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    SCN10A sodium voltage-gated channel alpha subunit 10 [ Homo sapiens (human) ]

    Gene ID: 6336, updated on 23-Nov-2017
    Official Symbol
    SCN10Aprovided by HGNC
    Official Full Name
    sodium voltage-gated channel alpha subunit 10provided by HGNC
    Primary source
    HGNC:HGNC:10582
    See related
    Ensembl:ENSG00000185313 MIM:604427; Vega:OTTHUMG00000048245
    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
    PN3; SNS; hPN3; FEPS2; Nav1.8
    Summary
    The protein encoded by this gene is a tetrodotoxin-resistant voltage-gated sodium channel alpha subunit. The properties of the channel formed by the encoded transmembrane protein can be altered by interaction with different beta subunits. This protein may be involved in the onset of pain associated with peripheral neuropathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    Location:
    3p22.2
    Exon count:
    27
    Annotation release Status Assembly Chr Location
    108 current GRCh38.p7 (GCF_000001405.33) 3 NC_000003.12 (38697110..38794010, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38738837..38835501, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ribosomal protein L18a pseudogene 7 Neighboring gene sodium voltage-gated channel alpha subunit 5 Neighboring gene uncharacterized LOC105377034 Neighboring gene uncharacterized LOC107986042

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Jun 15 11:32:44 2016

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Associated conditions

    Description Tests
    Episodic pain syndrome, familial, 2
    MedGen: C3809893 OMIM: 615551 GeneReviews: Not available
    Compare labs

    NHGRI GWAS Catalog

    Description
    Common variants at SCN5A-SCN10A and HEY2 are associated with Brugada syndrome, a rare disease with high risk of sudden cardiac death.
    NHGRI GWA Catalog
    Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction.
    NHGRI GWA Catalog
    Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
    NHGRI GWA Catalog
    Genetic determinants of P wave duration and PR segment.
    NHGRI GWA Catalog
    Genetic variation in SCN10A influences cardiac conduction.
    NHGRI GWA Catalog
    Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk.
    NHGRI GWA Catalog
    Genome-wide association studies of the PR interval in African Americans.
    NHGRI GWA Catalog
    Genome-wide association study of electrocardiographic parameters identifies a new association for PR interval and confirms previously reported associations.
    NHGRI GWA Catalog
    Genome-wide association study of PR interval.
    NHGRI GWA Catalog
    Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science.
    NHGRI GWA Catalog
    Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    NHGRI GWA Catalog
    Meta-analysis followed by replication identifies loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with systemic lupus erythematosus in Asians.
    NHGRI GWA Catalog
    Novel loci associated with PR interval in a genome-wide association study of 10 African American cohorts.
    NHGRI GWA Catalog
    Several common variants modulate heart rate, PR interval and QRS duration.
    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...
    • 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
    ion channel binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    voltage-gated ion channel activity IEA
    Inferred from Electronic Annotation
    more info
     
    voltage-gated sodium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    AV node cell action potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    bundle of His cell action potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    membrane depolarization during action potential IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    neuronal action potential IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    odontogenesis of dentin-containing tooth IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of atrial cardiac muscle cell membrane depolarization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of cardiac muscle contraction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of heart rate IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    sensory perception TAS
    Traceable Author Statement
    more info
    PubMed 
    sensory perception of pain IEA
    Inferred from Electronic Annotation
    more info
     
    sodium ion transmembrane transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Component Evidence Code Pubs
    clathrin complex IEA
    Inferred from Electronic Annotation
    more info
     
    extracellular exosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    voltage-gated sodium channel complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Preferred Names
    sodium channel protein type 10 subunit alpha
    Names
    peripheral nerve sodium channel 3
    sodium channel protein type X subunit alpha
    sodium channel, voltage-gated, type X, alpha polypeptide
    sodium channel, voltage-gated, type X, alpha subunit
    voltage-gated sodium channel subunit alpha Nav1.8

    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_031891.2 RefSeqGene

      Range
      5001..101665
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001293306.2NP_001280235.2  sodium channel protein type 10 subunit alpha isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
      Source sequence(s)
      AC116038, AC137625, AF117907
      UniProtKB/Swiss-Prot
      Q9Y5Y9
      Conserved Domains (5) summary
      cd13433
      Location:14181470
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11681426
      Ion_trans; Ion transport protein
      pfam06512
      Location:9041146
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:463534
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17411798
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    2. NM_001293307.2NP_001280236.2  sodium channel protein type 10 subunit alpha isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter, compared to isoform 1.
      Source sequence(s)
      AC116038, AC137625, AF117907
      UniProtKB/Swiss-Prot
      Q9Y5Y9
      Conserved Domains (4) summary
      cd13433
      Location:13211373
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:10711329
      Ion_trans; Ion transport protein
      pfam06512
      Location:8061049
      Na_trans_assoc; Sodium ion transport-associated
      pfam16905
      Location:16441701
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    3. NM_006514.3NP_006505.3  sodium channel protein type 10 subunit alpha isoform 1

      See identical proteins and their annotated locations for NP_006505.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC137625, AF117907
      Consensus CDS
      CCDS33736.1
      UniProtKB/Swiss-Prot
      Q9Y5Y9
      Related
      ENSP00000390600.2, OTTHUMP00000045936, ENST00000449082.2, OTTHUMT00000109745
      Conserved Domains (5) summary
      cd13433
      Location:14191471
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11691427
      Ion_trans; Ion transport protein
      pfam06512
      Location:9041147
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:463534
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17421799
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 108

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

    Reference GRCh38.p7 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p7 Primary Assembly

      Range
      38697110..38794010 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533994.2XP_011532296.1  sodium channel protein type 10 subunit alpha isoform X3

      Conserved Domains (4) summary
      cd13433
      Location:13241376
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:10741332
      Ion_trans; Ion transport protein
      pfam06512
      Location:8091052
      Na_trans_assoc; Sodium ion transport-associated
      pfam16905
      Location:16471704
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    2. XM_011533993.2XP_011532295.1  sodium channel protein type 10 subunit alpha isoform X2

      Conserved Domains (5) summary
      cd13433
      Location:14211473
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11711429
      Ion_trans; Ion transport protein
      pfam06512
      Location:9071149
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:466537
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17441801
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    3. XM_005265371.3XP_005265428.1  sodium channel protein type 10 subunit alpha isoform X1

      Conserved Domains (5) summary
      cd13433
      Location:14221474
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11721430
      Ion_trans; Ion transport protein
      pfam06512
      Location:9071150
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:466537
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17451802
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated

    Alternate CHM1_1.1

    Genomic

    1. NC_018914.2 Alternate CHM1_1.1

      Range
      38690433..38787099 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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