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    SCN3A sodium channel, voltage-gated, type III, alpha subunit [ Homo sapiens (human) ]

    Gene ID: 6328, updated on 9-Jun-2013
    Official Symbol
    SCN3Aprovided by HGNC
    Official Full Name
    sodium channel, voltage-gated, type III, alpha subunitprovided by HGNC
    Primary source
    HGNC:10590
    See related
    Ensembl:ENSG00000153253; HPRD:01671; MIM:182391; Vega:OTTHUMG00000044171
    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
    NAC3; Nav1.3
    Summary
    Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
    Location :
    2q24
    Sequence :
    Chromosome: 2; NC_000002.11 (165944030..166060577, complement)
    See SCN3A in Epigenomics, MapViewer

    Chromosome 2 - NC_000002.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA, H/ACA box 70F Neighboring gene cordon-bleu WH2 repeat protein-like 1 Neighboring gene solute carrier family 38, member 11 Neighboring gene sodium channel, voltage-gated, type II, alpha subunit Neighboring gene MAPRE1 pseudogene 3 Neighboring gene cysteine-serine-rich nuclear protein 3

    Go to nucleotideGraphics FASTA GenBank

    Go to reference sequence details

    Related articles in PubMed

    1. Duplication of the sodium channel gene cluster on 2q24 in children with early onset epilepsy. Goeggel Simonetti B, et al. Epilepsia, 2012 Dec. PMID 23016767.
    2. Upregulated expression of voltage-gated sodium channel Nav1.3 in cortical lesions of patients with focal cortical dysplasia type IIb. Yu S, et al. Neuroreport, 2012 May 9. PMID 22494998.
    3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. Rose JE, et al. Mol Med, 2010 Jul-Aug. PMID 20379614.
    4. Array-CGH detection of a de novo 2.8 Mb deletion in 2q24.2-->q24.3 in a girl with autistic features and developmental delay. Chen CP, et al. Eur J Med Genet, 2010 Jul-Aug. PMID 20346423.
    5. Abnormal expression of voltage-gated sodium channels Nav1.7, Nav1.3 and Nav1.8 in trigeminal neuralgia. Siqueira SR, et al. Neuroscience, 2009 Dec 1. PMID 19699781.

    See all (22) citations in PubMed

    See citations in PubMed for homologs of this gene provided by HomoloGene

    GeneRIFs: Gene References Into Functions What's a GeneRIF?

    1. This study demonistrated that associated with a duplication of the SCN2A and SCN3A gene cluster on 2q24 in patient with early onset epilepsy.
      Title: Duplication of the sodium channel gene cluster on 2q24 in children with early onset epilepsy.
    2. Upregulation of Nav1.3 protein and a specific cellular distribution of Nav1.3 proteins in focal cortical dysplasia type IIb(FCDIIb) lesion tissue samples suggest that Nav1.3 may be involved in the generation of epileptic activity in FCDIIb.
      Title: Upregulated expression of voltage-gated sodium channel Nav1.3 in cortical lesions of patients with focal cortical dysplasia type IIb.
    3. Deletions in SCN3A gene is associated with autistic features and developmental delay.
      Title: Array-CGH detection of a de novo 2.8 Mb deletion in 2q24.2-->q24.3 in a girl with autistic features and developmental delay.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. In trigeminal neuralgia (TN) there is a reduction in the expression of Nav1.7 and an increase in the expression of Nav1.3, Nav1.8 expression not significantly different; TN can be, at least in part, a channelopathy.
      Title: Abnormal expression of voltage-gated sodium channels Nav1.7, Nav1.3 and Nav1.8 in trigeminal neuralgia.
    6. The association of antiepileptic drugs responsiveness with genetic polymorphisms was investigated and any association with mRNA expression of the neuronal sodium channels was correlated.
      Title: Multidrug resistance in epilepsy and polymorphisms in the voltage-gated sodium channel genes SCN1A, SCN2A, and SCN3A: correlation among phenotype, genotype, and mRNA expression.
    7. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Multidrug resistance in epilepsy and polymorphisms in the voltage-gated sodium channel genes SCN1A, SCN2A, and SCN3A: correlation among phenotype, genotype, and mRNA expression.
    8. Characterization of 5' untranslated regions SCN3A, and identification of cis-conserved noncoding sequences.
      Title: Characterization of 5' untranslated regions of the voltage-gated sodium channels SCN1A, SCN2A, and SCN3A and identification of cis-conserved noncoding sequences.
    9. in autism families, two polymorphic coding variants of SCN3A are described
      Title: Sodium channels SCN1A, SCN2A and SCN3A in familial autism.
    Submit: New GeneRIF Correction

    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Products Interactant Other Gene Complex Source Pubs Description
    Q9NY46 Q07954 LRP1    HPRD  PubMed  
    BioGRID:112233 BioGRID:110215 LRP1    BioGRID  PubMed Two-hybrid 
    BioGRID:112233 BioGRID:110216 LRP2    BioGRID  PubMed Two-hybrid 
    BioGRID:112233 BioGRID:113579 LRP8    BioGRID  PubMed Two-hybrid 
    BioGRID:112233 BioGRID:201723 Nedd4    BioGRID  PubMed Reconstituted Complex 
    • 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...
    • 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...

    Markers

    Genotypes

    Homology

    Clone Names

    • KIAA1356

    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
    sodium ion transport NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    cytoplasm IEA
    Inferred from Electronic Annotation
    more info
    		  
    voltage-gated sodium channel complex NAS
    Non-traceable Author Statement
    more info
    		  
    Preferred Names
    sodium channel protein type 3 subunit alpha
    Names
    sodium channel protein type 3 subunit alpha
    brain III voltage-gated sodium channel
    voltage-gated sodium channel subtype III
    sodium channel protein type III subunit alpha
    sodium channel protein brain III subunit alpha
    voltage-gated sodium channel subunit alpha Nav1.3
    sodium channel, voltage-gated, type III, 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.

    mRNA and Protein(s)

    1. NM_001081676.1 → NP_001075145.1  sodium channel protein type 3 subunit alpha isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2), also known as 12v1, SCN3A-s, or the adult form, uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform 2).
      Source sequence(s)
      AC013463, AF035686, AF225986, AJ251507, AL079365, BM681920, DA796981
      UniProtKB/TrEMBL
      Q9C007
      UniProtKB/Swiss-Prot
      Q9NY46
      Conserved Domains (4) summary
      pfam00520
      Location:1193 – 1418
      Blast Score: 372
      Ion_trans; Ion transport protein
      pfam06512
      Location:949 – 1167
      Blast Score: 620
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510 – 624
      Blast Score: 403
      DUF3451; Domain of unknown function (DUF3451)
      cl16916
      Location:1659 – 1694
      Blast Score: 86
      ChtBD1; Hevein or type 1 chitin binding domain

    2. NM_001081677.1 → NP_001075146.1  sodium channel protein type 3 subunit alpha isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3), also known as the neonatal form, uses an alternate in-frame splice site in the central coding region and an alternate form of an exon in the 5' coding region, compared to variant 1. The resulting isoform (3) is shorter than isoform 1, and contains one amino acid substitution relative to isoform 2.
      Source sequence(s)
      AC013463, AF035686, AJ251507, AL079365, BM681920, DA772987
      Consensus CDS
      CCDS46440.1
      UniProtKB/Swiss-Prot
      Q9NY46
      Related
      ENSP00000353206, ENST00000360093
      Conserved Domains (4) summary
      pfam00520
      Location:1193 – 1418
      Blast Score: 371
      Ion_trans; Ion transport protein
      pfam06512
      Location:949 – 1167
      Blast Score: 621
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510 – 624
      Blast Score: 403
      DUF3451; Domain of unknown function (DUF3451)
      cl16916
      Location:1659 – 1694
      Blast Score: 86
      ChtBD1; Hevein or type 1 chitin binding domain

    3. NM_006922.3 → NP_008853.3  sodium channel protein type 3 subunit alpha isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1), also known as 12v4, represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC013463, AF035686, AF225987, AJ251507, AL079365, BM681920, DA796981
      Consensus CDS
      CCDS33312.1
      UniProtKB/Swiss-Prot
      Q9NY46
      Related
      ENSP00000283254, OTTHUMP00000041047, ENST00000283254, OTTHUMT00000102655
      Conserved Domains (4) summary
      pfam00520
      Location:1242 – 1467
      Blast Score: 376
      Ion_trans; Ion transport protein
      pfam06512
      Location:998 – 1216
      Blast Score: 622
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510 – 711
      Blast Score: 637
      DUF3451; Domain of unknown function (DUF3451)
      cl16916
      Location:1708 – 1743
      Blast Score: 86
      ChtBD1; Hevein or type 1 chitin binding domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 104

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

    Reference GRCh37.p10 Primary Assembly

    Genomic

    1. NC_000002.11 Reference GRCh37.p10 Primary Assembly

      Range
      165944030..166060577, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate HuRef

    Genomic

    1. AC_000134.1 Alternate HuRef

      Range
      157826522..157942999, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate CHM1_1.0

    Genomic

    1. NC_018913.1 Alternate CHM1_1.0

      Range
      165341003..165457549, complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    genomic ABBA01004916.1 (21414..36486) None
    genomic ABBA01004917.1 None
    genomic AC013463.7 AAY15072.1
    genomic AF330135.1 AAG53414.1
      AAG53415.1
    genomic AMYH01011226.1 (282162..398708) None
    genomic CH471058.2 EAX11331.1
      EAX11332.1
      EAX11333.1
      EAX11334.1
      EAX11335.1
    genomic S69887.1 AAB30530.1
    mRNA AB037777.1 BAA92594.1
    mRNA AF035685.1 AAC29514.1
    mRNA AF035686.1 AAC29515.1
    mRNA AF225986.1 AAK00218.1
    mRNA AF225987.1 AAK00219.1
    mRNA AF239921.1 AAF44690.1
    mRNA AJ251507.1 CAB85895.1
    mRNA AJ276139.1 CAC03582.1
    mRNA AJ276140.1 CAC03583.1
    mRNA AJ277394.1 CAC03586.1
    mRNA AK299757.1 BAG61646.1
    mRNA AK301853.1 BAG63295.1
    mRNA AL079365.1 None
    mRNA BM681920.1 None
    mRNA DA772987.1 None
    mRNA DA796981.1 None
    mRNA DQ993537.1 None
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NY46.2 GenPept UniProtKB/Swiss-Prot:Q9NY46

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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      Supplemental Content

      Table of contents

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      • BioAssay
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        BioAssay, by Protein Target
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      • BioSystems
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      • CCDS
        Links from Gene to CCDS are established if a gene encodes a protein sequence that is a member of a Consensus CDS (CCDS).
      • Conserved Domains
        Conserved Domain Database Links between Entrez Gene and Conserved Domain Database (CDD) are calculated from the domains annotated by the CDD group on Reference Sequence proteins.
      • dbVar
        Link from Gene to dbVar
      • EST
        Link to related EST entry
      • Full text in PMC
        PMC links
      • Full text in PMC_nucleotide
        Full text in PubMedCentral identified from shared sequence links
      • Genome
        Genome records having the gene annotated on corresponding genomic reference sequence.
      • GEO Profiles
        Related GEO
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        GTR associated with a gene
      • HomoloGene
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      • Map Viewer
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      • Nucleotide
        Link to related Nucleotide entry
      • OMIM
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      • Probe
        Related Probe entry
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        Link to related protein entry
      • PubChem Compound
        PubChem Compounds
      • PubChem Substance
        PubChem Substances
      • PubMed
        Links between Gene and PubMed are the result of the following: 1. Manual curation within NCBI. Part of the process of generating a REVIEWED RefSeq is an analysis of the current literature. Papers that are seminal in defining the gene, its sequence, and its function are added to the record at that time. Alert users point out gaps or errors in papers associated with a Gene record. These messages are reviewed and implemented as required. 2. Integration of information from other public databases. Gene integrates gene-citation from resources external to NCBI such as model organism-specific databases, Gene Ontology (GO), groups curating interactions, and sequence databases. The assumption in using these source is that they report citations specific to a gene in a known species. Gene does not process citations from OMIM automatically, because many of citations in OMIM refer to studies of genes in species other than human.
      • PubMed (GeneRIF)
        GeneRIF -- Gene Reference Into Function Staff of the Index Section in the National Library of Medicine review the current literature. When they find articles focused on the structure and function of a gene, they write a brief summary of the impact of the paper and make the connection between the citation (PubMed) and Gene. An interface exists for interested users to submit such data as well. http://www.ncbi.nlm.nih.gov/projects/GeneRIF/GeneRIFhelp.html
      • PubMed (OMIM)
        Links are provided when Gene has a link to a record in OMIM, and OMIM explicitly cites these publications in PubMed.
      • PubMed(nucleotide/PMC)
        Citations in PubMed identified from shared sequence and PMC links.
      • RefSeq Proteins
        Link to Protein RefSeqs
      • RefSeq RNAs
        Link to Nucleotide RefSeq RNAs
      • SNP
        Related SNP records
      • SNP: GeneView
        SNPs linked from GeneView
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        Gene Genotype Report
      • Taxonomy
        Link to related taxonomy entry
      • UniGene
        Links are provided between Gene and UniGene when both databases calculate links to the same mRNA record (gi).
      • UniSTS
        Related UniSTS records

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