Variant ID 639
Entrez Gene ID 6323
Gene SCN1A (GeneCards)
Location hg19 2:166911148-166911148
hg38 2:166054638-166054638
Disease Autism Spectrum Disorders (view all the variants in this disease)
Method HiSeq 2000
Mutation(HGVS format) NC_000002.11:g.166911148 C>T (Genome Assembly: hg19)

Other information

Exon or Intron NA
Position in protein NA
Amino acid changes in protein NA > NA
Position in cDNA 602
Changes in cDNA G > A
mRNA accession NM_001202435.1
mRNA length 8426
Reference length 243199373

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
EIGEN score 0.994
CADD Raw score (version 1.3) 5.774528 (Deleterious)
FATHMM raw prediction score 0.99103 (Tolerated)
SIFT score 0 (Deleterious)
LRT score 0 (Deleterious)
MutationTaster score 1 (Deleterious)
MutatioinAssessor score 2.96 (Deleterious)
PROVEAN score -4.84 (Deleterious)
MetaSVM score 1.081 (Deleterious)
MetaLR score 0.977 (Deleterious)
MCAP score 0.956 (Deleterious)
FitCons score 0.487 (Highly Significant p < 0.003 )
Genomic Evolutionary Rate Profiling (GERP) score 5.24
PhyloP score based on multiple alignment of 100 vertebrates 9.999
PhastCons score based on multiple alignment of 100 vertebrates 1
SiPhy log transformed odds ratio on multiple alignment of 29 mammals 19.174
Deleterious probability by DeFine 0.94 (Deleterious)
Entrez Gene ID 6323 (NCBI Gene)
Official Gene Symbol SCN1A (GeneCards)
Number of variants in SCN1A in this database 187 (view all the variants)
Full name sodium voltage-gated channel alpha subunit 1
Band 2q24.3
Other IDs Vega: OTTHUMG00000044173
OMIM: 182389
HGNC: HGNC:10585
Ensembl: ENSG00000144285
Other names FEB3, FHM3, NAC1, SCN1, SMEI, EIEE6, FEB3A, HBSCI, GEFSP2, Nav1.1
Summary Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodium channel alpha subunit, which has four homologous domains, each of which contains six transmembrane regions. Allelic variants of this gene are associated with generalized epilepsy with febrile seizures and epileptic encephalopathy. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript. [provided by RefSeq, Oct 2015]

Individual #1

Individual ID 26637798.01 (view all the variants in this individual)
Pubmed ID 26637798
Whose mosaic mutation Female Patient  
Phenotype 3  
Disease Autism Spectrum Disorders (view all the variants in this disease)
OMIM ID 209850

Publication #1: 26637798

Pubmed ID 26637798
Title Targeted DNA Sequencing from Autism Spectrum Disorder Brains Implicates Multiple Genetic Mechanisms.
Journal Neuron
Publication date 2015.12
Disease Autism Spectrum Disorders
Number of cases Male cases: 1; Female cases: 1;