Variant ID 445
Entrez Gene ID 6323
Gene SCN1A (GeneCards)
Location hg19 2:166901591-166901591
hg38 2:166045081-166045081
Disease Severe myoclonic epilepsy of infancy (view all the variants in this disease)
Method TaqMAMA
Mutation(HGVS format) NC_000002.11:g.166901591 G>A (Genome Assembly: hg19)

Other information

Exon or Intron Exon
Exon number 10
Position in protein 542
Amino acid changes in protein R > Z
Position in cDNA 1624
Changes in cDNA C > T
mRNA accession NM_001202435.1
mRNA length 6030
Reference length 243199373

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
Variant IDs in COSMIC (version 89) 1264980
Variant occurences in COSMIC 1(oesophagus)
EIGEN score -0.162
CADD Raw score (version 1.3) 6.224617 (Deleterious)
FATHMM raw prediction score 0.95144 (Tolerated)
LRT score 0.001 (Deleterious)
MutationTaster score 1 (Deleterious)
FitCons score 0.56 (Highly Significant p < 0.003 )
Genomic Evolutionary Rate Profiling (GERP) score -1.05
PhyloP score based on multiple alignment of 100 vertebrates 2.218
PhastCons score based on multiple alignment of 100 vertebrates 0.979
SiPhy log transformed odds ratio on multiple alignment of 29 mammals 21.227
Deleterious probability by DeFine 0.8045 (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 16541393.01 (view all the variants in this individual)
Pubmed ID 16541393
Whose mosaic mutation Mother  
Phenotype 1  
Number of affected children 2 ( male: 1; female: 1; )
Disease Severe myoclonic epilepsy of infancy (view all the variants in this disease)
OMIM ID 607208

Publication #1: 16541393

Pubmed ID 16541393
Title Parental mosaicism can cause recurrent transmission of SCN1A mutations associated with severe myoclonic epilepsy of infancy
Journal Human Mutation
Publication date 2006.04
Disease Severe myoclonic epilepsy of infancy
Number of cases Male cases: 1; Female cases: 1;