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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
  • Alliance
  • Transcription Start Sites
    5 TSS
Location &
Maps
more
  • Sequence Map
    Chr2:66270782-66440837 bp, - strand
  • From NCBI annotation of GRCm38

    View this region in JBrowse

  • Genome Browsers
  • Genetic Map
    Chromosome 2, 39.13 cM
  • Mapping Data
    7 experiments
Strain
Comparison
more
  • SNPs within 2kb
    717 from dbSNP Build 142
  • Strain Annotations
    18
  • RFLP
For selected strains:
Strain Gene Model ID Feature Type Coordinates Select Strains
C57BL/6J MGI_C57BL6J_98246
protein coding gene Chr2:66270778-66440840 (-)
129S1/SvImJ MGP_129S1SvImJ_G0025784
protein coding gene Chr2:66125444-66288736 (-)
A/J MGP_AJ_G0025760
protein coding gene Chr2:63546797-63706809 (-)
AKR/J MGP_AKRJ_G0025730
protein coding gene Chr2:65273432-65446646 (-)
BALB/cJ MGP_BALBcJ_G0025755
protein coding gene Chr2:63729161-63892409 (-)
C3H/HeJ MGP_C3HHeJ_G0025516
protein coding gene Chr2:65460372-65624988 (-)
C57BL/6NJ MGP_C57BL6NJ_G0026202
protein coding gene Chr2:68066175-68245388 (-)
CAROLI/EiJ MGP_CAROLIEiJ_G0023606
protein coding gene Chr2:60907116-61060205 (-)
CAST/EiJ MGP_CASTEiJ_G0024980
protein coding gene Chr2:65512230-65702109 (-)
CBA/J MGP_CBAJ_G0025496
protein coding gene Chr2:70601978-70791684 (-)
DBA/2J MGP_DBA2J_G0025627
protein coding gene Chr2:63185341-63355833 (-)
FVB/NJ MGP_FVBNJ_G0025589
protein coding gene Chr2:62612047-62773836 (-)
LP/J MGP_LPJ_G0025715
protein coding gene Chr2:65947886-66124526 (-)
NOD/ShiLtJ MGP_NODShiLtJ_G0025620
protein coding gene Chr2:72581659-72765606 (-)
NZO/HlLtJ MGP_NZOHlLtJ_G0026259
protein coding gene Chr2:65345391-65512279 (-)
PWK/PhJ MGP_PWKPhJ_G0024721
protein coding gene Chr2:63011309-63175575 (-)
SPRET/EiJ MGP_SPRETEiJ_G0024528
protein coding gene Chr2:65509274-65683768 (-)
WSB/EiJ MGP_WSBEiJ_G0025048
protein coding gene Chr2:65714652-65886833 (-)



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
    UniProt: P35498

  • Chr Location
    2q24.3; chr2:165989160-166149216 (-)  GRCh38.p7

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

Human Disease Mouse Models
      
IDs
View 5 models
      
IDs
View 3 models
      
IDs
Click on a disease name to see all genes associated with that disease.

  • Mutations/Alleles
    4 with disease annotations
  • References
    5 with disease annotations
Mutations,
Alleles, and
Phenotypes
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  • Phenotype Summary
    59 phenotypes from 10 alleles in 17 genetic backgrounds
    9 phenotypes from multigenic genotypes
    1 images
    47 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
immune system
integument
limbs/digits/tail
liver/biliary system
mortality/aging
muscle
neoplasm
nervous system
pigmentation
renal/urinary system
reproductive system
respiratory system
skeleton
taste/olfaction
vision/eye

Click cells to view annotations.
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
RNA binding
signaling receptor activity
signaling receptor binding
transcription
transferase
transporter
Biological Process

carbohydrate derivative metabolism
cell death
cell differentiation
cell proliferation
cellular component organization
establishment of localization
homeostatic process
immune system process
lipid metabolic process
nucleic acid-templated transcription
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
  • Comparison Matrix
  • Interactions
    less
    Sequences &
    Gene Models
    less
    Representative SequencesLengthStrain/SpeciesFlank
    genomic 20265 NCBI Gene Model | MGI Sequence Detail 170056 C57BL/6J ±  kb
    transcript NM_001313997 RefSeq | MGI Sequence Detail 8320 C57BL/6  
    polypeptide A2APX8 UniProt | EBI | MGI Sequence Detail 2009 Not Applicable  
    For the selected sequence
    Protein
    Information
    less
    • UniProt
      7 Sequences
    • Protein Ontology
      PR:000002095 sodium channel protein type 1 subunit alpha
    • InterPro Domains
      IPR005821 Ion transport domain
      IPR010526 Sodium ion transport-associated
      IPR027359 Voltage-dependent channel domain superfamily
      IPR024583 Voltage-gated Na+ ion channel, cytoplasmic domain
      IPR008051 Voltage gated sodium channel, alpha-1 subunit
      IPR001696 Voltage gated sodium channel, alpha subunit
    Molecular
    Reagents
    less
    • All nucleic 17
      cDNA 9
      Primer pair 7
      Other 1

      Microarray probesets 6
    Other
    Accession IDs
    less
    MGD-MRK-14319
    References
    more
    • Summaries
      All 95
      Developmental Gene Expression 6
      Diseases 5
      Gene Ontology 15
      Phenotypes 47
    • 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:265046 Favero M, et al., A Transient Developmental Window of Fast-Spiking Interneuron Dysfunction in a Mouse Model of Dravet Syndrome. J Neurosci. 2018 Sep 5;38(36):7912-7927

    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
    11/06/2018
    MGI 6.13
    The Jackson Laboratory