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Scn9a Gene Detail
Summary
  • Symbol
    Scn9a
  • Name
    sodium channel, voltage-gated, type IX, alpha
  • Synonyms
    PN1
  • Feature Type
    protein coding gene
  • IDs
    MGI:107636
    NCBI Gene: 20274
  • Alliance
    gene page
  • Transcription Start Sites
    1 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:66310424-66465306 bp, - strand
    From Ensembl annotation of GRCm39
  • View this region in JBrowse
  • Genome Browsers
    Ensembl | UCSC | NCBI
  • Genetic Map
    Chromosome 2, 39.13 cM
  • Mapping Data
    8 experiments
Strain
Comparison
more
  • SNPs within 2kb
    4990 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
    4
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_107636
 protein coding gene Chr2:66310424-66465456 (-)
129S1/SvImJ MGP_129S1SvImJ_G0025785
 protein coding gene Chr2:66331392-66498552 (-)
A/J MGP_AJ_G0025761
 protein coding gene Chr2:63748874-63903079 (-)
AKR/J MGP_AKRJ_G0025731
 protein coding gene Chr2:65493900-65664026 (-)
BALB/cJ MGP_BALBcJ_G0025756
 protein coding gene Chr2:63933664-64098987 (-)
C3H/HeJ MGP_C3HHeJ_G0025517
 protein coding gene Chr2:65662505-65832200 (-)
C57BL/6NJ MGP_C57BL6NJ_G0026203
 protein coding gene Chr2:68296853-68467107 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0023607
 protein coding gene Chr2:61095694-61250447 (-)
CAST/EiJ MGP_CASTEiJ_G0024981
 protein coding gene Chr2:65749463-65926445 (-)
CBA/J MGP_CBAJ_G0025497
 protein coding gene Chr2:70846626-71026845 (-)
DBA/2J MGP_DBA2J_G0025628
 protein coding gene Chr2:63393981-63556894 (-)
FVB/NJ MGP_FVBNJ_G0025590
 protein coding gene Chr2:62816164-62977788 (-)
LP/J MGP_LPJ_G0025716
 protein coding gene Chr2:66163940-66324372 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0025621
 protein coding gene Chr2:72815793-73004525 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0026260
 protein coding gene Chr2:65549196-65726081 (-)
PWK/PhJ MGP_PWKPhJ_G0024722
 protein coding gene Chr2:63216817-63379079 (-)
SPRET/EiJ MGP_SPRETEiJ_G0024529
 protein coding gene Chr2:65721247-65892642 (-)
WSB/EiJ MGP_WSBEiJ_G0025049
 protein coding gene Chr2:65927791-66108965 (-)



Homology
more
  • Human Ortholog
    SCN9A, sodium voltage-gated channel alpha subunit 9
  • Vertebrate Orthologs
    3
Vertebrate Orthology Source
Alliance of Genome Resources
  • Human Ortholog
    SCN9A, sodium voltage-gated channel alpha subunit 9
  • Synonyms
    ETHA, FEB3B, GEFSP7, HSAN2D, Nav1.7, NE-NA, NENA, PN1, SFNP
  • Links
    NCBI Gene ID: 6335
    neXtProt AC: NX_Q15858
    UniProt: Q15858

  • Chr Location
    2q24.3; chr2:166195185-166376001 (-)  GRCh38
Human Diseases
more
  • Diseases
    2 with human SCN9A associations

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

Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    26 phenotypes from 6 alleles in 9 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.
Mice homozygous for a knock-out allele exhibit prenatal/neonatal lethality. Mice homozygous for a knock-in allele exhibit increased susceptibility to electrically induced seizures.
Gene Ontology
(GO)
Classifications
less
  • All GO Annotations
    36
  • 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
    805
  • Tissues
    56
  • cDNA Data
    15
  • Literature Summary
    7
  • Comparison Matrix
    Gene Expression + Phenotype
    • Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic ENSMUSG00000075316 Ensembl Gene Model | MGI Sequence Detail 154883 C57BL/6J ±  kb
    transcript ENSMUST00000100064 Ensembl | MGI Sequence Detail 9840 Not Applicable  
    polypeptide ENSMUSP00000097642 Ensembl | MGI Sequence Detail 1984 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      10 Sequences
    • Protein Ontology
      PR:000002104 sodium channel protein type 9 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
      Q62205 7 sites, 5 N-linked glycans (7 sites)
    Molecular
    Reagents
    less
    • All nucleic 22
      Genomic 2
      cDNA 16
      Primer pair 2
      Other 2

      Microarray probesets 8
    Other
    Accession IDs
    less
    MGD-MRK-36210
    References
    more
    • Summaries
      All 75
      Developmental Gene Expression 7
      Gene Ontology 12
      Phenotypes 30
    • Earliest
      J:45865 D'Arcangelo G, et al., Neuronal growth factor regulation of two different sodium channel types through distinct signal transduction pathways. J Cell Biol. 1993 Aug;122(4):915-21
    • Latest
      J:353573 Bangash MA, et al., Analgesic targets identified in mouse sensory neuron somata and terminal pain translatomes. Cell Rep. 2024 Aug 27;43(8):114614
    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
    11/19/2024
    MGI 6.24     		The Jackson Laboratory