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    SCN1A sodium voltage-gated channel alpha subunit 1 [ Homo sapiens (human) ]

    Gene ID: 6323, updated on 3-Jul-2016
    Official Symbol
    SCN1Aprovided by HGNC
    Official Full Name
    sodium voltage-gated channel alpha subunit 1provided 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
    Voltage-dependent sodium channels are heteromeric complexes that regulate sodium exchange between intracellular and extracellular spaces and are essential for the generation and propagation of action potentials in muscle cells and neurons. Each sodium channel is composed of a large pore-forming, glycosylated alpha subunit and two smaller beta subunits. This gene encodes a sodium channel alpha subunit, which has four homologous domains, each of which contains six transmembrane regions. Allelic variants of this gene are associated with generalized epilepsy with febrile seizures and epileptic encephalopathy. 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, Oct 2015]
    Orthologs
    Location:
    2q24.3
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 2 NC_000002.12 (165989160..166149216, 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 LOC101929680 Neighboring gene RNA, 7SK small nuclear pseudogene 152 Neighboring gene sodium voltage-gated channel alpha subunit 9

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Copy number response

    Description
    Copy number response
    Triplosensitivity

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

    ClinGen Genome Curation Page
    Haploinsufficency

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

    ClinGen Genome Curation PagePubMed

    NHGRI GWAS Catalog

    Description
    Common variants associated with general and MMR vaccine-related febrile seizures.
    NHGRI GWA Catalog
    Epilepsy, hippocampal sclerosis and febrile seizures linked by common genetic variation around SCN1A.
    NHGRI GWA Catalog
    Genetic determinants of common epilepsies: a meta-analysis of genome-wide association studies.
    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...
    • Cardiac conduction, organism-specific biosystem (from REACTOME)
      Cardiac conduction, organism-specific biosystemThe normal sequence of contraction of atria and ventricles of the heart require activation of groups of cardiac cells. The mechanism must elicit rapid changes in heart rate and respond to changes in ...
    • 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...
    • Muscle contraction, organism-specific biosystem (from REACTOME)
      Muscle contraction, organism-specific biosystemIn this module, the processes by which calcium binding triggers actin - myosin interactions and force generation in smooth and striated muscle tissues are annotated.
    • Phase 0 - rapid depolarisation, organism-specific biosystem (from REACTOME)
      Phase 0 - rapid depolarisation, organism-specific biosystemPhase 0 is the rapid depolarisation phase in which electrical stimulation of a cell initiates events involving the influx and efflux of ions resulting in the production of a cell's action potential. ...
    Products Interactant Other Gene Complex Source Pubs Description

    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    sodium ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    voltage-gated sodium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    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
     
    positive regulation of defense response to virus by host IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of postsynaptic membrane potential IEA
    Inferred from Electronic Annotation
    more info
     
    sodium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    sodium ion transport NAS
    Non-traceable Author Statement
    more info
    PubMed 
    xenophagy IMP
    Inferred from Mutant Phenotype
    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 I subunit alpha
    sodium channel protein, brain I alpha subunit
    sodium channel voltage gated type 1 alpha subunit
    sodium channel, voltage gated, type I alpha subunit
    sodium channel, voltage-gated, type I, alpha polypeptide
    sodium channel, voltage-gated, type I, alpha subunit
    voltage-gated sodium channel subunit alpha Nav1.1

    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 RefSeqGene

      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 identical proteins and their annotated locations for 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
      ENSP00000407030, ENST00000423058
      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 identical proteins and their annotated locations for 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
      Related
      ENSP00000386312, OTTHUMP00000205012, ENST00000409050, OTTHUMT00000333750
      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 identical proteins and their annotated locations for 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 identical proteins and their annotated locations for 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 108 details...

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p7 Primary Assembly

      Range
      165989160..166149216 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017004651.1XP_016860140.1  

    2. XM_011511602.2XP_011509904.1  

      See identical proteins and their annotated locations for XP_011509904.1

      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)
    3. XM_011511606.2XP_011509908.1  

      See identical proteins and their annotated locations for XP_011509908.1

      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)
    4. XM_017004644.1XP_016860133.1  

      Related
      ENSP00000303540, OTTHUMP00000041051, ENST00000303395, OTTHUMT00000102661
    5. XM_017004652.1XP_016860141.1  

    6. XM_017004654.1XP_016860143.1  

    7. XM_017004653.1XP_016860142.1  

    8. XM_011511605.2XP_011509907.1  

      Conserved Domains (4) summary
      cd13433
      Location:14721524
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:12421470
      Ion_trans; Ion transport protein
      pfam06512
      Location:9941216
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:509707
      DUF3451; Domain of unknown function (DUF3451)
    9. XM_017004650.1XP_016860139.1  

    10. XM_017004649.1XP_016860138.1  

    11. XM_017004648.1XP_016860137.1  

    12. XM_017004646.1XP_016860135.1  

    13. XM_017004645.1XP_016860134.1  

    14. XM_017004647.1XP_016860136.1  

    15. XM_011511604.2XP_011509906.1  

      See identical proteins and their annotated locations for XP_011509906.1

      UniProtKB/Swiss-Prot
      P35498
      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)

    RNA

    1. XR_001738884.1 RNA Sequence

    2. XR_001738885.1 RNA Sequence

    3. XR_001738883.1 RNA Sequence

    Alternate CHM1_1.1

    Genomic

    1. NC_018913.2 Alternate CHM1_1.1

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