Developmental Brain Disorder Gene Database

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Missense

SCN1A

HGNC:10585 (protein-coding gene)

sodium voltage-gated channel alpha subunit 1

Unique Cases:
151
Disorders:
ID, ASD, EP, CP
Last Updated:
January 4, 2024

Summary
Cases
Publications
External

Gene Summary:

Gene Function
Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient (PubMed:14672992). Plays a key role in brain, probably by regulating the moment when neurotransmitters are released in neurons. Involved in sensory perception of mechanical pain: activation in ... (Source: Uniprot)
Previous symbols
SCN1, FEB3
Alias symbols
Nav1.1, GEFSP2, HBSCI, NAC1, SMEI
Chromosomal Location
2q24.3
Genomic Coordinates
GRCh37:chr2:166845670-167005642
GRCh38:chr2:165984641-166149161
Associated Disorders
Intellectual Disability, Autism, Epilepsy, Cerebral Palsy

Predictive Scores:

HI Score (Decipher)

9.08

pLI (gnomAD)

1.00

LOEUF (gnomAD)

0.07

Classifications from External Sources:

SFARI Score (SFARI)

1

DDG2P Classification (DDG2P)

No Classification

ClinGen Classification (ClinGen)

Strong1

Definitive2

Moderate1

GenCC Classification (GenCC)

Definitive6 Moderate2 Strong5 Supportive6

Publications:

Kang KW et. al., Genetic characteristics of non-familial epilepsy., PeerJ, 2019
Benson KA et. al., A comparison of genomic diagnostics in adults and children with epilepsy and comorbid intellectual disability., Eur J Hum Genet, 2020
Snoeijen-Schouwenaars FM et. al., Diagnostic exome sequencing in 100 consecutive patients with both epilepsy and intellectual disability., Epilepsia, 2019
Demos M et. al., Diagnostic Yield and Treatment Impact of Targeted Exome Sequencing in Early-Onset Epilepsy., Front Neurol, 2019
Costain G et. al., Clinical Application of Targeted Next-Generation Sequencing Panels and Whole Exome Sequencing in Childhood Epilepsy., Neuroscience, 2019
Ostrander BEP et. al., Whole-genome analysis for effective clinical diagnosis and gene discovery in early infantile epileptic encephalopathy., NPJ Genom Med, 2018
Xie H et. al., De novo SCN1A, SCN8A, and CLCN2 mutations in childhood absence epilepsy., Epilepsy Res, 2019
Papuc SM et. al., The role of recessive inheritance in early-onset epileptic encephalopathies: a combined whole-exome sequencing and copy number study., Eur J Hum Genet, 2019
Arafat A et. al., Unexplained Early Infantile Epileptic Encephalopathy in Han Chinese Children: Next-Generation Sequencing and Phenotype Enriching., Sci Rep, 2017
Kothur K et. al., Diagnostic yield of targeted massively parallel sequencing in children with epileptic encephalopathy., Seizure, 2018
Stojanovic JR et. al., Diagnostic and Clinical Utility of Clinical Exome Sequencing in Children With Moderate and Severe Global Developmental Delay / Intellectual Disability., J Child Neurol, 2020
Kim SY et. al., Dissecting the phenotypic and genetic spectrum of early childhood-onset generalized epilepsies., Seizure, 2019
Wang Y et. al., Genetic Variants Identified from Epilepsy of Unknown Etiology in Chinese Children by Targeted Exome Sequencing., Sci Rep, 2017
Long S et. al., The Clinical and Genetic Features of Co-occurring Epilepsy and Autism Spectrum Disorder in Chinese Children., Front Neurol, 2019
Sahli M et. al., Clinical exome sequencing identifies two novel mutations of the SCN1A and SCN2A genes in Moroccan patients with epilepsy: a case series., J Med Case Rep, 2019
Fernández-Marmiesse A et. al., Rare Variants in 48 Genes Account for 42% of Cases of Epilepsy With or Without Neurodevelopmental Delay in 246 Pediatric Patients., Front Neurosci, 2019
Balicza P et. al., Comprehensive Analysis of Rare Variants of 101 Autism-Linked Genes in a Hungarian Cohort of Autism Spectrum Disorder Patients., Front Genet, 2019
Chérot E et. al., Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients., Clin Genet, 2018
Ko A et. al., Targeted gene panel and genotype-phenotype correlation in children with developmental and epileptic encephalopathy., Epilepsy Res, 2018
Balciuniene J et. al., Use of a Dynamic Genetic Testing Approach for Childhood-Onset Epilepsy., JAMA Netw Open, 2019
Takata A et. al., Comprehensive analysis of coding variants highlights genetic complexity in developmental and epileptic encephalopathy., Nat Commun, 2019
Chan CK et. al., Whole exome sequencing identifies a novel SCN1A mutation in genetic (idiopathic) generalized epilepsy and juvenile myoclonic epilepsy subtypes., Neurol Sci, 2020
Arteche-López A et. al., Towards a Change in the Diagnostic Algorithm of Autism Spectrum Disorders: Evidence Supporting Whole Exome Sequencing as a First-Tier Test., Genes (Basel), 2021
Salinas V et. al., Clinical next generation sequencing in developmental and epileptic encephalopathies: Diagnostic relevance of data re-analysis and variants re-interpretation., Eur J Med Genet, 2021
Zaganas I et. al., Genetic cause of epilepsy in a Greek cohort of children and young adults with heterogeneous epilepsy syndromes., Epilepsy Behav Rep, 2021
Mei H et. al., Genetic Spectrum Identified by Exome Sequencing in a Chinese Pediatric Cerebral Palsy Cohort., J Pediatr, 2022
Suzuki T et. al., A recurrent PJA1 variant in trigonocephaly and neurodevelopmental disorders., Ann Clin Transl Neurol, 2020
Atlı E et. al., Investigation of the Genetic Etiology in Idiopathic Generalized Epileptic Disorders by Targeted Next-Generation Sequencing Technique., Balkan Med J, 2022
Varesio C et. al., Diagnostic Yield and Cost-Effectiveness of "Dynamic" Exome Analysis in Epilepsy with Neurodevelopmental Disorders: A Tertiary-Center Experience in Northern Italy., Diagnostics (Basel), 2021

NCBI: Gene

Integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
NCBI: Gene

Gene Reviews

An international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families.
Gene Reviews

DECIPHER

DECIPHER (DatabasE of genomiC varIation and Phenotype in Humans using Ensembl Resources) is an interactive web-based database which incorporates a suite of tools designed to aid the interpretation of genomic variants. DECIPHER enhances clinical diagnosis by retrieving information from a variety of bioinformatics resources relevant to the variant found in the patient.
DECIPHER

SFARI

SFARI Gene is an evolving online database designed to permit quick entrée into the genetics of autism, and to help researchers track the ever-expanding genetic risk factors that emerge in the literature.
SFARI

ClinGen

ClinGen is a National Institutes of Health (NIH)-funded resource dedicated to building an authoritative central resource that defines the clinical relevance of genes and variants for use in precision medicine and research.
ClinGen

GenCC

The GenCC DB provides information pertaining to the validity of gene-disease relationships, with a current focus on Mendelian diseases.
GenCC

gnomAD

The Genome Aggregation Database (gnomAD) is a resource developed by an international coalition of investigators, with the goal of aggregating and harmonizing both exome and genome sequencing data from a wide variety of large-scale sequencing projects, and making summary data available for the wider scientific community.
gnomAD
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