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Scn2a Gene Detail
Summary
  • Symbol
    Scn2a
  • Name
    sodium channel, voltage-gated, type II, alpha
  • Synonyms
    A230052E19Rik, Nav1.2, Scn2a1
  • Feature Type
    protein coding gene
  • IDs
    MGI:98248
    NCBI Gene: 110876
  • Alliance
    gene page
  • Transcription Start Sites
    7 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:65451115-65597791 bp, + strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 2, 38.61 cM
  • Mapping Data
    11 experiments
Strain
Comparison
more
  • SNPs within 2kb
    3945 from dbSNP Build 142
  • Strain Annotations
    18
  • PCR
    1
  • RFLP
    2
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_98248
 protein coding gene Chr2:65451108-65597791 (+)
129S1/SvImJ MGP_129S1SvImJ_G0025780
 protein coding gene Chr2:65436785-65575371 (+)
A/J MGP_AJ_G0025756
 protein coding gene Chr2:62916491-63056916 (+)
AKR/J MGP_AKRJ_G0025726
 protein coding gene Chr2:64600582-64754626 (+)
BALB/cJ MGP_BALBcJ_G0025751
 protein coding gene Chr2:63070990-63216774 (+)
C3H/HeJ MGP_C3HHeJ_G0025512
 protein coding gene Chr2:64791965-64934121 (+)
C57BL/6NJ MGP_C57BL6NJ_G0026198
 protein coding gene Chr2:67369520-67522890 (+)
CAROLI/EiJ MGP_CAROLIEiJ_G0023602
 protein coding gene Chr2:60272107-60401806 (+)
CAST/EiJ MGP_CASTEiJ_G0024976
 protein coding gene Chr2:64822515-64963371 (+)
CBA/J MGP_CBAJ_G0025492
 protein coding gene Chr2:69904070-70052332 (+)
DBA/2J MGP_DBA2J_G0025623
 protein coding gene Chr2:62540223-62681985 (+)
FVB/NJ MGP_FVBNJ_G0025585
 protein coding gene Chr2:61969423-62110014 (+)
LP/J MGP_LPJ_G0025711
 protein coding gene Chr2:65261809-65410475 (+)
NOD/ShiLtJ MGP_NODShiLtJ_G0025616
 protein coding gene Chr2:71856348-72000271 (+)
NZO/HlLtJ MGP_NZOHlLtJ_G0026255
 protein coding gene Chr2:64660210-64807332 (+)
PWK/PhJ MGP_PWKPhJ_G0024717
 protein coding gene Chr2:62360092-62497669 (+)
SPRET/EiJ MGP_SPRETEiJ_G0024524
 protein coding gene Chr2:64823443-64971500 (+)
WSB/EiJ MGP_WSBEiJ_G0025044
 protein coding gene Chr2:65040311-65176971 (+)



Homology
more
  • Human Ortholog
    SCN2A, sodium voltage-gated channel alpha subunit 2
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SCN2A, sodium voltage-gated channel alpha subunit 2
  • Synonyms
    BFIC3, BFIS3, BFNIS, DEE11, EA9, EIEE11, HBA, HBSCI, HBSCII, NAC2, Na(v)1.2, Nav1.2, SCN2A1, SCN2A2
  • Links
    NCBI Gene ID: 6326
    UniProt: Q99250

  • Chr Location
    2q24.3; chr2:165194993-165392310 (+)  GRCh38
Human Diseases
more
  • Diseases
    1 with Scn2a mouse models; 3 with human SCN2A associations

Human Disease Mouse Models
      
IDs
 View 1 model
      
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    1 with disease annotations
  • References
    1 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    18 phenotypes from 2 alleles in 2 genetic backgrounds
    30 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.
Homozygotes for a targeted mutation exhibit excess neuronal apoptosis (especially in the brainstem), reduced neuronal sodium channel currents in vitro, and severe hypoxia resulting in neonatal lethality.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    65
  • GO References
    17
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
    744
  • Tissues
    12
  • cDNA Data
    8
  • Literature Summary
    11
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000075318 Ensembl Gene Model | MGI Sequence Detail 146677 C57BL/6J ±  kb
    transcript ENSMUST00000028377 Ensembl | MGI Sequence Detail 8935 Not Applicable  
    polypeptide ENSMUSP00000028377 Ensembl | MGI Sequence Detail 2006 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      13 Sequences
    • Protein Ontology
      PR:000002098 sodium channel protein type 2 subunit alpha
      (term hierarchy)
    • InterPro Domains
      IPR005821 Ion transport domain
      IPR000048 IQ motif, EF-hand binding site
      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
      B1AWN6 10 sites, 3 N-linked glycans (3 sites), 1 O-linked glycan (1 site)
    Molecular
    Reagents
    less
    • All nucleic 19
      cDNA 11
      Primer pair 8

      Microarray probesets 18
    Other
    Accession IDs
    less
    MGD-MRK-14321, MGI:2444703
    References
    more
    • Summaries
      All 93
      Developmental Gene Expression 11
      Diseases 1
      Gene Ontology 17
      Phenotypes 30
    • Earliest
      J:10031 Litt M, et al., Localization of a human brain sodium channel gene (SCN2A) to chromosome 2. Genomics. 1989 Aug;5(2):204-8
    • Latest
      J:363170 Keith RE, et al., Perirhinal cortex abnormalities impair hippocampal plasticity and learning in Scn2a, Fmr1, and Cdkl5 autism mouse models. Sci Adv. 2025 Mar 7;11(10):eadt0780
    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
    03/25/2025
    MGI 6.24     		The Jackson Laboratory