. GS levels are regulated post-translationally by an N-terminal degron that enables the ubiquitin-mediated degradation of GS in a glutamine-induced manner. GS deficiency in humans is known to lead to neurological defects and death in infancy, yet how dysregulation of the degron-mediated control of GS levels might affect neurodevelopment is unknown. We ascertained nine individuals with severe developmental delay, seizures, and white matter abnormalities but normal plasma and cerebrospinal fluid biochemistry with de novo variants in GLUL. Seven out of nine were start-loss variants and two out of nine disrupted 5' UTR splicing resulting in splice exclusion of the initiation codon. Using transfection-based expression systems and mass spectrometry, these variants were shown to lead to translation initiation of GS from methionine 18, downstream of the N-terminal degron motif, resulting in a protein that is stable and enzymatically competent but insensitive to negative feedback by glutamine. Analysis of human single-cell transcriptomes demonstrated that GLUL is widely expressed in neuro- and glial-progenitor cells and mature astrocytes but not in post-mitotic neurons. One individual with a start-loss GLUL variant demonstrated periventricular nodular heterotopia, a neuronal migration disorder, yet overexpression of stabilized GS in mice using in utero electroporation demonstrated no migratory deficits. These findings underline the importance of tight regulation of glutamine metabolism during neurodevelopment in humans.


Subject(s)
Epilepsy, Generalized , Glutamate-Ammonia Ligase , Glutamine , Animals , Humans , Mice , Brain/metabolism , Epilepsy, Generalized/genetics , Glutamate-Ammonia Ligase/genetics , Glutamate-Ammonia Ligase/metabolism , Glutamates/metabolism , Glutamine/genetics , Glutamine/metabolism
2.
Am J Hum Genet ; 109(4): 750-758, 2022 04 07.
Article in English | MEDLINE | ID: mdl-35202563

ABSTRACT

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.


Subject(s)
Histones , Zebrafish , Animals , Chromatin , DNA , Histones/metabolism , Humans , Syndrome , Zebrafish/genetics , Zebrafish/metabolism
3.
Am J Med Genet A ; : e63779, 2024 Jun 10.
Article in English | MEDLINE | ID: mdl-38853608

ABSTRACT

Pathogenic variants in FLNA cause a diversity of X-linked developmental disorders associated with either preserved or diminished levels of filamin A protein and are conceptualized dichotomously as relating to underlying gain- or loss-of-function pathogenic mechanisms. Hemizygosity for germline deletions or truncating variants in FLNA is generally considered to result in embryonic lethality. Structurally, filamin A is composed of an N-terminal actin-binding region, followed by 24 immunoglobulin-like repeat units. The repeat domains are separated into distinct segments by two regions of low-complexity known as hinge-1 and hinge-2. Hinge-1 is proposed to confer flexibility to the otherwise rigid protein and is a target for cleavage by calpain with the resultant filamin fragments mediating crucial cellular signaling processes. Here, three families with pathogenic variants in FLNA that impair the function of hinge-1 in males are described, leading to distinct clinical phenotypes. One large in-frame deletion that includes the hinge leads to frontometaphyseal dysplasia in affected males and females, while two germline truncating variants located within the exon encoding hinge 1 result in phenotypes in males that are explained by exon skipping and under-expression of a transcript that deletes hinge-1 from the resultant protein. These three variants affecting hinge-1 indicate that this domain does not mediate cellular functions that, when deficientresult in embryonic lethality in males and that germline truncating variants in this region of FLNA can result in viable phenotypes in males.

4.
J Med Genet ; 60(12): 1224-1234, 2023 Nov 27.
Article in English | MEDLINE | ID: mdl-37586838

ABSTRACT

BACKGROUND: KBG syndrome is caused by haploinsufficiency of ANKRD11 and is characterised by macrodontia of upper central incisors, distinctive facial features, short stature, skeletal anomalies, developmental delay, brain malformations and seizures. The central nervous system (CNS) and skeletal features remain poorly defined. METHODS: CNS and/or skeletal imaging were collected from molecularly confirmed individuals with KBG syndrome through an international network. We evaluated the original imaging and compared our results with data in the literature. RESULTS: We identified 53 individuals, 44 with CNS and 40 with skeletal imaging. Common CNS findings included incomplete hippocampal inversion and posterior fossa malformations; these were significantly more common than previously reported (63.4% and 65.9% vs 1.1% and 24.7%, respectively). Additional features included patulous internal auditory canal, never described before in KBG syndrome, and the recurrence of ventriculomegaly, encephalic cysts, empty sella and low-lying conus medullaris. We found no correlation between these structural anomalies and epilepsy or intellectual disability. Prevalent skeletal findings comprised abnormalities of the spine including scoliosis, coccygeal anomalies and cervical ribs. Hand X-rays revealed frequent abnormalities of carpal bone morphology and maturation, including a greater delay in ossification compared with metacarpal/phalanx bones. CONCLUSION: This cohort enabled us to describe the prevalence of very heterogeneous neuroradiological and skeletal anomalies in KBG syndrome. Knowledge of the spectrum of such anomalies will aid diagnostic accuracy, improve patient care and provide a reference for future research on the effects of ANKRD11 variants in skeletal and brain development.


Subject(s)
Abnormalities, Multiple , Bone Diseases, Developmental , Intellectual Disability , Tooth Abnormalities , Humans , Intellectual Disability/diagnosis , Intellectual Disability/genetics , Abnormalities, Multiple/diagnosis , Abnormalities, Multiple/genetics , Bone Diseases, Developmental/diagnostic imaging , Bone Diseases, Developmental/genetics , Tooth Abnormalities/diagnostic imaging , Tooth Abnormalities/genetics , Facies , Phenotype , Repressor Proteins/genetics , Transcription Factors , Neuroimaging
5.
Intern Med J ; 54(3): 388-397, 2024 Mar.
Article in English | MEDLINE | ID: mdl-37732891

ABSTRACT

BACKGROUND: The complexities of mitochondrial disease make epidemiological studies challenging, yet this information is important in understanding the healthcare burden and addressing service and educational needs. Existing studies are limited to quaternary centres or focus on a single genotype or phenotype and estimate disease prevalence at 12.5 per 100 000. New Zealand's (NZ) size and partially integrated national healthcare system make it amenable to a nationwide prevalence study. AIM: To estimate the prevalence of molecularly confirmed and suspected mitochondrial disease on 31 December 2015 in NZ. METHODS: Cases were identified from subspecialists and laboratory databases and through interrogation of the Ministry of Health National Minimum Dataset with a focus on presentations between 2000 and 2015. Patient records were reviewed, and those with a diagnosis of 'mitochondrial disease' who were alive and residing in NZ on the prevalence date were included. These were divided into molecularly confirmed and clinically suspected cases. Official NZ estimated resident population data were used to calculate prevalence. RESULTS: Seven hundred twenty-three unique national health index numbers were identified. Five hundred five were excluded. The minimum combined prevalence for mitochondrial disease was 4.7 per 100 000 (95% confidence interval (CI): 4.1-5.4). The minimum prevalence for molecularly confirmed and suspected disease was 2.9 (95% CI 2.4-3.4) and 1.8 (95% CI 1.4-2.2) cases per 100 000 respectively. CONCLUSIONS: Within the limitations of this study, comparison to similar prevalence studies performed by specialist referral centres suggests mitochondrial disease is underdiagnosed in NZ. This highlights a need for improved education and referral pathways for mitochondrial disease in NZ.


Subject(s)
Delivery of Health Care , Humans , Cross-Sectional Studies , New Zealand/epidemiology , Prevalence
6.
Am J Med Genet A ; 191(5): 1164-1209, 2023 May.
Article in English | MEDLINE | ID: mdl-36779427

ABSTRACT

The "Nosology of genetic skeletal disorders" has undergone its 11th revision and now contains 771 entries associated with 552 genes reflecting advances in molecular delineation of new disorders thanks to advances in DNA sequencing technology. The most significant change as compared to previous versions is the adoption of the dyadic naming system, systematically associating a phenotypic entity with the gene it arises from. We consider this a significant step forward as dyadic naming is more informative and less prone to errors than the traditional use of list numberings and eponyms. Despite the adoption of dyadic naming, efforts have been made to maintain strong ties to the MIM catalog and its historical data. As with the previous versions, the list of disorders and genes in the Nosology may be useful in considering the differential diagnosis in the clinic, directing bioinformatic analysis of next-generation sequencing results, and providing a basis for novel advances in biology and medicine.

7.
EMBO Rep ; 21(5): e48204, 2020 05 06.
Article in English | MEDLINE | ID: mdl-32207244

ABSTRACT

During embryonic development, excitatory projection neurons migrate in the cerebral cortex giving rise to organised layers. Periventricular heterotopia (PH) is a group of aetiologically heterogeneous disorders in which a subpopulation of newborn projection neurons fails to initiate their radial migration to the cortex, ultimately resulting in bands or nodules of grey matter lining the lateral ventricles. Although a number of genes have been implicated in its cause, currently they only satisfactorily explain the pathogenesis of the condition for 50% of patients. Novel gene discovery is complicated by the extreme genetic heterogeneity recently described to underlie its cause. Here, we study the neurodevelopmental role of endothelin-converting enzyme-2 (ECE2) for which two biallelic variants have been identified in two separate patients with PH. Our results show that manipulation of ECE2 levels in human cerebral organoids and in the developing mouse cortex leads to ectopic localisation of neural progenitors and neurons. We uncover the role of ECE2 in neurogenesis, and mechanistically, we identify its involvement in the generation and secretion of extracellular matrix proteins in addition to cytoskeleton and adhesion.


Subject(s)
Neurogenesis , Periventricular Nodular Heterotopia , Cell Movement/genetics , Cerebral Cortex , Female , Humans , Neurogenesis/genetics , Neurons , Pregnancy
8.
Hum Mutat ; 42(8): 1030-1041, 2021 08.
Article in English | MEDLINE | ID: mdl-34082468

ABSTRACT

PCDH19 is a nonclustered protocadherin molecule involved in axon bundling, synapse function, and transcriptional coregulation. Pathogenic variants in PCDH19 cause infantile-onset epilepsy known as PCDH19-clustering epilepsy or PCDH19-CE. Recent advances in DNA-sequencing technologies have led to a significant increase in the number of reported PCDH19-CE variants, many of uncertain significance. We aimed to determine the best approaches for assessing the disease relevance of missense variants in PCDH19. The application of the American College of Medical Genetics and Association for Molecular Pathology (ACMG-AMP) guidelines was only 50% accurate. Using a training set of 322 known benign or pathogenic missense variants, we identified MutPred2, MutationAssessor, and GPP as the best performing in silico tools. We generated a protein structural model of the extracellular domain and assessed 24 missense variants. We also assessed 24 variants using an in vitro reporter assay. A combination of these tools was 93% accurate in assessing known pathogenic and benign PCDH19 variants. We increased the accuracy of the ACMG-AMP classification of 45 PCDH19 variants from 50% to 94%, using these tools. In summary, we have developed a robust toolbox for the assessment of PCDH19 variant pathogenicity to improve the accuracy of PCDH19-CE variant classification.


Subject(s)
Cadherins , Epilepsy , Cadherins/genetics , Humans , Mutation, Missense , Protocadherins , Sequence Analysis, DNA
9.
Am J Hum Genet ; 102(6): 1115-1125, 2018 06 07.
Article in English | MEDLINE | ID: mdl-29805041

ABSTRACT

Spondylocarpotarsal synostosis syndrome (SCTS) is characterized by intervertebral fusions and fusion of the carpal and tarsal bones. Biallelic mutations in FLNB cause this condition in some families, whereas monoallelic variants in MYH3, encoding embryonic heavy chain myosin 3, have been implicated in dominantly inherited forms of the disorder. Here, five individuals without FLNB mutations from three families were hypothesized to be affected by recessive SCTS on account of sibling recurrence of the phenotype. Initial whole-exome sequencing (WES) showed that all five were heterozygous for one of two independent splice-site variants in MYH3. Despite evidence indicating that three of the five individuals shared two allelic haplotypes encompassing MYH3, no second variant could be located in the WES datasets. Subsequent genome sequencing of these three individuals demonstrated a variant altering a 5' UTR splice donor site (rs557849165 in MYH3) not represented by exome-capture platforms. When the cohort was expanded to 16 SCTS-affected individuals without FLNB mutations, nine had truncating mutations transmitted by unaffected parents, and six inherited the rs557849165 variant in trans, an observation at odds with the population allele frequency for this variant. The rs557849165 variant disrupts splicing in the 5' UTR but is still permissive of MYH3 translational initiation, albeit with reduced efficiency. Although some MYH3 variants cause dominant SCTS, these data indicate that others (notably truncating variants) do not, except in the context of compound heterozygosity for a second hypomorphic allele. These observations make genetic diagnosis challenging in the context of simplex presentations of the disorder.


Subject(s)
Abnormalities, Multiple/genetics , Genes, Recessive , Lumbar Vertebrae/abnormalities , Musculoskeletal Diseases/genetics , Mutation/genetics , Myosin Heavy Chains/genetics , Scoliosis/congenital , Synostosis/genetics , Thoracic Vertebrae/abnormalities , Alleles , Chromosome Mapping , Female , Filamins/genetics , Haplotypes/genetics , Heterozygote , Humans , Male , Pedigree , Phenotype , RNA Splicing/genetics , Scoliosis/genetics , Syndrome , Exome Sequencing
10.
Am J Med Genet A ; 185(4): 1317-1320, 2021 04.
Article in English | MEDLINE | ID: mdl-33372358

ABSTRACT

A Sri Lankan male child with supraorbital hyperostosis, broad nasal bridge, small mandible, severe kyphoscoliosis, distal joint contractures of the hands and long second and third toes is described. A hemizygous pathogenic variant in exon 22 of the filamin A (FLNA) gene [NM_001110556.1: c.3557C>T; which leads to a nonsynonymous substitution of serine by leucine at codon 1186 in the FLNA protein; NP_001104026.1: p.Ser1186Leu] was identified. The clinical features observed in this patient were consistent with the cardinal manifestations seen in frontometaphyseal dysplasia 1 (FMD1). However, characteristic extra skeletal manifestations such as cardiac defects, uropathy, and hearing impairment which have previously been reported in association with this condition were absent in this patient.


Subject(s)
Bone Diseases, Developmental/genetics , Filamins/genetics , Forehead/abnormalities , Genetic Predisposition to Disease , Osteochondrodysplasias/genetics , Abnormalities, Multiple/genetics , Abnormalities, Multiple/pathology , Bone Diseases, Developmental/pathology , Child , Exons/genetics , Forehead/pathology , Humans , Male , Micrognathism/genetics , Micrognathism/pathology , Mutation, Missense/genetics , Osteochondrodysplasias/pathology , Phenotype , Sri Lanka/epidemiology
11.
Am J Med Genet A ; 185(12): 3675-3682, 2021 12.
Article in English | MEDLINE | ID: mdl-34272929

ABSTRACT

Pathogenic variation in the X-linked gene FLNA causes a wide range of human developmental phenotypes. Loss-of-function is usually male embryonic-lethal, and most commonly results in a neuronal migration disorder in affected females. Gain-of-function variants cause a spectrum of skeletal dysplasias that present with variable additional, often distinctive, soft-tissue anomalies in males and females. Here we present two, unrelated, male individuals with novel, intronic variants in FLNA that are predicted to be pathogenic. Their phenotypes are reminiscent of the gain-of-function spectrum without the skeletal manifestations. Most strikingly, they manifest urethral anomalies, cardiac malformations, and keloid scarring, all commonly encountered features of frontometaphyseal dysplasia. Both variants prevent inclusion of exon 40 into the FLNA transcript, predicting the in-frame deletion of 42 amino acids, however the abundance of FLNA protein was equivalent to that observed in healthy individuals. Loss of these 42 amino acids removes sites that mediate key FLNA functions, including binding of some ligands and phosphorylation. This phenotype further expands the spectrum of the FLNA filaminopathies.


Subject(s)
Filamins/genetics , Forehead/abnormalities , Genetic Diseases, X-Linked/genetics , Genetic Predisposition to Disease , Osteochondrodysplasias/genetics , Child , Cicatrix/complications , Cicatrix/genetics , Cicatrix/physiopathology , Exons/genetics , Forehead/physiopathology , Genes, X-Linked , Genetic Diseases, X-Linked/physiopathology , Genetic Variation/genetics , Humans , Infant , Keloid/complications , Keloid/genetics , Keloid/physiopathology , Loss of Function Mutation/genetics , Male , Mutation/genetics , Osteochondrodysplasias/physiopathology , Pedigree , Phenotype , Phosphorylation/genetics , Urethra/abnormalities , Urethra/physiopathology
12.
Am J Med Genet A ; 185(12): 3814-3820, 2021 12.
Article in English | MEDLINE | ID: mdl-34254723

ABSTRACT

Terminal osseous dysplasia with pigmentary defects (TODPD), also known as digitocutaneous dysplasia, is one of the X-linked filaminopathies caused by a variety of FLNA-variants. TODPD is characterized by skeletal defects, skin fibromata and dysmorphic facial features. So far, only a single recurrent variant (c.5217G>A;p.Val1724_Thr1739del) in FLNA has found to be responsible for TODPD. We identified a novel c.5217+5G>C variant in FLNA in a female proband with skeletal defects, skin fibromata, interstitial lung disease, epilepsy, and restrictive cardiomyopathy. This variant causes mis-splicing of exon 31 predicting the production of a FLNA-protein with an in-frame-deletion of 16 residues identical to the miss-splicing-effect of the recurrent TODPD c.5217G>A variant. This mis-spliced transcript was explicitly detected in heart tissue, but was absent from blood, skin, and lung. X-inactivation analyses showed extreme skewing with almost complete inactivation of the mutated allele (>90%) in these tissues, except for heart. The mother of the proband, who also has fibromata and skeletal abnormalities, is also carrier of the FLNA-variant and was diagnosed with noncompaction cardiomyopathy after cardiac screening. No other relevant variants in cardiomyopathy-related genes were found. Here we describe a novel variant in FLNA (c.5217+5G>C) as the second pathogenic variant responsible for TODPD. Cardiomyopathy has not been described as a phenotypic feature of TODPD before.


Subject(s)
Cardiomyopathies/genetics , Filamins/genetics , Fingers/abnormalities , Genetic Diseases, X-Linked/genetics , Genetic Predisposition to Disease , Limb Deformities, Congenital/genetics , Osteochondrodysplasias/genetics , Pigmentation Disorders/genetics , Toes/abnormalities , Cardiomyopathies/complications , Cardiomyopathies/pathology , Child, Preschool , Female , Fingers/pathology , Genes, X-Linked/genetics , Genetic Diseases, X-Linked/complications , Genetic Diseases, X-Linked/pathology , Humans , Infant , Limb Deformities, Congenital/complications , Limb Deformities, Congenital/pathology , Mutation/genetics , Osteochondrodysplasias/complications , Osteochondrodysplasias/pathology , Phenotype , Pigmentation Disorders/complications , Pigmentation Disorders/pathology , Sequence Deletion/genetics , Toes/pathology , X Chromosome Inactivation/genetics
13.
PLoS Genet ; 14(5): e1007281, 2018 05.
Article in English | MEDLINE | ID: mdl-29738522

ABSTRACT

Periventricular nodular heterotopia (PVNH) is a malformation of cortical development commonly associated with epilepsy. We exome sequenced 202 individuals with sporadic PVNH to identify novel genetic risk loci. We first performed a trio-based analysis and identified 219 de novo variants. Although no novel genes were implicated in this initial analysis, PVNH cases were found overall to have a significant excess of nonsynonymous de novo variants in intolerant genes (p = 3.27x10-7), suggesting a role for rare new alleles in genes yet to be associated with the condition. Using a gene-level collapsing analysis comparing cases and controls, we identified a genome-wide significant signal driven by four ultra-rare loss-of-function heterozygous variants in MAP1B, including one de novo variant. In at least one instance, the MAP1B variant was inherited from a parent with previously undiagnosed PVNH. The PVNH was frontally predominant and associated with perisylvian polymicrogyria. These results implicate MAP1B in PVNH. More broadly, our findings suggest that detrimental mutations likely arising in immediately preceding generations with incomplete penetrance may also be responsible for some apparently sporadic diseases.


Subject(s)
Genetic Predisposition to Disease/genetics , Loss of Function Mutation , Microtubule-Associated Proteins/genetics , Periventricular Nodular Heterotopia/genetics , Brain/abnormalities , Brain/diagnostic imaging , Female , Heterozygote , Humans , Magnetic Resonance Imaging , Male , Exome Sequencing/methods
14.
Hum Mutat ; 41(5): 865-883, 2020 05.
Article in English | MEDLINE | ID: mdl-32108395

ABSTRACT

The X-linked filaminopathies represent a diverse group of clinical conditions, all caused by variants in the gene FLNA. FLNA encodes the widely expressed actin binding protein, filamin A that has multiple roles during embryonic development including cell migration, mechanical sensing, and cell signaling. In this review, we discuss the 10 distinct X-linked filaminopathy conditions that between them affect almost all organ systems, including the brain, skeleton, heart, and skin, highlighting the critical role of this protein in human development. We review each of the phenotypes and discuss their pathogenesis, where known. Assigning pathogenicity to variants in FLNA can prove difficult, especially for missense variants and small indels, in-part because of the X-linked nature of the phenotypes, the overlap of phenotypic features between conditions, and poor understanding of the function of certain protein domains. We outline here approaches to characterize phenotypes, highlight hotspot regions within FLNA commonly mutated in these conditions, and approaches to resolving some variants of uncertain significance.


Subject(s)
Filamins/genetics , Genes, X-Linked , Genetic Association Studies , Genetic Predisposition to Disease , Muscular Dystrophies/diagnosis , Muscular Dystrophies/etiology , Mutation , Phenotype , Alleles , Diagnosis, Differential , Facies , Filamins/metabolism , Gain of Function Mutation , Gene Expression Regulation , Genetic Testing , Genetic Variation , Humans , Male , Muscular Dystrophies/metabolism , Organ Specificity/genetics , Radiography , Signal Transduction
15.
Hum Mutat ; 41(7): 1238-1249, 2020 07.
Article in English | MEDLINE | ID: mdl-32112660

ABSTRACT

Int22h1/Int22h2-mediated Xq28 duplication syndrome is a relatively new X-linked intellectual disability syndrome, arising from duplications of the subregion flanked by intron 22 homologous regions 1 and 2 on the q arm of chromosome X. Its primary manifestations include variable cognitive deficits, distinct facial dysmorphia, and neurobehavioral abnormalities that mainly include hyperactivity, irritability, and autistic behavior. Affected males are hemizygous for the duplication, which explains their often more severe manifestations compared with heterozygous females. In this report, we describe the cases of nine individuals recently identified having the syndrome, highlighting unique and previously unreported findings of this syndrome. Specifically, we report for the first time in this syndrome, two cases with de novo duplications, three receiving prenatal diagnosis with the syndrome, and three others having atypical versions of the duplication. Among the latter, one proband has a shortened version spanning only the centromeric half of the typical duplication, while the other two cases have a nearly identical length duplication as the classical duplication, with the exception that their duplication's breakpoints are telomerically shifted by about 0.2 Mb. Finally, we shed light on two new manifestations in this syndrome, vertebral anomalies and multiple malignancies, which possibly expand the phenotypic spectrum of the syndrome.


Subject(s)
Chromosome Duplication , Genetic Diseases, X-Linked/genetics , Intellectual Disability/genetics , Child , Child, Preschool , Female , Humans , Infant , Male , Middle Aged , Prenatal Diagnosis , Syndrome
16.
Hum Mutat ; 41(9): 1645-1661, 2020 09.
Article in English | MEDLINE | ID: mdl-32623794

ABSTRACT

The family of Tre2-Bub2-Cdc16 (TBC)-domain containing GTPase activating proteins (RABGAPs) is not only known as key regulatorof RAB GTPase activity but also has GAP-independent functions. Rab GTPases are implicated in membrane trafficking pathways, such as vesicular trafficking. We report biallelic loss-of-function variants in TBC1D2B, encoding a member of the TBC/RABGAP family with yet unknown function, as the underlying cause of cognitive impairment, seizures, and/or gingival overgrowth in three individuals from unrelated families. TBC1D2B messenger RNA amount was drastically reduced, and the protein was absent in fibroblasts of two patients. In immunofluorescence analysis, ectopically expressed TBC1D2B colocalized with vesicles positive for RAB5, a small GTPase orchestrating early endocytic vesicle trafficking. In two independent TBC1D2B CRISPR/Cas9 knockout HeLa cell lines that serve as cellular model of TBC1D2B deficiency, epidermal growth factor internalization was significantly reduced compared with the parental HeLa cell line suggesting a role of TBC1D2B in early endocytosis. Serum deprivation of TBC1D2B-deficient HeLa cell lines caused a decrease in cell viability and an increase in apoptosis. Our data reveal that loss of TBC1D2B causes a neurodevelopmental disorder with gingival overgrowth, possibly by deficits in vesicle trafficking and/or cell survival.


Subject(s)
GTPase-Activating Proteins/genetics , Gingival Overgrowth/genetics , Neurodevelopmental Disorders/genetics , Seizures/genetics , Adult , Child , Endocytosis , Female , HeLa Cells , Humans , Infant , Loss of Function Mutation , Male , Pedigree , Exome Sequencing , Young Adult
17.
Am J Hum Genet ; 101(1): 139-148, 2017 Jul 06.
Article in English | MEDLINE | ID: mdl-28686853

ABSTRACT

We report 15 individuals with de novo pathogenic variants in WDR26. Eleven of the individuals carry loss-of-function mutations, and four harbor missense substitutions. These 15 individuals comprise ten females and five males, and all have intellectual disability with delayed speech, a history of febrile and/or non-febrile seizures, and a wide-based, spastic, and/or stiff-legged gait. These subjects share a set of common facial features that include a prominent maxilla and upper lip that readily reveal the upper gingiva, widely spaced teeth, and a broad nasal tip. Together, these features comprise a recognizable facial phenotype. We compared these features with those of chromosome 1q41q42 microdeletion syndrome, which typically contains WDR26, and noted that clinical features are consistent between the two subsets, suggesting that haploinsufficiency of WDR26 contributes to the pathology of 1q41q42 microdeletion syndrome. Consistent with this, WDR26 loss-of-function single-nucleotide mutations identified in these subjects lead to nonsense-mediated decay with subsequent reduction of RNA expression and protein levels. We derived a structural model of WDR26 and note that missense variants identified in these individuals localize to highly conserved residues of this WD-40-repeat-containing protein. Given that WDR26 mutations have been identified in ∼1 in 2,000 of subjects in our clinical cohorts and that WDR26 might be poorly annotated in exome variant-interpretation pipelines, we would anticipate that this disorder could be more common than currently appreciated.


Subject(s)
Facies , Gait/genetics , Haploinsufficiency/genetics , Intellectual Disability/genetics , Proteins/genetics , Seizures/genetics , Adaptor Proteins, Signal Transducing , Amino Acid Sequence , Base Sequence , Child, Preschool , Chromosome Deletion , Female , Growth and Development/genetics , Humans , Intellectual Disability/complications , Male , Mutation/genetics , Proteins/chemistry , RNA Stability/genetics , Seizures/complications , Syndrome
18.
J Cell Sci ; 131(8)2018 04 13.
Article in English | MEDLINE | ID: mdl-29654161

ABSTRACT

During development, cycles of spatiotemporal remodeling of higher-order networks of actin filaments contribute to control cell fate specification and differentiation. Programs for controlling these dynamics are hard-wired into actin-regulatory proteins. The filamin family of actin-binding proteins exert crucial mechanotransduction and signaling functions in tissue morphogenesis. Filamin-B (FLNB) is a key player in chondrocyte progenitor differentiation for endochondral ossification. Biallelic loss-of-function mutations or gain-of-function mutations in FLNB cause two groups of skeletal disorders that can be attributed to either the loss of repressive function on TGF-ß signaling or a disruption in mechanosensory properties, respectively. In this Review, we highlight a unique family of vertebrate-specific short-lived filamin-binding proteins, the refilins (refilin-A and refilin-B), that modulate filamin-dependent actin crosslinking properties. Refilins are downstream TGF-ß effectors in epithelial cells. Double knockout of both refilin-A and refilin-B in mice results in precocious ossification of some axial skeletal elements, leading to malformations that are similar to those seen in FLNB-deficient mice. Based on these findings, we present a model summarizing the role of refilins in regulating the mechanosensory functions of FLNB during skeletal development. We also discuss the possible contribution of refilins to FLNB-related skeletal pathologies that are associated with gain-of-function mutations.


Subject(s)
Actin Cytoskeleton/metabolism , Filamins/metabolism , Microfilament Proteins/metabolism , Animals , Cell Differentiation/physiology , Humans
19.
J Inherit Metab Dis ; 43(4): 871-879, 2020 07.
Article in English | MEDLINE | ID: mdl-32049367

ABSTRACT

Pathogenic variants in the Golgi localised alpha 1,6 fucosyltransferase, FUT8, cause a rare inherited metabolic disorder known as FUT8-CDG. To date, only three affected individuals have been reported presenting with a constellation of symptoms including intrauterine growth restriction, severe delays in growth and development, other neurological impairments, significantly shortened limbs, respiratory complications, and shortened lifespan. Here, we report an additional four unrelated affected individuals homozygous for novel pathogenic variants in FUT8. Analysis of serum N-glycans revealed a complete lack of core fucosylation, an important diagnostic biomarker of FUT8-CDG. Our data expands both the molecular and clinical phenotypes of FUT8-CDG and highlights the importance of identifying a reliable biomarker for confirming potentially pathogenic variants.


Subject(s)
Congenital Disorders of Glycosylation/genetics , Fucose/metabolism , Fucosyltransferases/genetics , Polysaccharides/metabolism , Congenital Disorders of Glycosylation/metabolism , Female , Fucosyltransferases/deficiency , Humans , Male , Mass Spectrometry , Phenotype , Exome Sequencing
20.
Am J Hum Genet ; 99(2): 392-406, 2016 08 04.
Article in English | MEDLINE | ID: mdl-27426733

ABSTRACT

Frontometaphyseal dysplasia (FMD) is a progressive sclerosing skeletal dysplasia affecting the long bones and skull. The cause of FMD in some individuals is gain-of-function mutations in FLNA, although how these mutations result in a hyperostotic phenotype remains unknown. Approximately one half of individuals with FMD have no identified mutation in FLNA and are phenotypically very similar to individuals with FLNA mutations, except for an increased tendency to form keloid scars. Using whole-exome sequencing and targeted Sanger sequencing in 19 FMD-affected individuals with no identifiable FLNA mutation, we identified mutations in two genes-MAP3K7, encoding transforming growth factor ß (TGF-ß)-activated kinase (TAK1), and TAB2, encoding TAK1-associated binding protein 2 (TAB2). Four mutations were found in MAP3K7, including one highly recurrent (n = 15) de novo mutation (c.1454C>T [ p.Pro485Leu]) proximal to the coiled-coil domain of TAK1 and three missense mutations affecting the kinase domain (c.208G>C [p.Glu70Gln], c.299T>A [p.Val100Glu], and c.502G>C [p.Gly168Arg]). Notably, the subjects with the latter three mutations had a milder FMD phenotype. An additional de novo mutation was found in TAB2 (c.1705G>A, p.Glu569Lys). The recurrent mutation does not destabilize TAK1, or impair its ability to homodimerize or bind TAB2, but it does increase TAK1 autophosphorylation and alter the activity of more than one signaling pathway regulated by the TAK1 kinase complex. These findings show that dysregulation of the TAK1 complex produces a close phenocopy of FMD caused by FLNA mutations. Furthermore, they suggest that the pathogenesis of some of the filaminopathies caused by FLNA mutations might be mediated by misregulation of signaling coordinated through the TAK1 signaling complex.


Subject(s)
Forehead/abnormalities , MAP Kinase Kinase Kinases/genetics , MAP Kinase Kinase Kinases/metabolism , Mutation/genetics , Osteochondrodysplasias/genetics , Signal Transduction/genetics , Adaptor Proteins, Signal Transducing/genetics , Adaptor Proteins, Signal Transducing/metabolism , Female , Filamins/genetics , Humans , MAP Kinase Signaling System/genetics , Male , NF-kappa B/metabolism , Osteochondrodysplasias/metabolism , Phosphorylation , Protein Binding , Protein Multimerization
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