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Scn1a Gene Detail
Summary
  • Symbol
    Scn1a
  • Name
    sodium channel, voltage-gated, type I, alpha
  • Synonyms
    Nav1.1
  • Feature Type
    protein coding gene
  • IDs
    MGI:98246
    NCBI Gene: 20265
  • Alliance
    genome feature page
  • Transcription Start Sites
    6 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:66101125-66271181 bp, - strand
    From NCBI annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 2, 39.13 cM
  • Mapping Data
    7 experiments
Strain
Comparison
more
  • SNPs within 2kb
    4703 from dbSNP Build 142
  • Strain Annotations
    19
  • RFLP
    1
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_98246
 protein coding gene Chr2:66101122-66271184 (-)
129S1/SvImJ ENSMUSG00200036558
 protein coding gene Chr2:63176336-63256685 (-)
A/J ENSMUSG00195019791
 protein coding gene Chr2:63297749-63378230 (-)
AKR/J ENSMUSG00220036017
 protein coding gene Chr2:63251960-63332425 (-)
BALB/cJ ENSMUSG00180037174
 protein coding gene Chr2:63256591-63337060 (-)
C3H/HeJ ENSMUSG00175037068
 protein coding gene Chr2:63333053-63413445 (-)
C57BL/6NJ ENSMUSG00215027509
 protein coding gene Chr2:63196057-63276509 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0023606
 protein coding gene Chr2:60907116-61060205 (-)
CAST/EiJ ENSTCUG00005009075
 protein coding gene Chr2:62603024-62684380 (-)
CBA/J ENSMUSG00210031675
 protein coding gene Chr2:63376052-63456428 (-)
DBA/2J ENSMUSG00185039906
 protein coding gene Chr2:63231584-63312014 (-)
FVB/NJ ENSMUSG00205033456
 protein coding gene Chr2:62736690-62817136 (-)
JF1/MsJ ENSUMUG00000005397
 protein coding gene Chr2:62911511-62990248 (-)
LP/J ENSMUSG00230022505
 protein coding gene Chr2:65057787-65138238 (-)
NOD/ShiLtJ ENSMUSG00190035285
 protein coding gene Chr2:63295290-63375720 (-)
NZO/HlLtJ ENSMUSG00225015187
 protein coding gene Chr2:72780296-72860726 (-)
PWK/PhJ ENSLUMG00010031061
 protein coding gene Chr2:63056397-63137333 (-)
SPRET/EiJ ENSMSPG00010031104
 protein coding gene Chr2:64369157-64504126 (-)
WSB/EiJ ENSIUOG00005018066
 protein coding gene Chr2:63356488-63436791 (-)



Homology
more
  • Human Ortholog
    SCN1A, sodium voltage-gated channel alpha subunit 1
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SCN1A, sodium voltage-gated channel alpha subunit 1
  • Synonyms
    DEE6, DEE6A, DEE6B, DRVT, EIEE6, FEB3, FEB3A, FHM3, GEFSP2, HBSCI, NAC1, Nav1.1, SCN1, SMEI
  • Links
    NCBI Gene ID: 6323
    UniProt: P35498

  • Chr Location
    2q24.3; chr2:165984641-166182806 (-)  GRCh38
Human Diseases
more
  • Diseases
    3 with Scn1a mouse models; 5 with human SCN1A associations

Human Disease Mouse Models
      
IDs
 View 8 models
IDs
 View 5 models
      
IDs
 View 2 models
      
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    7 with disease annotations
  • References
    10 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    83 phenotypes from 12 alleles in 20 genetic backgrounds
    11 phenotypes from multigenic genotypes
    1 images
    181 phenotype references
Phenotype Overview

adipose tissue
behavior/neurological
cardiovascular system
cellular
craniofacial
digestive/alimentary system
embryo
endocrine/exocrine glands
growth/size/body
hearing/vestibular/ear
hematopoietic system
homeostasis/metabolism
integument
immune system
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
neoplasm
vision/eye

Click cells to view annotations.
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. Heterozygosity for a human familial hemiplegic migraine type 3 (FHM3) associated mutation leads to cortical spreading depolarization (CSD) and is lethal in juveniles and young adults.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    67
  • GO References
    18
Molecular Function

carbohydrate derivative binding
cytoskeletal protein binding
DNA binding
enzyme regulator
hydrolase
ligase
lipid binding
oxidoreductase
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell differentiation
cell population proliferation
cellular component organization
DNA-templated transcription
establishment of localization
homeostatic process
immune system process
lipid metabolic process
programmed cell death
protein metabolic process
response to stimulus
signaling
system development
Cellular Component

cell projection
cytoplasmic vesicle
cytoskeleton
cytosol
endoplasmic reticulum
endosome
extracellular region
Golgi apparatus
mitochondrion
membraneless organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
protein-containing complex
synapse
vacuole
Click cells to view annotations.
Expression
less
Expression Overview

early conceptus
embryo ectoderm
embryo endoderm
embryo mesoderm
embryo mesenchyme
extraembryonic component
alimentary system
auditory system
branchial arches
cardiovascular system
connective tissue
endocrine system
exocrine system
hemolymphoid system
integumental system
limbs
liver and biliary system
musculoskeletal system
nervous system
olfactory system
reproductive system
respiratory system
urinary system
visual system
Click cells to view annotations.


  • Assay Results
    631
  • Tissues
    16
  • cDNA Data
    7
  • Literature Summary
    9
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 20265 NCBI Gene Model | MGI Sequence Detail 170057 C57BL/6J ±  kb
    transcript NM_001313997 RefSeq | MGI Sequence Detail 8320 ZRU/MplStud  
    polypeptide A2APX8 UniProt | EBI | MGI Sequence Detail 2009 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      7 Sequences
    • Protein Ontology
      PR:000002095 sodium channel protein type 1 subunit alpha
      (term hierarchy)
    • InterPro Domains
      IPR005821 Ion transport domain
      IPR058542 SCN5A-like, C-terminal IQ motif
      IPR010526 Sodium ion transport-associated domain
      IPR027359 Voltage-dependent channel domain superfamily
      IPR043203 Voltage-gated cation channel calcium and sodium
      IPR024583 Voltage-gated Na+ ion channel, cytoplasmic domain
      IPR008051 Voltage gated sodium channel, alpha-1 subunit
      IPR001696 Voltage gated sodium channel, alpha subunit
      IPR044564 Voltage-gated sodium channel alpha subunit, inactivation gate
    • GlyGen
      A2APX8 11 sites, 6 N-linked glycans (6 sites), 1 O-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 17
      cDNA 9
      Primer pair 7
      Other 1

      Microarray probesets 6
    Other
    Accession IDs
    less
    MGD-MRK-14319
    References
    more
    • Summaries
      All 269
      Developmental Gene Expression 9
      Diseases 10
      Gene Ontology 18
      Phenotypes 181
    • 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:392461 Huang Y, et al., cGAS-mediated type I IFN signaling contributes to disease progression in drug-refractory epilepsy. Nat Neurosci. 2026 Sep;29(9):2124-2138
    Contributing Projects:
    Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/15/2026
    MGI 6.29     		The Jackson Laboratory