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SCN1A sodium channel, voltage-gated, type I, alpha subunit [ Homo sapiens (human) ]

Gene ID: 6323, updated on 11-Sep-2014
Official Symbol
SCN1Aprovided by HGNC
Official Full Name
sodium channel, voltage-gated, type I, alpha subunitprovided by HGNC
Primary source
HGNC:HGNC:10585
See related
Ensembl:ENSG00000144285; HPRD:01669; MIM:182389; Vega:OTTHUMG00000044173
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FEB3; FHM3; NAC1; SCN1; SMEI; EIEE6; FEB3A; HBSCI; GEFSP2; Nav1.1
Summary
The vertebrate sodium channel is a voltage-gated ion channel essential for the generation and propagation of action potentials, mainly in nerve and muscle. Voltage-sensitive sodium channels are heteromeric complexes consisting of a large central pore-forming glycosylated alpha subunit, and two smaller auxiliary beta subunits. This gene encodes the large alpha subunit, and mutations in this gene have been associated with several epilepsy, convulsion and migraine disorders. Alternative splicing results in multiple transcript variants. The RefSeq Project has decided to create four representative RefSeq records. Three of the transcript variants are supported by experimental evidence and the fourth contains alternate 5' untranslated exons, the exact combination of which have not been experimentally confirmed for the full-length transcript.[provided by RefSeq, Jan 2011]
See SCN1A in Epigenomics, MapViewer
Location:
2q24.3
Exon count:
28
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 2 NC_000002.12 (165989160..166149132, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (166845670..167005642, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC100506124 Neighboring gene tetratricopeptide repeat domain 21B Neighboring gene TTC21B antisense RNA 1 Neighboring gene uncharacterized LOC102724058 Neighboring gene uncharacterized LOC102724058 Neighboring gene uncharacterized LOC101929680 Neighboring gene sodium channel, voltage-gated, type IX, alpha subunit Neighboring gene sodium channel, voltage-gated, type VII, alpha subunit

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated (2012-07-06)

ISCA Genome Curation Page
Haploinsufficency

Sufficient evidence for dosage pathogenicity (Last evaluated (2012-07-06)

ISCA Genome Curation PagePubMed

NHGRI GWAS Catalog

Description
Epilepsy, hippocampal sclerosis and febrile seizures linked by common genetic variation around SCN1A.
NHGRI GWA Catalog
Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
NHGRI GWA Catalog
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13).
NHGRI GWA Catalog
  • Axon guidance, organism-specific biosystem (from REACTOME)
    Axon guidance, organism-specific biosystemAxon guidance / axon pathfinding is the process by which neurons send out axons to reach the correct targets. Growing axons have a highly motile structure at the growing tip called the growth cone, w...
  • Developmental Biology, organism-specific biosystem (from REACTOME)
    Developmental Biology, organism-specific biosystemAs a first step towards capturing the array of processes by which a fertilized egg gives rise to the diverse tissues of the body, examples of three kinds of processes have been annotated. These are a...
  • Dopaminergic synapse, organism-specific biosystem (from KEGG)
    Dopaminergic synapse, organism-specific biosystemDopamine (DA) is an important and prototypical slow neurotransmitter in the mammalian brain, where it controls a variety of functions including locomotor activity, motivation and reward, learning an...
  • Dopaminergic synapse, conserved biosystem (from KEGG)
    Dopaminergic synapse, conserved biosystemDopamine (DA) is an important and prototypical slow neurotransmitter in the mammalian brain, where it controls a variety of functions including locomotor activity, motivation and reward, learning an...
  • Interaction between L1 and Ankyrins, organism-specific biosystem (from REACTOME)
    Interaction between L1 and Ankyrins, organism-specific biosystemAnkyrins are a family of adaptor proteins that couple membrane proteins such as voltage gated Na+ channels and the Na+/K+ anion exchanger to the spectrin actin cytoskeleton. Ankyrins are encoded by t...
  • L1CAM interactions, organism-specific biosystem (from REACTOME)
    L1CAM interactions, organism-specific biosystemThe L1 family of cell adhesion molecules (L1CAMs) are a subfamily of the immunoglobulin superfamily of transmembrane receptors, comprised of four structurally related proteins: L1, Close Homolog of L...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
voltage-gated sodium channel activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
adult walking behavior IEA
Inferred from Electronic Annotation
more info
 
membrane depolarization during action potential IBA
Inferred from Biological aspect of Ancestor
more info
 
neuromuscular process controlling posture IEA
Inferred from Electronic Annotation
more info
 
neuronal action potential IBA
Inferred from Biological aspect of Ancestor
more info
 
neuronal action potential propagation IEA
Inferred from Electronic Annotation
more info
 
regulation of ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
sodium ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
sodium ion transmembrane transport NAS
Non-traceable Author Statement
more info
PubMed 
sodium ion transport NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
T-tubule IEA
Inferred from Electronic Annotation
more info
 
Z disc ISS
Inferred from Sequence or Structural Similarity
more info
 
axon initial segment IEA
Inferred from Electronic Annotation
more info
 
intercalated disc IEA
Inferred from Electronic Annotation
more info
 
neuronal cell body IEA
Inferred from Electronic Annotation
more info
 
node of Ranvier IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
voltage-gated sodium channel complex IEA
Inferred from Electronic Annotation
more info
 
Preferred Names
sodium channel protein type 1 subunit alpha
Names
sodium channel protein type 1 subunit alpha
sodium channel protein type I subunit alpha
sodium channel protein, brain I alpha subunit
sodium channel voltage gated type 1 alpha subunit
voltage-gated sodium channel subunit alpha Nav1.1
sodium channel, voltage-gated, type I, alpha polypeptide

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_011906.1 

    Range
    820..89480
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_8

mRNA and Protein(s)

  1. NM_001165963.1NP_001159435.1  sodium channel protein type 1 subunit alpha isoform 1

    See proteins identical to NP_001159435.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes encodes the longest isoform (1).
    Source sequence(s)
    AB093548, AC010127
    Consensus CDS
    CCDS54413.1
    UniProtKB/Swiss-Prot
    P35498
    Related
    ENSP00000303540, OTTHUMP00000041051, ENST00000303395, OTTHUMT00000102661
    Conserved Domains (4) summary
    cd13433
    Location:14841536
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12541482
    Ion_trans; Ion transport protein
    pfam06512
    Location:10061228
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510719
    DUF3451; Domain of unknown function (DUF3451)
  2. NM_001165964.1NP_001159436.1  sodium channel protein type 1 subunit alpha isoform 3

    See proteins identical to NP_001159436.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AB098335, AC010127
    Consensus CDS
    CCDS54414.1
    UniProtKB/Swiss-Prot
    P35498
    Conserved Domains (4) summary
    cd13433
    Location:14561508
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12261454
    Ion_trans; Ion transport protein
    pfam06512
    Location:9781200
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510691
    DUF3451; Domain of unknown function (DUF3451)
  3. NM_001202435.1NP_001189364.1  sodium channel protein type 1 subunit alpha isoform 1

    See proteins identical to NP_001189364.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) represents a transcript with 5' untranslated exons, compared to variant 1. The RefSeq Project created this record to better support clinical studies but the exact combination of exons and splice sites still needs to be experimentally confirmed. Variants 1 and 4 encode the same isoform.
    Source sequence(s)
    AC010127, AC107082
    Consensus CDS
    CCDS54413.1
    UniProtKB/Swiss-Prot
    P35498
    Conserved Domains (4) summary
    cd13433
    Location:14841536
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12541482
    Ion_trans; Ion transport protein
    pfam06512
    Location:10061228
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510719
    DUF3451; Domain of unknown function (DUF3451)
  4. NM_006920.4NP_008851.3  sodium channel protein type 1 subunit alpha isoform 2

    See proteins identical to NP_008851.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice junction at the 3' end of an exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AB093549, AC010127, AF225985
    Consensus CDS
    CCDS33316.1
    UniProtKB/Swiss-Prot
    P35498
    Related
    ENSP00000364554, OTTHUMP00000041052, ENST00000375405, OTTHUMT00000102662
    Conserved Domains (4) summary
    cd13433
    Location:14731525
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12431471
    Ion_trans; Ion transport protein
    pfam06512
    Location:9951217
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510708
    DUF3451; Domain of unknown function (DUF3451)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000002.12 

    Range
    165989160..166149132
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000134.1 

    Range
    158727062..158886965
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018913.2 

    Range
    166851977..167011835
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)