About   Help   FAQ
Scn5a Gene Detail
Summary
  • Symbol
    Scn5a
  • Name
    sodium channel, voltage-gated, type V, alpha
  • Synonyms
    mH1, Nav1.5, Nav1.5c, SkM2
Location &
Maps
more
  • Sequence Map
    Chr9:119312474-119408082 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 9, 71.33 cM
  • Mapping Data
    3 experiments
Strain
Comparison
more
  • SNPs within 2kb
    2771 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    2
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_98251
 protein coding gene Chr9:119312470-119408096 (-)
129S1/SvImJ MGP_129S1SvImJ_G0035421
 protein coding gene Chr9:122266254-122366620 (-)
A/J MGP_AJ_G0035402
 protein coding gene Chr9:117705719-117803855 (-)
AKR/J MGP_AKRJ_G0035335
 protein coding gene Chr9:120785779-120887601 (-)
BALB/cJ MGP_BALBcJ_G0035398
 protein coding gene Chr9:117577856-117682839 (-)
C3H/HeJ MGP_C3HHeJ_G0035106
 protein coding gene Chr9:121247841-121345223 (-)
C57BL/6NJ MGP_C57BL6NJ_G0035921
 protein coding gene Chr9:125603617-125703872 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0032803
 protein coding gene Chr9:114906011-115004374 (-)
CAST/EiJ MGP_CASTEiJ_G0034409
 protein coding gene Chr9:121242833-121343577 (-)
CBA/J MGP_CBAJ_G0035073
 protein coding gene Chr9:130322672-130424082 (-)
DBA/2J MGP_DBA2J_G0035232
 protein coding gene Chr9:117150875-117246814 (-)
FVB/NJ MGP_FVBNJ_G0035179
 protein coding gene Chr9:116015773-116118331 (-)
LP/J MGP_LPJ_G0035311
 protein coding gene Chr9:122605446-122706259 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0035220
 protein coding gene Chr9:131279403-131374892 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0035940
 protein coding gene Chr9:121165730-121263543 (-)
PWK/PhJ MGP_PWKPhJ_G0034115
 protein coding gene Chr9:117582259-117680533 (-)
SPRET/EiJ MGP_SPRETEiJ_G0033951
 protein coding gene Chr9:121265523-121366729 (-)
WSB/EiJ MGP_WSBEiJ_G0034530
 protein coding gene Chr9:121049143-121146219 (-)



Homology
more
  • Human Ortholog
    SCN5A, sodium voltage-gated channel alpha subunit 5
  • Vertebrate Orthologs
    4
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SCN5A, sodium voltage-gated channel alpha subunit 5
  • Synonyms
    CDCD2, CMD1E, CMPD2, HB1, HB2, HBBD, HH1, ICCD, IVF, LQT3, Nav1.5, PFHB1, SSS1, VF1
  • Links
    NCBI Gene ID: 6331
    neXtProt AC: NX_Q14524
    UniProt: Q14524

  • Chr Location
    3p22.2; chr3:38548057-38649743 (-)  GRCh38
Human Diseases
more
  • Diseases
    4 with Scn5a mouse models; 8 with human SCN5A associations

Human Disease Mouse Models
      
IDs
 View 2 models
IDs
 View 4 models
IDs
 View 2 models
IDs
 View 2 models
      
IDs
 View 2 models
IDs
IDs
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    8 with disease annotations
  • References
    9 with disease annotations
Mutations,
Alleles, and
Phenotypes
less
  • Phenotype Summary
    49 phenotypes from 7 alleles in 10 genetic backgrounds
    19 phenotypes from multigenic genotypes
    1 images
    68 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.
Mice homozygous for mutations in this gene die prenatally usually during organogenesis and may display decreased embryo size and abnormal cardiovascular system physiology. Heterozygous mice typically display abnormal heartbeats and defects in the function of the impulse conduction system.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    132
  • GO References
    27
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
    974
  • Tissues
    55
  • cDNA Data
    15
  • Literature Summary
    37
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000032511 Ensembl Gene Model | MGI Sequence Detail 95609 C57BL/6J ±  kb
    transcript ENSMUST00000065196 Ensembl | MGI Sequence Detail 8287 Not Applicable  
    polypeptide ENSMUSP00000066228 Ensembl | MGI Sequence Detail 2020 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      10 Sequences
    • Protein Ontology
      PR:000002101 sodium channel protein type 5 subunit alpha
      (term hierarchy)
    • InterPro Domains
      IPR005821 Ion transport domain
      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
      IPR008053 Voltage gated sodium channel, alpha-5 subunit
      IPR001696 Voltage gated sodium channel, alpha subunit
      IPR044564 Voltage-gated sodium channel alpha subunit, inactivation gate
    • GlyGen
      Q9JJV9 15 sites, 6 N-linked glycans (5 sites)
    Molecular
    Reagents
    less
    • All nucleic 26
      cDNA 17
      Primer pair 9

      Microarray probesets 3
    Other
    Accession IDs
    less
    MGD-MRK-14324
    References
    more
    • Summaries
      All 173
      Developmental Gene Expression 37
      Diseases 9
      Gene Ontology 27
      Phenotypes 68
    • Earliest
      J:13592 Schleef M, et al., Chromosomal localization and genomic cloning of the mouse alpha-tropomyosin gene Tpm-1. Genomics. 1993 Aug;17(2):519-21
    • Latest
      J:362202 Ono M, et al., Feeding behavior modifies the circadian variation in RR and QT intervals by distinct mechanisms in mice. Am J Physiol Regul Integr Comp Physiol. 2024 Jul 1;327(1):R109-R121
    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
    Warranty Disclaimer, Privacy Notice, Licensing, & Copyright
    Send questions and comments to User Support.     		last database update
    03/25/2025
    MGI 6.24     		The Jackson Laboratory