Variant ID 30223
Entrez Gene ID 6323
Gene SCN1A (GeneCards)
Location hg19 2:166848437-166848437
hg38 2:165991927-165991927
Disease Dravet syndrome (view all the variants in this disease)
Method smMIP
Mutation(HGVS format) NC_000002.11:g.166848437 G>A (Genome Assembly: hg19)

Other information

Exon or Intron Exon
Position in protein 1783
Amino acid changes in protein A > V
Position in cDNA 5348
Changes in cDNA C > T
mRNA accession NM_001165963.1
mRNA length NA
Reference length 243199373

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
SNP ID (dbSNP ID version 137) rs121917921
Variant IDs in COSMIC (version 89) 1153520
Variant occurences in COSMIC 2(large_intestine)|1(endometrium)
EIGEN score 1.0233
CADD Raw score (version 1.3) 5.345563 (Deleterious)
FATHMM raw prediction score 0.99483 (Tolerated)
SIFT score 0 (Deleterious)
LRT score 0 (Deleterious)
MutationTaster score 1 (Deleterious)
MutatioinAssessor score 3.32 (Deleterious)
PROVEAN score -3.68 (Deleterious)
MetaSVM score 1.047 (Deleterious)
MetaLR score 0.985 (Deleterious)
MCAP score 0.962 (Deleterious)
FitCons score 0.487 (Highly Significant p < 0.003 )
Genomic Evolutionary Rate Profiling (GERP) score 5.69
PhyloP score based on multiple alignment of 100 vertebrates 9.926
PhastCons score based on multiple alignment of 100 vertebrates 1
SiPhy log transformed odds ratio on multiple alignment of 29 mammals 19.823
Deleterious probability by iFish2 0.4272 (Neutral)
Deleterious probability by DeFine 0.9507 (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 29460957.04 (view all the variants in this individual)
Pubmed ID 29460957
Whose mosaic mutation Female Patient  
Origin of mosaic mutation in patients de novo
Phenotype 3  
Disease Dravet syndrome (view all the variants in this disease)
OMIM ID 604403

Publication #1: 29460957

Pubmed ID 29460957
Title Mosaicism of de novo pathogenic SCN1A variants in epilepsy is a frequent phenomenon that correlates with variable phenotypes
Journal Epilepsia
Publication date 2018.01
Disease SCN1A related epileptic encephalopathy
Number of cases Male cases: 7; Female cases: 3;