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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
  • Gene Overview
    MyGene.info: SCN1A
Location & Maps
more
  • Sequence Map
    Chr2:66270778-66440840 bp, - strand
  • From VEGA annotation of GRCm38

    Mouse Genome Browser

  • Download
    Sequence
      170063 bp   ±  kb flank

  • Genome Browsers
  • Genetic Map
    Chromosome 2, 39.13 cM
  • Mapping Data
    7 experiments
Homology
more
  • Human Ortholog
    SCN1A, sodium voltage-gated channel alpha subunit 1
  • Vertebrate Orthologs
    8
  • Human Ortholog
    SCN1A, sodium voltage-gated channel alpha subunit 1
    Orthology source: HomoloGene, HGNC
  • Synonyms
    EIEE6, FEB3, FEB3A, FHM3, GEFSP2, HBSCI, NAC1, Nav1.1, SCN1, SMEI
  • Links
    NCBI Gene ID: 6323
    neXtProt AC: NX_P35498

  • Chr Location
    2q24.3; chr2:165989160-166149272 (-)  GRCh38.p2

Human Diseases
more
  • Diseases
    2 with Scn1a mouse models; 3 with human SCN1A associations

Human Disease Mouse Models
       Epileptic Encephalopathy, Early Infantile, 6; EIEE6   OMIM: 607208 View 7 models
       Generalized Epilepsy with Febrile Seizures Plus, Type 1; GEFSP1   OMIM: 604233 View 4 models
       Generalized Epilepsy with Febrile Seizures Plus, Type 2; GEFSP2   OMIM: 604403
Migraine, Familial Hemiplegic, 3; FHM3   OMIM: 609634
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    7 with disease annotations
  • References
    12 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    56 phenotypes from 9 alleles in 15 genetic backgrounds
    11 phenotypes from multigenic genotypes
    1 images
    32 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.
  • All Mutations and Alleles
    14
  • Chemically induced (other)
    1
  • Gene trapped
    1
  • Targeted
    12
  • Genomic Mutations
    1 involving Scn1a
  • Incidental Mutations
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.
Gene Ontology
(GO)
Classifications
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  • All GO Annotations
  • GO References
Molecular Function

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

nucleic acid-templated transcription
carbohydrate derivative metabolism
cell death
cell differentiation
cell proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
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
non-membrane-bounded organelle
nucleus
organelle envelope
organelle lumen
plasma membrane
synapse
vacuole
Click cells to view annotations.
Expression
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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
  • Tissues
  • cDNA Data
  • Literature Summary
Interactions
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Sequences &
Gene Models
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Representative SequencesLengthStrain/SpeciesFlank
genomic OTTMUSG00000013102 VEGA Gene Model | MGI Sequence Detail 170063 C57BL/6J ±  kb
transcript OTTMUST00000031616 VEGA | MGI Sequence Detail 8386 Not Applicable  
polypeptide OTTMUSP00000014085 VEGA | MGI Sequence Detail 2009 Not Applicable  
For the selected sequence
Polymorphisms
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  • SNPs within 2kb
    717 from dbSNP Build 142
  • RFLP
Protein
Information
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  • UniProt
    9 Sequences
  • InterPro Domains
    IPR005821 Ion transport domain
    IPR010526 Sodium ion transport-associated
    IPR027359 Voltage-dependent channel, four helix bundle domain
    IPR024583 Voltage-gated Na+ ion channel, cytoplasmic domain
    IPR028325 Voltage-gated potassium channel
    IPR008051 Voltage gated sodium channel, alpha-1 subunit
    IPR001696 Voltage gated sodium channel, alpha subunit
Molecular
Reagents
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  • All nucleic 16
    cDNA 8
    Primer pair 7
    Other 1

    Microarray probesets 6
Other
Accession IDs
less
MGD-MRK-14319
References
more
  • Summaries
    All 72
    Developmental Gene Expression 5
    Diseases 12
    Gene Ontology 14
    Phenotypes 32
  • 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:235304 Osteen JD, et al., Selective spider toxins reveal a role for the Nav1.1 channel in mechanical pain. Nature. 2016 Jun 23;534(7608):494-9

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
11/29/2016
MGI 6.06
The Jackson Laboratory