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Scn3a Gene Detail
Summary
  • Symbol
    Scn3a
  • Name
    sodium channel, voltage-gated, type III, alpha
  • Synonyms
    LOC381367, Nav1.3
  • Feature Type
    protein coding gene
  • IDs
    MGI:98249
    NCBI Gene: 20269
  • Alliance
    genome feature page
  • Transcription Start Sites
    6 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:65288607-65397971 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 2, 38.55 cM
  • Mapping Data
    11 experiments
Strain
Comparison
more
  • SNPs within 2kb
    2987 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_98249
 protein coding gene Chr2:65287462-65397971 (-)
129S1/SvImJ ENSMUSG00200035958
 protein coding gene Chr2:62360078-62439908 (-)
A/J ENSMUSG00195020342
 protein coding gene Chr2:62490726-62570817 (-)
AKR/J ENSMUSG00220034013
 protein coding gene Chr2:62443181-62523265 (-)
BALB/cJ ENSMUSG00180039292
 protein coding gene Chr2:62436102-62515923 (-)
C3H/HeJ ENSMUSG00175032801
 protein coding gene Chr2:62501262-62581358 (-)
C57BL/6NJ ENSMUSG00215028568
 protein coding gene Chr2:62381972-62461797 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0023601
 protein coding gene Chr2:60120291-60234259 (-)
CAST/EiJ ENSTCUG00005008292
 protein coding gene Chr2:61805668-61885041 (-)
CBA/J ENSMUSG00210031284
 protein coding gene Chr2:62538674-62618772 (-)
DBA/2J ENSMUSG00185036975
 protein coding gene Chr2:62411107-62496515 (-)
FVB/NJ ENSMUSG00205029525
 protein coding gene Chr2:61930414-62010517 (-)
JF1/MsJ ENSUMUG00000005161
 protein coding gene Chr2:62082140-62161875 (-)
LP/J ENSMUSG00230019139
 protein coding gene Chr2:64243888-64323698 (-)
NOD/ShiLtJ ENSMUSG00190027819
 protein coding gene Chr2:62485237-62564584 (-)
NZO/HlLtJ ENSMUSG00225015207
 protein coding gene Chr2:71973200-72053288 (-)
PWK/PhJ ENSLUMG00010032633
 protein coding gene Chr2:62240104-62320395 (-)
SPRET/EiJ ENSMSPG00010030372
 protein coding gene Chr2:63531706-63642851 (-)
WSB/EiJ ENSIUOG00005018152
 protein coding gene Chr2:62535416-62621556 (-)



Homology
more
  • Human Ortholog
    SCN3A, sodium voltage-gated channel alpha subunit 3
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SCN3A, sodium voltage-gated channel alpha subunit 3
  • Synonyms
    DEE62, EIEE62, FFEVF4, NAC3, Nav1.3
  • Links
    NCBI Gene ID: 6328
    UniProt: Q9NY46

  • Chr Location
    2q24.3; chr2:165087526-165204050 (-)  GRCh38
Human Diseases
more
  • Diseases
    2 with human SCN3A associations

Human Disease Mouse Models
      
IDs
IDs
Click on a disease name to see all genes associated with that disease.

Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    6 phenotypes from 3 alleles in 3 genetic backgrounds
    17 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 mutation of this gene results in lethality of most mutants by weaning. Heterozygous mice exhibit improved glucose tolerance.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    38
  • GO References
    12
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
    630
  • Tissues
    11
  • cDNA Data
    22
  • Literature Summary
    6
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000057182 Ensembl Gene Model | MGI Sequence Detail 109365 C57BL/6J ±  kb
    transcript ENSMUST00000100069 Ensembl | MGI Sequence Detail 8550 Not Applicable  
    polypeptide ENSMUSP00000097647 Ensembl | MGI Sequence Detail 1947 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      11 Sequences
    • Protein Ontology
      PR:000002099 sodium channel protein type 3 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
      IPR001696 Voltage gated sodium channel, alpha subunit
      IPR044564 Voltage-gated sodium channel alpha subunit, inactivation gate
    • GlyGen
      A2ASI5 10 sites, 5 N-linked glycans (3 sites)
    Molecular
    Reagents
    less
    • All nucleic 32
      cDNA 23
      Primer pair 9

      Microarray probesets 5
    Other
    Accession IDs
    less
    MGD-MRK-14322, MGI:2685846
    References
    more
    • Summaries
      All 72
      Developmental Gene Expression 6
      Gene Ontology 12
      Phenotypes 17
    • 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:362505 Ambroziak W, et al., Thermally induced neuronal plasticity in the hypothalamus mediates heat tolerance. Nat Neurosci. 2025 Feb;28(2):346-360
    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)
    Citing These Resources
    Funding Information
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    Send questions and comments to User Support.     		last database update
    09/01/2026
    MGI 6.24     		The Jackson Laboratory