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1.
Am J Hum Genet ; 108(1): 186-193, 2021 01 07.
Article in English | MEDLINE | ID: mdl-33417887

ABSTRACT

POLR3B encodes the second-largest catalytic subunit of RNA polymerase III, an enzyme involved in transcription. Bi-allelic pathogenic variants in POLR3B are a well-established cause of hypomyelinating leukodystrophy. We describe six unrelated individuals with de novo missense variants in POLR3B and a clinical presentation substantially different from POLR3-related leukodystrophy. These individuals had afferent ataxia, spasticity, variable intellectual disability and epilepsy, and predominantly demyelinating sensory motor peripheral neuropathy. Protein modeling and proteomic analysis revealed a distinct mechanism of pathogenicity; the de novo POLR3B variants caused aberrant association of individual enzyme subunits rather than affecting overall enzyme assembly or stability. We expand the spectrum of disorders associated with pathogenic variants in POLR3B to include a de novo heterozygous POLR3B-related disorder.


Subject(s)
Ataxia/genetics , Hereditary Central Nervous System Demyelinating Diseases/genetics , RNA Polymerase III/genetics , Adolescent , Adult , Cerebellar Ataxia/genetics , Child , Child, Preschool , Female , Genes, Recessive/genetics , Heterozygote , Humans , Male , Mutation, Missense/genetics , Proteomics/methods , Young Adult
2.
Am J Hum Genet ; 108(10): 2006-2016, 2021 10 07.
Article in English | MEDLINE | ID: mdl-34626583

ABSTRACT

Spermatogenesis-associated 5 like 1 (SPATA5L1) represents an orphan gene encoding a protein of unknown function. We report 28 bi-allelic variants in SPATA5L1 associated with sensorineural hearing loss in 47 individuals from 28 (26 unrelated) families. In addition, 25/47 affected individuals (53%) presented with microcephaly, developmental delay/intellectual disability, cerebral palsy, and/or epilepsy. Modeling indicated damaging effect of variants on the protein, largely via destabilizing effects on protein domains. Brain imaging revealed diminished cerebral volume, thin corpus callosum, and periventricular leukomalacia, and quantitative volumetry demonstrated significantly diminished white matter volumes in several individuals. Immunofluorescent imaging in rat hippocampal neurons revealed localization of Spata5l1 in neuronal and glial cell nuclei and more prominent expression in neurons. In the rodent inner ear, Spata5l1 is expressed in the neurosensory hair cells and inner ear supporting cells. Transcriptomic analysis performed with fibroblasts from affected individuals was able to distinguish affected from controls by principal components. Analysis of differentially expressed genes and networks suggested a role for SPATA5L1 in cell surface adhesion receptor function, intracellular focal adhesions, and DNA replication and mitosis. Collectively, our results indicate that bi-allelic SPATA5L1 variants lead to a human disease characterized by sensorineural hearing loss (SNHL) with or without a nonprogressive mixed neurodevelopmental phenotype.


Subject(s)
Cerebral Palsy/pathology , Epilepsy/pathology , Genetic Predisposition to Disease , Genetic Variation , Hearing Loss/pathology , Intellectual Disability/pathology , Muscle Spasticity/pathology , ATPases Associated with Diverse Cellular Activities/genetics , Adolescent , Adult , Alleles , Animals , Cerebral Palsy/etiology , Cerebral Palsy/metabolism , Child, Preschool , Epilepsy/etiology , Epilepsy/metabolism , Female , Hearing Loss/etiology , Hearing Loss/metabolism , Humans , Infant , Infant, Newborn , Intellectual Disability/etiology , Intellectual Disability/metabolism , Male , Muscle Spasticity/etiology , Muscle Spasticity/metabolism , Rats , Young Adult
3.
Am J Med Genet A ; 194(8): e63610, 2024 08.
Article in English | MEDLINE | ID: mdl-38517161

ABSTRACT

Primrose syndrome (PS) is a rare genetic disease characterized by developmental delay, intellectual disability, sensorineural hearing loss, and dysmorphic features. PS is caused by de novo pathogenic variants in the ZBTB20 gene, which encodes a transcription factor modulating neurogenesis. We describe resolution with sertraline of neurobehavioral difficulties in a 17-year-old Hispanic male with PS with de novo heterozygous c.1916G > A (p.C639Y) variant of ZBTB20. Neurobehavioral difficulties included aggression towards self and others, irritability, tearfulness, and mood liability that did not respond to behavioral interventions or aripiprazole. Treatment with sertraline, a medication indicated for psychiatric disorders including anxiety and depression, led to the resolution of neurobehavioral difficulties after 2 weeks of initiation of medication. The treatment course suggests that selective serotonin reuptake inhibitors, such as sertraline, may be a useful tool for neurobehavioral difficulties in PS over antipsychotics that are accompanied by complex side effect profiles, and suggest that anxiety is the primary cause of the neurobehavioral difficulties in this patient.


Subject(s)
Intellectual Disability , Sertraline , Transcription Factors , Humans , Sertraline/therapeutic use , Male , Adolescent , Intellectual Disability/genetics , Intellectual Disability/drug therapy , Transcription Factors/genetics , Hearing Loss, Sensorineural/genetics , Hearing Loss, Sensorineural/drug therapy , Selective Serotonin Reuptake Inhibitors/therapeutic use , Abnormalities, Multiple/genetics , Abnormalities, Multiple/drug therapy , Abnormalities, Multiple/psychology , Calcinosis , Ear Diseases , Muscular Atrophy , Nerve Tissue Proteins
4.
Epilepsy Behav ; 150: 109584, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38096660

ABSTRACT

SYNGAP1-related disorder (SYNGAP1-RD) is a neurodevelopmental disorder that is commonly associated with epilepsy, autism spectrum disorder (ASD), and disruptive behaviors. In this study, behavior problems in 11 consecutive patients with SYNGAP1-RD are described and quantified based on a behavioral screening conducted within the context of a multi-disciplinary tertiary care specialty clinic visit. The behavioral phenotype was then compared to published samples of behavior problems in ASD and other genetic cause of epilepsy occurring in the context of neurodevelopmental disorders using results from the Aberrant Behavior Checklist-Community (ABC-C), an empirically derived outcome measure. We report common antecedent and consequent events surrounding problem behavior across individuals. Additionally, we report on the management approach of caregivers and the impact of problem behaviors on the family. Our results suggest a number of commonalities between behavioral profiles in SYNGAP1-RD with ASD and other genetic causes of developmental and epileptic encephalopathies, and also highlight severe behavior problems as a specific behavioral phenotype of SYNGAP1-RD.


Subject(s)
Autism Spectrum Disorder , Epilepsy , Neurodevelopmental Disorders , Problem Behavior , Humans , Autism Spectrum Disorder/complications , Autism Spectrum Disorder/genetics , Autism Spectrum Disorder/therapy , Tertiary Healthcare , Epilepsy/complications , Epilepsy/genetics , Epilepsy/therapy , ras GTPase-Activating Proteins
5.
Cell Mol Life Sci ; 80(11): 345, 2023 Nov 03.
Article in English | MEDLINE | ID: mdl-37921875

ABSTRACT

AMPA receptors are members of the glutamate receptor family and mediate a fast component of excitatory synaptic transmission at virtually all central synapses. Thus, their functional characteristics are a critical determinant of brain function. We evaluate intolerance of each GRIA gene to genetic variation using 3DMTR and report here the functional consequences of 52 missense variants in GRIA1-4 identified in patients with various neurological disorders. These variants produce changes in agonist EC50, response time course, desensitization, and/or receptor surface expression. We predict that these functional and localization changes will have important consequences for circuit function, and therefore likely contribute to the patients' clinical phenotype. We evaluated the sensitivity of variant receptors to AMPAR-selective modulators including FDA-approved drugs to explore potential targeted therapeutic options.


Subject(s)
Nervous System Diseases , Humans , Nervous System Diseases/genetics , Synaptic Transmission/physiology , Receptors, AMPA/genetics , Receptors, AMPA/metabolism , Synapses/metabolism
6.
Am J Med Genet C Semin Med Genet ; 193(3): e32058, 2023 09.
Article in English | MEDLINE | ID: mdl-37534867

ABSTRACT

This study focused on the development and initial psychometric evaluation of a set of online, webcam-collected, and artificial intelligence-derived patient performance measures for neurodevelopmental genetic syndromes (NDGS). Initial testing and qualitative input was used to develop four stimulus paradigms capturing social and cognitive processes, including social attention, receptive vocabulary, processing speed, and single-word reading. The paradigms were administered to a sample of 375 participants, including 163 with NDGS, 56 with idiopathic neurodevelopmental disability (NDD), and 156 neurotypical controls. Twelve measures were created from the four stimulus paradigms. Valid completion rates varied from 87 to 100% across measures, with lower but adequate completion rates in participants with intellectual disability. Adequate to excellent internal consistency reliability (α = 0.67 to 0.95) was observed across measures. Test-retest reproducibility at 1-month follow-up and stability at 4-month follow-up was fair to good (r = 0.40-0.73) for 8 of the 12 measures. All gaze-based measures showed evidence of convergent and discriminant validity with parent-report measures of other cognitive and behavioral constructs. Comparisons across NDGS groups revealed distinct patterns of social and cognitive functioning, including people with PTEN mutations showing a less impaired overall pattern and people with SYNGAP1 mutations showing more attentional, processing speed, and social processing difficulties relative to people with NFIX mutations. Webcam-collected performance measures appear to be a reliable and potentially useful method for objective characterization and monitoring of social and cognitive processes in NDGS and idiopathic NDD. Additional validation work, including more detailed convergent and discriminant validity analyses and examination of sensitivity to change, is needed to replicate and extend these observations.


Subject(s)
Artificial Intelligence , Intellectual Disability , Humans , Reproducibility of Results , Intelligence , Psychometrics
7.
Ann Neurol ; 92(5): 895-901, 2022 11.
Article in English | MEDLINE | ID: mdl-35947102

ABSTRACT

NOTCH1 belongs to the NOTCH family of proteins that regulate cell fate and inflammatory responses. Somatic and germline NOTCH1 variants have been implicated in cancer, Adams-Oliver syndrome, and cardiovascular defects. We describe 7 unrelated patients grouped by the presence of leukoencephalopathy with calcifications and heterozygous de novo gain-of-function variants in NOTCH1. Immunologic profiling showed upregulated CSF IP-10, a cytokine secreted downstream of NOTCH1 signaling. Autopsy revealed extensive leukoencephalopathy and microangiopathy with vascular calcifications. This evidence implicates that heterozygous gain-of-function variants in NOTCH1 lead to a chronic central nervous system (CNS) inflammatory response resulting in a calcifying microangiopathy with leukoencephalopathy. ANN NEUROL 2022;92:895-901.


Subject(s)
Ectodermal Dysplasia , Leukoencephalopathies , Humans , Receptor, Notch1/genetics , Receptor, Notch1/metabolism , Chemokine CXCL10 , Central Nervous System/metabolism
8.
Am J Med Genet A ; 191(7): 1741-1757, 2023 07.
Article in English | MEDLINE | ID: mdl-37045800

ABSTRACT

There are few well-validated measures that are appropriate for assessing the full range of neurobehavioral presentations in PTEN hamartoma tumor syndrome (PHTS) and other neurodevelopmental genetic syndromes (NDGS). As potential therapeutics are developed, having reliable, valid, free, and easily accessible measures to track a range of neurobehavioral domains will be crucial for future clinical trials. This study focused on the development and initial psychometric evaluation of a set of freely available informant-report survey scales for PHTS-the Neurobehavioral Evaluation Tool (NET). Concept elicitation, quantitative ratings, and cognitive interviewing processes were conducted with stakeholders and clinician-scientist experts, used to identify the most important neurobehavioral domains for this population, and to ensure items were appropriate for the full range of individuals with PHTS. Results of this process identified a PHTS neurobehavioral impact model with 11 domains. The final NET scales assessing these domains were administered to a sample of 384 participants (median completion time = 20.6 min), including 32 people with PHTS, 141 with other NDGS, 47 with idiopathic neurodevelopmental disorder (NDD), and 164 neurotypical controls. Initial psychometric results for the total scores of each scale indicated very good model (ω = 0.83-0.99) and internal consistency reliability (α = 0.82-0.98) as well as excellent test-retest reproducibility at 1-month follow-up (r = 0.78-0.98) and stability at 4-month follow-up (r = 0.76-0.96). Conditional reliability estimates indicated very strong measurement precision in key score ranges for assessing PHTS and other people with NDGS and/or idiopathic NDD. Comparisons across domains between PHTS and the other groups revealed specific patterns of symptoms and functioning, including lower levels of challenging behavior and more developed daily living and executive functioning skills relative to other NDGS. The NET appears to be a reliable and potentially useful tool for clinical characterization and monitoring of neurobehavioral symptoms in PHTS and may also have utility in the assessment of other NDGS and idiopathic NDD. Additional validation work, including convergent and discriminant validity analyses, are needed to replicate and extend these observations.


Subject(s)
Hamartoma Syndrome, Multiple , Humans , Hamartoma Syndrome, Multiple/diagnosis , Hamartoma Syndrome, Multiple/genetics , Hamartoma Syndrome, Multiple/pathology , Reproducibility of Results , PTEN Phosphohydrolase/genetics
9.
Brain ; 145(6): 1939-1948, 2022 06 30.
Article in English | MEDLINE | ID: mdl-35773235

ABSTRACT

Biallelic pathogenic variants in SZT2 result in a neurodevelopmental disorder with shared features, including early-onset epilepsy, developmental delay, macrocephaly, and corpus callosum abnormalities. SZT2 is as a critical scaffolding protein in the amino acid sensing arm of the mTORC1 signalling pathway. Due to its large size (3432 amino acids), lack of crystal structure, and absence of functional domains, it is difficult to determine the pathogenicity of SZT2 missense and in-frame deletions, but these variants are increasingly detected and reported by clinical genetic testing in individuals with epilepsy. To exemplify this latter point, here we describe a cohort of 12 individuals with biallelic SZT2 variants and phenotypic overlap with SZT2-related neurodevelopmental disorders. However, the majority of individuals carried one or more SZT2 variants of uncertain significance (VUS), highlighting the need for functional characterization to determine, which, if any, of these VUS were pathogenic. Thus, we developed a novel individualized platform to identify SZT2 loss-of-function variants in the context of mTORC1 signalling and reclassify VUS. Using this platform, we identified a recurrent in-frame deletion (SZT2 p.Val1984del) which was determined to be a loss-of-function variant and therefore likely pathogenic. Haplotype analysis revealed that this single in-frame deletion is a founder variant in those of Ashkenazi Jewish ancestry. Moreover, this approach allowed us to tentatively reclassify all of the VUS in our cohort of 12 individuals, identifying five individuals with biallelic pathogenic or likely pathogenic variants. Clinical features of these five individuals consisted of early-onset seizures (median 24 months), focal seizures, developmental delay and macrocephaly similar to previous reports. However, we also show a widening of the phenotypic spectrum, as none of the five individuals had corpus callosum abnormalities, in contrast to previous reports. Overall, we present a rapid assay to resolve VUS in SZT2, identify a founder variant in individuals of Ashkenazi Jewish ancestry, and demonstrate that corpus callosum abnormalities is not a hallmark feature of this condition. Our approach is widely applicable to other mTORopathies including the most common causes of the focal genetic epilepsies, DEPDC5, TSC1/2, MTOR and NPRL2/3.


Subject(s)
Epilepsies, Partial , Epilepsy , Megalencephaly , Epilepsy/genetics , Humans , Mechanistic Target of Rapamycin Complex 1/genetics , Megalencephaly/genetics , Nerve Tissue Proteins/genetics , Tumor Suppressor Proteins/genetics
10.
J Med Genet ; 59(7): 669-677, 2022 07.
Article in English | MEDLINE | ID: mdl-34321324

ABSTRACT

BACKGROUND: Variants in HECW2 have recently been reported to cause a neurodevelopmental disorder with hypotonia, seizures and impaired language; however, only six variants have been reported and the clinical characteristics have only broadly been defined. METHODS: Molecular and clinical data were collected from clinical and research cohorts. Massive parallel sequencing was performed and identified individuals with a HECW2-related neurodevelopmental disorder. RESULTS: We identified 13 novel missense variants in HECW2 in 22 unpublished cases, of which 18 were confirmed to have a de novo variant. In addition, we reviewed the genotypes and phenotypes of previously reported and new cases with HECW2 variants (n=35 cases). All variants identified are missense, and the majority of likely pathogenic and pathogenic variants are located in or near the C-terminal HECT domain (88.2%). We identified several clustered variants and four recurrent variants (p.(Arg1191Gln);p.(Asn1199Lys);p.(Phe1327Ser);p.(Arg1330Trp)). Two variants, (p.(Arg1191Gln);p.(Arg1330Trp)), accounted for 22.9% and 20% of cases, respectively. Clinical characterisation suggests complete penetrance for hypotonia with or without spasticity (100%), developmental delay/intellectual disability (100%) and developmental language disorder (100%). Other common features are behavioural problems (88.9%), vision problems (83.9%), motor coordination/movement (75%) and gastrointestinal issues (70%). Seizures were present in 61.3% of individuals. Genotype-phenotype analysis shows that HECT domain variants are more frequently associated with cortical visual impairment and gastrointestinal issues. Seizures were only observed in individuals with variants in or near the HECT domain. CONCLUSION: We provide a comprehensive review and expansion of the genotypic and phenotypic spectrum of HECW2 disorders, aiding future molecular and clinical diagnosis and management.


Subject(s)
Intellectual Disability , Neurodevelopmental Disorders , Ubiquitin-Protein Ligases , Genotype , Humans , Intellectual Disability/genetics , Muscle Hypotonia/genetics , Muscle Hypotonia/pathology , Neurodevelopmental Disorders/genetics , Phenotype , Seizures/genetics , Ubiquitin-Protein Ligases/genetics
11.
Ann Gen Psychiatry ; 22(1): 45, 2023 Nov 06.
Article in English | MEDLINE | ID: mdl-37932739

ABSTRACT

BACKGROUND: There is a critical need for effective treatment of the core symptoms of autism spectrum disorder (ASD). The purinergic antagonist suramin may improve core symptoms through restoration of normal mitochondrial function and reduction of neuro-inflammation via its known antagonism of P2X and P2Y receptors. Nonclinical studies in fragile X knockout mice and the maternal immune activation model support these hypotheses. METHODS: We conducted a 14 week, randomized, double-blind, placebo-controlled proof -of-concept study (N = 52) to test the efficacy and safety of suramin intravenous infusions in boys aged 4-15 years with moderate to severe ASD. The study had 3 treatment arms: 10 mg/kg suramin, 20 mg/kg suramin, and placebo given at baseline, week 4, and week 8. The Aberrant Behavior Checklist of Core Symptoms (ABC-Core) (subscales 2, 3, and 5) was the primary endpoint and the Clinical Global Impressions-Improvement (CGI-I) was a secondary endpoint. RESULTS: Forty-four subjects completed the study. The 10 mg/kg suramin group showed a greater, but statistically non-significant, numeric improvement (- 12.5 ± 3.18 [mean ± SE]) vs. placebo (- 8.9 ± 2.86) in ABC-Core at Week 14. The 20 mg/kg suramin group did not show improvement over placebo. In exploratory analyses, the 10 mg/kg arm showed greater ABC Core differences from placebo in younger subjects and among those with less severe symptoms. In CGI-I, the 10 mg/kg arm showed a statistically significant improvement from baseline (2.8 ± 0.30 [mean ± SE]) compared to placebo (1.7 ± 0.27) (p = 0.016). The 20 mg/kg arm had a 2.0 ± 0.28 improvement in CGI-I, which was not statistically significant compared to placebo (p = 0.65). CONCLUSION: Suramin was generally safe and well tolerated over 14 weeks; most adverse events were mild to moderate in severity. Trial Registration Registered with the South African Health Authority, registration number DOH-27-0419-6116. CLINICALTRIALS: Gov registration ID is NCT06058962, last update posted 2023-09-28.

12.
Am J Hum Genet ; 105(3): 640-657, 2019 09 05.
Article in English | MEDLINE | ID: mdl-31402090

ABSTRACT

The identification of genetic variants implicated in human developmental disorders has been revolutionized by second-generation sequencing combined with international pooling of cases. Here, we describe seven individuals who have diverse yet overlapping developmental anomalies, and who all have de novo missense FBXW11 variants identified by whole exome or whole genome sequencing and not reported in the gnomAD database. Their phenotypes include striking neurodevelopmental, digital, jaw, and eye anomalies, and in one individual, features resembling Noonan syndrome, a condition caused by dysregulated RAS signaling. FBXW11 encodes an F-box protein, part of the Skp1-cullin-F-box (SCF) ubiquitin ligase complex, involved in ubiquitination and proteasomal degradation and thus fundamental to many protein regulatory processes. FBXW11 targets include ß-catenin and GLI transcription factors, key mediators of Wnt and Hh signaling, respectively, critical to digital, neurological, and eye development. Structural analyses indicate affected residues cluster at the surface of the loops of the substrate-binding domain of FBXW11, and the variants are predicted to destabilize the protein and/or its interactions. In situ hybridization studies on human and zebrafish embryonic tissues demonstrate FBXW11 is expressed in the developing eye, brain, mandibular processes, and limb buds or pectoral fins. Knockdown of the zebrafish FBXW11 orthologs fbxw11a and fbxw11b resulted in embryos with smaller, misshapen, and underdeveloped eyes and abnormal jaw and pectoral fin development. Our findings support the role of FBXW11 in multiple developmental processes, including those involving the brain, eye, digits, and jaw.


Subject(s)
Brain/abnormalities , Eye Abnormalities/genetics , Fingers/abnormalities , Mutation, Missense , Phenotype , Ubiquitin-Protein Ligases/genetics , beta-Transducin Repeat-Containing Proteins/genetics , Adolescent , Adult , Child , Child, Preschool , Female , Humans , Male
13.
Am J Hum Genet ; 104(2): 203-212, 2019 02 07.
Article in English | MEDLINE | ID: mdl-30612693

ABSTRACT

Using exome sequencing, we have identified de novo variants in MAPK8IP3 in 13 unrelated individuals presenting with an overlapping phenotype of mild to severe intellectual disability. The de novo variants comprise six missense variants, three of which are recurrent, and three truncating variants. Brain anomalies such as perisylvian polymicrogyria, cerebral or cerebellar atrophy, and hypoplasia of the corpus callosum were consistent among individuals harboring recurrent de novo missense variants. MAPK8IP3 has been shown to be involved in the retrograde axonal-transport machinery, but many of its specific functions are yet to be elucidated. Using the CRISPR-Cas9 system to target six conserved amino acid positions in Caenorhabditis elegans, we found that two of the six investigated human alterations led to a significantly elevated density of axonal lysosomes, and five variants were associated with adverse locomotion. Reverse-engineering normalized the observed adverse effects back to wild-type levels. Combining genetic, phenotypic, and functional findings, as well as the significant enrichment of de novo variants in MAPK8IP3 within our total cohort of 27,232 individuals who underwent exome sequencing, we implicate de novo variants in MAPK8IP3 as a cause of a neurodevelopmental disorder with intellectual disability and variable brain anomalies.


Subject(s)
Adaptor Proteins, Signal Transducing/genetics , Brain/abnormalities , Brain/metabolism , Intellectual Disability/genetics , Mutation , Nerve Tissue Proteins/genetics , Adaptor Proteins, Signal Transducing/chemistry , Adaptor Proteins, Signal Transducing/metabolism , Adolescent , Animals , Brain/diagnostic imaging , CRISPR-Cas Systems , Caenorhabditis elegans/genetics , Caenorhabditis elegans/physiology , Child , Child, Preschool , Computer Simulation , Female , Humans , Intellectual Disability/diagnostic imaging , Locomotion , Lysosomes/metabolism , Male , Models, Molecular , Nerve Tissue Proteins/chemistry , Nerve Tissue Proteins/metabolism , Exome Sequencing , Young Adult
14.
Am J Hum Genet ; 103(5): 752-768, 2018 11 01.
Article in English | MEDLINE | ID: mdl-30388402

ABSTRACT

The nuclear factor I (NFI) family of transcription factors play an important role in normal development of multiple organs. Three NFI family members are highly expressed in the brain, and deletions or sequence variants in two of these, NFIA and NFIX, have been associated with intellectual disability (ID) and brain malformations. NFIB, however, has not previously been implicated in human disease. Here, we present a cohort of 18 individuals with mild ID and behavioral issues who are haploinsufficient for NFIB. Ten individuals harbored overlapping microdeletions of the chromosomal 9p23-p22.2 region, ranging in size from 225 kb to 4.3 Mb. Five additional subjects had point sequence variations creating a premature termination codon, and three subjects harbored single-nucleotide variations resulting in an inactive protein as determined using an in vitro reporter assay. All individuals presented with additional variable neurodevelopmental phenotypes, including muscular hypotonia, motor and speech delay, attention deficit disorder, autism spectrum disorder, and behavioral abnormalities. While structural brain anomalies, including dysgenesis of corpus callosum, were variable, individuals most frequently presented with macrocephaly. To determine whether macrocephaly could be a functional consequence of NFIB disruption, we analyzed a cortex-specific Nfib conditional knockout mouse model, which is postnatally viable. Utilizing magnetic resonance imaging and histology, we demonstrate that Nfib conditional knockout mice have enlargement of the cerebral cortex but preservation of overall brain structure and interhemispheric connectivity. Based on our findings, we propose that haploinsufficiency of NFIB causes ID with macrocephaly.


Subject(s)
Haploinsufficiency/genetics , Intellectual Disability/genetics , Megalencephaly/genetics , NFI Transcription Factors/genetics , Adolescent , Adult , Animals , Cerebral Cortex/pathology , Child , Child, Preschool , Codon, Nonsense/genetics , Cohort Studies , Corpus Callosum/pathology , Female , Humans , Male , Mice , Mice, Knockout , Polymorphism, Single Nucleotide/genetics , Young Adult
15.
Genet Med ; 23(10): 1912-1921, 2021 10.
Article in English | MEDLINE | ID: mdl-34113010

ABSTRACT

PURPOSE: In this study, we aimed to characterize the clinical phenotype of a SHANK1-related disorder and define the functional consequences of SHANK1 truncating variants. METHODS: Exome sequencing (ES) was performed for six individuals who presented with neurodevelopmental disorders. Individuals were ascertained with the use of GeneMatcher and Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER). We evaluated potential nonsense-mediated decay (NMD) of two variants by making knock-in cell lines of endogenous truncated SHANK1, and expressed the truncated SHANK1 complementary DNA (cDNA) in HEK293 cells and cultured hippocampal neurons to examine the proteins. RESULTS: ES detected de novo truncating variants in SHANK1 in six individuals. Evaluation of NMD resulted in stable transcripts, and the truncated SHANK1 completely lost binding with Homer1, a linker protein that binds to the C-terminus of SHANK1. These variants may disrupt protein-protein networks in dendritic spines. Dispersed localization of the truncated SHANK1 variants within the spine and dendritic shaft was also observed when expressed in neurons, indicating impaired synaptic localization of truncated SHANK1. CONCLUSION: This report expands the clinical spectrum of individuals with truncating SHANK1 variants and describes the impact these variants may have on the pathophysiology of neurodevelopmental disorders.


Subject(s)
Nerve Tissue Proteins , Neurodevelopmental Disorders , HEK293 Cells , Humans , Nerve Tissue Proteins/genetics , Neurodevelopmental Disorders/genetics , Neurons , Phenotype , Exome Sequencing
16.
Genet Med ; 23(2): 352-362, 2021 02.
Article in English | MEDLINE | ID: mdl-33106617

ABSTRACT

PURPOSE: Neurodevelopmental disorders (NDD) caused by protein phosphatase 2A (PP2A) dysfunction have mainly been associated with de novo variants in PPP2R5D and PPP2CA, and more rarely in PPP2R1A. Here, we aimed to better understand the latter by characterizing 30 individuals with de novo and often recurrent variants in this PP2A scaffolding Aα subunit. METHODS: Most cases were identified through routine clinical diagnostics. Variants were biochemically characterized for phosphatase activity and interaction with other PP2A subunits. RESULTS: We describe 30 individuals with 16 different variants in PPP2R1A, 21 of whom had variants not previously reported. The severity of developmental delay ranged from mild learning problems to severe intellectual disability (ID) with or without epilepsy. Common features were language delay, hypotonia, and hypermobile joints. Macrocephaly was only seen in individuals without B55α subunit-binding deficit, and these patients had less severe ID and no seizures. Biochemically more disruptive variants with impaired B55α but increased striatin binding were associated with profound ID, epilepsy, corpus callosum hypoplasia, and sometimes microcephaly. CONCLUSION: We significantly expand the phenotypic spectrum of PPP2R1A-related NDD, revealing a broader clinical presentation of the patients and that the functional consequences of the variants are more diverse than previously reported.


Subject(s)
Intellectual Disability , Microcephaly , Neurodevelopmental Disorders , Humans , Intellectual Disability/genetics , Muscle Hypotonia , Neurodevelopmental Disorders/epidemiology , Neurodevelopmental Disorders/genetics , Protein Phosphatase 2/genetics , Transcription Factors
18.
Genet Med ; 22(3): 538-546, 2020 03.
Article in English | MEDLINE | ID: mdl-31723249

ABSTRACT

PURPOSE: Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous neurodevelopmental disorders. We sought to delineate the clinical, molecular, and neuroimaging spectrum of a novel neurodevelopmental disorder caused by variants in the zinc finger protein 292 gene (ZNF292). METHODS: We ascertained a cohort of 28 families with ID due to putatively pathogenic ZNF292 variants that were identified via targeted and exome sequencing. Available data were analyzed to characterize the canonical phenotype and examine genotype-phenotype relationships. RESULTS: Probands presented with ID as well as a spectrum of neurodevelopmental features including ASD, among others. All ZNF292 variants were de novo, except in one family with dominant inheritance. ZNF292 encodes a highly conserved zinc finger protein that acts as a transcription factor and is highly expressed in the developing human brain supporting its critical role in neurodevelopment. CONCLUSION: De novo and dominantly inherited variants in ZNF292 are associated with a range of neurodevelopmental features including ID and ASD. The clinical spectrum is broad, and most individuals present with mild to moderate ID with or without other syndromic features. Our results suggest that variants in ZNF292 are likely a recurrent cause of a neurodevelopmental disorder manifesting as ID with or without ASD.


Subject(s)
Autism Spectrum Disorder/genetics , Carrier Proteins/genetics , Genetic Predisposition to Disease , Nerve Tissue Proteins/genetics , Neurodevelopmental Disorders/genetics , Adolescent , Autism Spectrum Disorder/diagnosis , Autism Spectrum Disorder/diagnostic imaging , Autism Spectrum Disorder/pathology , Child , Child, Preschool , Female , High-Throughput Nucleotide Sequencing/methods , Humans , Male , Neurodevelopmental Disorders/diagnosis , Neurodevelopmental Disorders/diagnostic imaging , Neurodevelopmental Disorders/pathology , Neuroimaging/methods , Exome Sequencing/methods
19.
Clin Genet ; 98(6): 571-576, 2020 12.
Article in English | MEDLINE | ID: mdl-33009664

ABSTRACT

The gamma-1 isoform of casein kinase 1, the protein encoded by CSNK1G1, is involved in the growth and morphogenesis of cells. This protein is expressed ubiquitously among many tissue types, including the brain, where it regulates the phosphorylation of N-methyl-D-aspartate receptors and plays a role in synaptic transmission. One prior individual with a de novo variant in CSNK1G presenting with severe developmental delay and early-onset epilepsy has been reported. Here we report an updated clinical history of this previously published case, as well as four additional individuals with de novo variants in CSNK1G1 identified via microarray-based comparative genomic hybridization, exome, or genome sequencing. All individuals (n = 5) had developmental delay. At least three individuals had diagnoses of autism spectrum disorder. All participants were noted to have dysmorphic facial features, although the reported findings varied widely and therefore may not clearly be recognizable. None of the participants had additional major malformations. Taken together, our data suggest that CSNK1G1 may be a cause of syndromic developmental delay and possibly autism spectrum disorder.


Subject(s)
Autism Spectrum Disorder/genetics , Developmental Disabilities/genetics , Genetic Predisposition to Disease , Adolescent , Adult , Autism Spectrum Disorder/pathology , Casein Kinase II/genetics , Child , Child, Preschool , Comparative Genomic Hybridization , Developmental Disabilities/pathology , Female , Heterozygote , Humans , Male , Whole Genome Sequencing , Young Adult
20.
J Genet Couns ; 28(2): 304-312, 2019 04.
Article in English | MEDLINE | ID: mdl-30680845

ABSTRACT

Despite its promising diagnostic yield, whole exome sequencing (WES) frequently introduces variant(s) of uncertain significance (VUS), which have been speculated to cause parental stress and anxiety. This study aimed to explore the psychosocial impact of receiving a VUS from pediatric WES on caregivers and to identify implications for clinical practice. Fourteen telephone interviews were conducted with parents or legal guardians who received VUS results from their child's WES to assess their understanding of the result, affective responses, perceived impact, and adaptation. Our content analysis showed that most participants had a good understanding of the purpose of the test and the majority of them recalled the result category. Most participants deemed the result had no impact thus far on their perception of their child's condition. However, one participant reported feelings of fear related to the VUS. Most participants experienced a range of emotions from receiving the result. The majority of participants reported that this result did not significantly alter their child's care or their ability to take care of their child, and three participants reported empowerment. Additionally, several participants expressed an interest in research studies and peer support groups dedicated to families with a VUS identified on WES. Our study elicited new information about the psychosocial impact of receiving a VUS from WES. This insight may help to guide pre- and post-WES counseling in the future.


Subject(s)
Exome Sequencing , Genetic Testing , Health Knowledge, Attitudes, Practice , Parents/psychology , Adult , Child , Female , Humans , Legal Guardians/psychology , Male , Middle Aged , Uncertainty
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