Variant ID 129
Entrez Gene ID 6323
Gene SCN1A (GeneCards)
Location hg19 2:166850661-166850661
hg38 2:165994151-165994151
Disease GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS; TYPE 2 (view all the variants in this disease)
Method ABI3730
Mutation(HGVS format) NC_000002.11:g.166850661 A>G (Genome Assembly: hg19)

Other information

Exon or Intron Exon
Position in protein 1616
Amino acid changes in protein I > T
Position in cDNA 4847
Changes in cDNA T > C
mRNA accession NM_001202435.1
mRNA length 6030
Reference length 243199373

Annotations and predictions

MAF in gnomAD genome (version 2.0.1) 0
EIGEN score 1.0038
CADD Raw score (version 1.3) 6.033221 (Deleterious)
FATHMM raw prediction score 0.98888 (Tolerated)
SIFT score 0 (Deleterious)
LRT score 0 (Deleterious)
MutationTaster score 1 (Deleterious)
MutatioinAssessor score 3.895 (Deleterious)
PROVEAN score -4.11 (Deleterious)
MetaSVM score 1.073 (Deleterious)
MetaLR score 0.977 (Deleterious)
MCAP score 0.943 (Deleterious)
FitCons score 0.487 (Highly Significant p < 0.003 )
Genomic Evolutionary Rate Profiling (GERP) score 5.9
PhyloP score based on multiple alignment of 100 vertebrates 9.218
PhastCons score based on multiple alignment of 100 vertebrates 1
SiPhy log transformed odds ratio on multiple alignment of 29 mammals 16.332
Deleterious probability by iFish2 0.6559 (Deleterious)
Deleterious probability by DeFine 0.9287 (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 22151702.01 (view all the variants in this individual)
Pubmed ID 22151702
Whose mosaic mutation Father  
Phenotype 1  
Number of affected children 2 ( male: 2; )
Disease GENERALIZED EPILEPSY WITH FEBRILE SEIZURES PLUS; TYPE 2 (view all the variants in this disease)
OMIM ID 604403

Publication #1: 22151702

Pubmed ID 22151702
Title Mosaic SCN1A mutations in familial partial epilepsy with antecedent febrile seizures
Journal Genes Brain and Behaviour
Publication date 2012.05
Disease Familial temporal lobe Epilepsy1
Number of cases Male cases: 2;