scholarly journals Further delineation of the phenotypic spectrum of pathogenic variants in MED13

2021 ◽  
Author(s):  
Inna S. Povolotskaya ◽  
Natalya V. Vetrova ◽  
Svetlana O. Zhikrivetskaya ◽  
Elizaveta V. Musatova ◽  
Valeriia S. Klestova ◽  
...  
Keyword(s):  
Genetic Testing ◽  
Genetic Variants ◽  
De Novo ◽  
Autism Spectrum ◽  
Specific Gene ◽  
Incomplete Penetrance ◽  
Cgg Repeat ◽  
Neurodevelopmental Disease ◽  
Pathogenic Variants ◽  
Phenotypic Spectrum

Abstract Introduction:Diagnostic yield of the genetic testing in search for the molecular basis of neurodevelopmental diseases remains low due to incomplete knowledge of the phenotypic spectrum of pathogenic variants in a specific gene. Recently the MED13 gene was linked to neurodevelopmental disease. Methods:Four families with children affected by autism spectrum disorder (ASD) were recruited to the study. Extensive genetic testing was performed for each proband: CGG repeat expansion analysis in FMR1 gene; whole exome sequencing (WES); array comparative genomic hybridization (aCGH); maternity and paternity confirmation. Genetic variants which were revealed by WES were verified with Sanger sequencing or aCGH in probands and their relatives. Results:Four rare heterozygous genetic variants in MED13 gene were identified in four unrelated patients with clinical features matching MED13-associated phenotype: intellectual disability (ID) of various degrees, speech delay, ASD and mild facial dysmorphisms. Three of the variants occurred de novo, while one was inherited maternally, in accordance with previous findings, suggesting incomplete penetrance. A patient with a de novo missense mutation in the intrinsic disordered region of MED13 developed seizures similarly to the only other reported patient with a pathogenic missense variant in this region. Limitations:Additional functional studies are needed to elucidate molecular mechanisms of the disease and distinguish between pathogenic and non-pathogenic variation.Conclusion:Our data strongly support the role of MED13 in neurodevelopmental disease by eliminating other common genetic defects. We expand the phenotypic spectrum of the disease causing variants: pathogenic missense variants in the intrinsic disordered region of MED13 may lead to a phenotype with seizures and incomplete penetrance of the maternally inherited variants may occur.

scholarly journals Detailed Clinical and Psychological Phenotype of the X-linked HNRNPH2-Related Neurodevelopmental Disorder

2021 ◽  
Vol 7 (1) ◽  
pp. e551
Author(s):  
Jennifer M. Bain ◽  
Olivia Thornburg ◽  
Cheryl Pan ◽  
Donnielle Rome-Martin ◽  
Lia Boyle ◽  
...  
Keyword(s):  
Language Impairment ◽  
De Novo ◽  
Neurodevelopmental Disorder ◽  
Retrospective Chart Review ◽  
Premature Death ◽  
Parent Report ◽  
Autism Spectrum ◽  
Pathogenic Variants ◽  
Motor Problems ◽  
Cortical Visual Impairment

ObjectiveTo expand the clinical phenotype of the X-linked HNRNPH2-related neurodevelopmental disorder in 33 individuals.MethodsParticipants were diagnosed with pathogenic or likely pathogenic variants in HNRNPH2 using American College of Medical Genetics and Genomics/Association of Molecular Pathology criteria, largely identified via clinical exome sequencing. Genetic reports were reviewed. Clinical data were collected by retrospective chart review and caregiver report including standardized parent report measures.ResultsWe expand our clinical characterization of HNRNPH2-related disorders to include 33 individuals, aged 2–38 years, both females and males, with 11 different de novo missense variants, most within the nuclear localization signal. The major features of the phenotype include developmental delay/intellectual disability, severe language impairment, motor problems, growth, and musculoskeletal disturbances. Minor features include dysmorphic features, epilepsy, neuropsychiatric diagnoses such as autism spectrum disorder, and cortical visual impairment. Although rare, we report early stroke and premature death with this condition.ConclusionsThe spectrum of X-linked HNRNPH2-related disorders continues to expand as the allelic spectrum and identification of affected males increases.

scholarly journals Varying intolerance of gene pathways to mutational classes explain genetic convergence across neuropsychiatric disorders

2016 ◽  
Author(s):  
Shahar Shohat ◽  
Eyal Ben-David ◽  
Sagiv Shifman
Keyword(s):  
Gene Expression ◽  
Genome Wide Association Study ◽  
De Novo ◽  
Expression Patterns ◽  
Neuropsychiatric Disorders ◽  
Autism Spectrum ◽  
Specific Gene ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Brain Gene Expression

AbstractGenetic susceptibility to Intellectual disability (ID), autism spectrum disorder (ASD) and schizophrenia (SCZ) often arises from mutations in the same genes, suggesting that they share common mechanisms. We studied genes with de novo mutations in the three disorders and genes implicated by SCZ genome-wide association study (GWAS). Using biological annotations and brain gene expression, we show that mutation class explains enrichment patterns more than specific disorder. Genes with loss of function mutations and genes with missense mutations were enriched with different pathways, shared with genes intolerant to mutations. Specific gene expression patterns were found for each disorder. ID genes were preferentially expressed in fetal cortex, ASD genes also in fetal cerebellum and striatum, and genes associated with SCZ were most significantly enriched in adolescent cortex. Our study suggests that convergence across neuropsychiatric disorders stems from vulnerable pathways to genetic variations, but spatiotemporal activity of genes contributes to specific phenotypes.

scholarly journals SAICAr-dependent and independent effects of ADSL deficiency on neurodevelopment

2020 ◽  
Author(s):  
Ilaria Dutto ◽  
Julian Gerhards ◽  
Antonio Herrera ◽  
Alexandra Junza ◽  
Oscar Yanes ◽  
...  
Keyword(s):  
De Novo ◽  
Autism Spectrum ◽  
Zebrafish Embryos ◽  
Biosynthesis Pathway ◽  
Purine Nucleotide ◽  
Adenylosuccinate Lyase ◽  
Dna Damage Signaling ◽  
Phenotypic Spectrum ◽  
Neurotoxic Effects ◽  
Independent Effects

AbstractAdenylosuccinate Lyase (ADSL) functions in the de novo purine biosynthesis pathway. ADSL deficiency (ADSLD) causes numerous neurodevelopmental pathologies, including microcephaly and autism spectrum disorder. ADSLD patients have normal purine nucleotide levels but exhibit accumulation of the dephosphorylated ADSL substrates SAICAr and S-Ado. SAICAr was implicated in the neurotoxic effects of ADSLD, although its role remains unknown. We examined the effects of ADSL depletion in human cells and found increased DNA damage signaling, that was rescued by nucleosides, and impaired primary ciliogenesis, that was rescued by reducing SAICAr. By analyzing ADSL deficient chicken and zebrafish embryos we observed impaired neurogenesis and microcephaly, and neuroprogenitor attrition in zebrafish was rescued by reducing SAICAr. Zebrafish embryos also displayed phenotypes commonly linked to ciliopathies. Our results suggest that both reduced purine levels and SAICAr accumulation contribute to neurodevelopmental pathology in ADSLD and defective ciliogenesis may influence the ADSLD phenotypic spectrum.

scholarly journals Novel de novo heterozygous mutation on SYNGAP1 from the Indian population

2020 ◽  
Author(s):  
Vijaya Verma ◽  
Amit Mandora ◽  
Abhijeet Botre ◽  
James Premdoss Clement
Keyword(s):  
Exome Sequencing ◽  
De Novo ◽  
Novel Mutation ◽  
Autism Spectrum ◽  
Current Treatment ◽  
Developmental Trajectory ◽  
Global Developmental Delay ◽  
Heterozygous Mutation ◽  
Specific Gene ◽  
De Novo Mutations

Abstract Background : Exome sequencing is a prominent tool to identify novel and deleterious mutations which could be nonsense, frameshift, and canonical splice-site mutations in a specific gene. De novo mutations in SYNGAP1 , which codes for synaptic RAS-GTPase activating the protein, causes Intellectual disability (ID) and Autism Spectrum Disorder (ASD). SYNGAP1 related ASD/ID is one of the rare diseases that is detrimental to the normal neuronal developmental and disrupts the global development of a child. Results: We report a case of a child of 2-year old with global developmental delay, microcephaly subtle dysmorphism, absence seizures, disrupted sleep, delay in learning a language, and eating problems. Upon further validation, the child has a few traits of ASD. Here, based on focused exome sequencing, we report a de novo heterozygous mutation in SYNGAP1 exon 11 with c. 1861 C>T (p.arg612ter). Currently, the child is on atorvastatin and has shown considerable improvement in global behaviour and cognitive development. The long-term follow up of the child’s development would contribute to the already existing knowledge of the developmental trajectory in individuals with SYNGAP1 heterozygous mutation. Conclusion: In this report, we discuss the finding of a novel mutation in one of the genes, SYNGAP1 , implicated in ASD/ID. In addition, we discuss the current treatment prescribed to the patient and the progress of global developmental of the child.

Neurodevelopmental phenotypes associated with pathogenic variants in SLC6A1

2021 ◽  
pp. jmedgenet-2021-107694
Author(s):  
Ashley Kahen ◽  
Haluk Kavus ◽  
Alexa Geltzeiler ◽  
Catherine Kentros ◽  
Cora Taylor ◽  
...  
Keyword(s):  
Developmental Delay ◽  
De Novo ◽  
Language Disorder ◽  
Synaptic Cleft ◽  
Binding Pocket ◽  
Autism Spectrum ◽  
Gamma Aminobutyric Acid ◽  
Vineland Adaptive Behavior Scales ◽  
Care Givers ◽  
Pathogenic Variants

BackgroundSLC6A1 encodes GAT-1, a major gamma-aminobutyric acid (GABA) transporter in the brain. GAT-1 maintains neurotransmitter homeostasis by removing excess GABA from the synaptic cleft. Pathogenic variants in SLC6A1 disrupt the reuptake of GABA and are associated with a neurobehavioural phenotype.MethodsMedical history interviews, seizure surveys, Vineland Adaptive Behavior Scales Second Edition and other behavioural surveys were completed by primary care givers of 28 participants in Simons Searchlight. All participants underwent clinical whole exome sequencing or gene panel sequencing. Additional cases from the medical literature with comparable data were included.ResultsWe identified 28 individuals with largely de novo pathogenic/likely pathogenic variants including missense (15/21 or 71%) and truncating variants (6/21 or 29%). Missense variants were largely clustered around the sixth and seventh transmembrane domains, which functions as a GABA binding pocket. The phenotype of individuals with pathogenic variants in SLC6A1 includes hypotonia, intellectual disability/developmental delay, language disorder/speech delay, autism spectrum disorder, sleep issues and seizures.ConclusionPathogenic variants in SLC6A1 are associated with a clinical phenotype of developmental delay, behaviour problems and seizures. Understanding of the genotype–phenotype correlation within SLC6A1 may provide opportunities to develop new treatments for GABA-related conditions.

STXBP1 encephalopathy

Neurology ◽  
2019 ◽  
Vol 93 (3) ◽  
pp. 114-123 ◽  
Author(s):  
Vanessa Lanoue ◽  
Ye Jin Chai ◽  
Julie Z. Brouillet ◽  
Sarah Weckhuysen ◽  
Elizabeth E. Palmer ◽  
...  
Keyword(s):  
Neurodegenerative Diseases ◽  
Neural Development ◽  
Early Onset ◽  
De Novo ◽  
Basic Research ◽  
Autism Spectrum ◽  
Epileptic Encephalopathy ◽  
Severe Form ◽  
Pathogenic Variants ◽  
Extrapyramidal Features

De novo pathogenic variants in STXBP1 encoding syntaxin1-binding protein (STXBP1, also known as Munc18-1) lead to a range of early-onset neurocognitive conditions, most commonly early infantile epileptic encephalopathy type 4 (EIEE4, also called STXBP1 encephalopathy), a severe form of epilepsy associated with developmental delay/intellectual disability. Other neurologic features include autism spectrum disorder and movement disorders. The progression of neurologic symptoms has been reported in a few older affected individuals, with the appearance of extrapyramidal features, reminiscent of early onset parkinsonism. Understanding the pathologic process is critical to improving therapies, as currently available antiepileptic drugs have shown limited success in controlling seizures in EIEE4 and there is no precision medication approach for the other neurologic features of the disorder. Basic research shows that genetic knockout of STXBP1 or other presynaptic proteins of the exocytic machinery leads to widespread perinatal neurodegeneration. The mechanism that regulates this effect is under scrutiny but shares intriguing hallmarks with classical neurodegenerative diseases, albeit appearing early during brain development. Most critically, recent evidence has revealed that STXBP1 controls the self-replicating aggregation of α-synuclein, a presynaptic protein involved in various neurodegenerative diseases that are collectively known as synucleinopathies, including Parkinson disease. In this review, we examine the tantalizing link among STXBP1 function, EIEE, and the neurodegenerative synucleinopathies, and suggest that neural development in EIEE could be further affected by concurrent synucleinopathic mechanisms.

scholarly journals Truncating Variant Burden in High Functioning Autism and Pleiotropic Effects of LRP1 Across Psychiatric Phenotypes

2018 ◽  
Author(s):  
Bàrbara Torrico ◽  
Alex D Shaw ◽  
Roberto Mosca ◽  
Norma Vivó-Luque ◽  
Amaia Hervás ◽  
...  
Keyword(s):  
Rare Variants ◽  
De Novo ◽  
High Functioning Autism ◽  
Meta Analysis ◽  
Autism Spectrum ◽  
Pleiotropic Effects ◽  
Psychiatric Diseases ◽  
High Functioning ◽  
Pathogenic Variants ◽  
Functional Consequences

AbstractPrevious research has implicated de novo (DN) and inherited truncating mutations in autism spectrum disorder (ASD). We aim to investigate whether the load of inherited truncating mutations contribute similarly to high functioning autism (HFA), and to characterise genes harbouring DN variants in HFA.We performed whole-exome sequencing (WES) in 20 HFA families (average IQ = 100). No difference was observed in the number of transmitted versus non-transmitted truncating alleles to HFA (117 vs 130, P = 0.32). Transmitted truncating and DN variants in HFA were not enriched in GO or KEGG categories, nor autism-related gene sets. However, in a HFA patient we identified a DN variant in a canonical splice site of LRP1, a post-synaptic density gene that is a target for the FMRP. This DN leads to in-frame skipping of exon-29, removing 2 of 6 blades of the β-propeller domain-4 of LRP1, with putative functional consequences. Results using large datasets implicate LRP1 across psychiatric diseases: i) DN are associated with ASD (P = 0.039) and schizophrenia (P = 0.008) from combined sequencing projects; ii) Common variants using Psychiatric Genomics Consortium GWAS datasets show gene-based association in schizophrenia (P = 6.6E-07) and across six psychiatric diseases (meta-analysis P = 8.1E-05); and iii) burden of ultra-rare pathogenic variants is higher in ASD (P = 1.2E-05), using WES from 6,135 schizophrenia patients, 1,778 ASD patients and 6,245 controls. Previous and current studies suggest an impact of truncating mutations restricted to severe ASD phenotypes associated with intellectual disability. We provide evidence for pleiotropic effects of common and rare variants in the LRP1 gene across psychiatric phenotypes.

scholarly journals Prevalence and Phenotypic Impact of Rare Likely Pathogenic Variants in Autism Spectrum Disorder

2020 ◽  
Author(s):  
Behrang Mahjani ◽  
Silvia De Rubeis ◽  
Christina Gustavsson Mahjani ◽  
Maureen Mulhern ◽  
Xinyi Xu ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
De Novo ◽  
Strong Association ◽  
Population Sample ◽  
Population Level ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Single Nucleotide Variants ◽  
Pathogenic Variants ◽  
Pathogenic Cnvs

Abstract Background: Copy number variants (CNVs) and single nucleotide variants (SNVs) are sources of risk for autism spectrum disorder (ASD). The distribution of such pathogenic variants in individuals with ASD and the characterization of those who carry such variants versus those who do not are understudied at the population level. We describe a population sample from Sweden, evaluating the distribution of likely pathogenic variants and their impact on medical, neurological, and psychiatric phenotypes.Methods: The genotyped sample consisted of 1,236 children born in Sweden with autistic disorder, a severe form of ASD (International Classification of Diseases, Tenth Revision, code F84.0.) Of these individuals, CNVs were called from 997, while SNVs were called from 808. Results: Out of 997 individuals from whom CNVs were called, 104 (10.4 %) carried one or more likely pathogenic CNV, including 15q11q13 (n=8), 15q13.3 (n=5), 16p13.11 (n=5), 16p11.11 (n=5), 22q11.2 (n=5). Of 808 individuals assessed by whole-exome sequencing, 69 (8.5%) had a likely pathogenic SNV, including in GRIN2B (n = 6), POGZ (n = 5), SATB1 (n=4), DYNC1H1 (n=4), and CREBBP (n=3). Fourteen individuals carried two likely pathogenic CNVs, and 5 carried a likely pathogenic CNV and SNV. Carriers of likely pathogenic CNVs or SNVs were more likely to have intellectual disability (ID), scholastic skill disorders, and epilepsy, with odds ratios of 2.31 (95%CI, 1.55,3.47), 1.98 (95%CI, 1.19,3.21), and 1.63 (95%CI, 1.08,2.44) respectively. Carriers of likely pathogenic CNVs also showed significant increased rates of congenital anomalies. We compared rates of likely pathogenic CNVs, SNVs, and phenotypes from genotyped AD subjects with and without ID: rates were not significantly different between groups. Limitations: As a case-control cohort, we did not have de novo information to aid in classification. More broadly, there were judgment calls involved in identifying likely pathogenic variants. For these reasons, some misclassification is possible. In addition, phenotypes are defined from medical registers, which may lead to underestimates of milder findings.Conclusions: People with ASD who carry likely pathogenic CNVs or SNVs show increased rates of various comorbidities, most prominently ID. Despite the strong association with ID, conditioning on its presence explains little of the variation for other comorbidities and physical traits.

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