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Gene Detail
sodium channel, voltage-gated, type I, alpha
Synonyms Nav1.1
Feature Type protein coding gene
Genetic Map
Chromosome 2
39.13 cM
Detailed Genetic Map ± 1 cM

Mapping data(7)
Sequence Map
Chr2:66270781-66440840 bp, - strand
From VEGA annotation of GRCm38

  170060 bp   ±  kb flank

VEGA Genome Browser | Ensembl Genome Browser | UCSC Browser | NCBI Map Viewer

Mouse Genome Browser
HomoloGene:21375  Vertebrate Homology Class
1 human; 1 mouse; 1 rat; 1 chimpanzee; 1 rhesus macaque; 1 cattle; 1 dog; 1 chicken

Protein SuperFamily: voltage-gated sodium channel
Gene Tree: Scn1a

Human Homolog SCN1A, sodium channel, voltage-gated, type I, alpha subunit
NCBI Gene ID 6323
neXtProt AC  NX_P35498
Human Synonyms  EIEE6, FEB3, FEB3A, FHM3, GEFSP2, HBSCI, NAC1, Nav1.1, SCN1, SMEI
Human Chr (Location)  2q24.3; chr2:165989160-166149132 (-)  GRCh38
Disease Associations  (3) Diseases Associated with Human SCN1A
alleles, and
All mutations/alleles(11) : Gene trapped(1) Targeted(10)
Incidental mutations (data from Mutagenetix , APF )
Homozygous null mice show postnatal lethality, seizures and behavioral deficits whereas heterozygotes die prematurely with seizures and abnormal electrophysiology. In addition, knock-in mice exhibit increased susceptibility to febrile and flurothyl-induced seizures, and reduced inhibitory signaling.
Human Diseases Modeled Using Mouse Scn1a (2)    Alleles Annotated to Human Diseases(6)    Phenotype Images(1)
Scn1a interacts with 404 markers (Mir1b, Mir7-1, Mir9-1, ...)
Gene Ontology
All GO classifications: (35 annotations)
Process action potential, adult walking behavior, ...
Component axon, axon initial segment, ...
Function potassium channel activity, sodium channel activity, ...
This is a GO Consortium Reference Genome Project gene.
External Resources: FuncBase
Literature Summary: (5 records)
Data Summary: Results (26)    Tissues (10)    Images (3)
Theiler Stages: 11, 13, 21, 23, 25, 27, 28
Assay TypeResults
RNA in situ 2
cDNA source data(6)
External Resources: Allen Institute   GEO   Expression Atlas
All nucleic(16) cDNA(8) Primer pair(7) Other(1)
Microarray probesets(6)
Other database
VEGA Gene ModelOTTMUSG00000013102 (Evidence)
Ensembl Gene ModelENSMUSG00000064329 (Evidence)
Entrez Gene20265 (Evidence)
DFCITC1590622, TC1613503, TC1634626, TC1639686, TC1647388, TC1652041
DoTSDT.101332726, DT.101721090, DT.40167515, DT.55212830, DT.94170918
NIA Mouse Gene IndexU022695
Consensus CDS ProjectCCDS38131.1
International Mouse Knockout Project StatusScn1a
Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000013102 VEGA Gene Model | MGI Sequence Detail 170060 C57BL/6J ±  kb
transcript OTTMUST00000031616 VEGA | MGI Sequence Detail 8386 Not Applicable 
polypeptide OTTMUSP00000014085 VEGA | MGI Sequence Detail 2009 Not Applicable 

For the selected sequences
All sequences(64) RefSeq(8) UniProt(8)
Polymorphisms RFLP(1) : SNPs within 2kb(725 from dbSNP Build 137)
InterPro IPR024583 Domain of unknown function DUF3451
InterPro IPR005821 Ion transport domain
InterPro IPR000048 IQ motif, EF-hand binding site
InterPro IPR010526 Sodium ion transport-associated
InterPro IPR003091 Voltage-dependent potassium channel
InterPro IPR027359 Voltage-dependent potassium channel, four helix bundle domain
InterPro IPR008051 Voltage gated sodium channel, alpha-1 subunit
InterPro IPR001696 Voltage gated sodium channel, alpha subunit
Protein Ontology PR:000002095 sodium channel protein type 1 subunit alpha
References (Earliest) J:11420 Malo D, et al., Three brain sodium channel alpha-subunit genes are clustered on the proximal segment of mouse chromosome 2. Genomics. 1991 Jul;10(3):666-72
(Latest) J:205479 Mistry AM, et al., Strain- and age-dependent hippocampal neuron sodium currents correlate with epilepsy severity in Dravet syndrome mice. Neurobiol Dis. 2014 Jan 14;65C:1-11
All references(64)
Disease annotation references (7)
accession IDs

Contributing Projects:
Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Tumor Biology (MTB), Gene Ontology (GO), MouseCyc
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last database update
MGI 5.19
The Jackson Laboratory