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

    Gene ID: 6336, updated on 17-Sep-2024

    Summary

    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; AllianceGenome:HGNC:10582
    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; 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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SCN10A in Genome Data Viewer
    Location:
    3p22.2
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38696807..38816217, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38709028..38828431, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38738298..38857708, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene VISTA enhancer hs2266 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38583605-38584141 Neighboring gene VISTA enhancer hs2267 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38589324-38590114 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38590115-38590903 Neighboring gene ribosomal protein L18a pseudogene 7 Neighboring gene VISTA enhancer hs2177 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:38623245-38624228 Neighboring gene sodium voltage-gated channel alpha subunit 5 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:38656451-38656951 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:38666894-38667075 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38669791-38670290 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr3:38682299-38683042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38684220-38684730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:38684731-38685239 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14214 Neighboring gene VISTA enhancer hs2268 Neighboring gene VISTA enhancer hs2619 Neighboring gene uncharacterized LOC105377034 Neighboring gene uncharacterized LOC107986042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14215 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:38877996-38878572 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:38912374-38913573 Neighboring gene sodium voltage-gated channel alpha subunit 11 Neighboring gene NANOG hESC enhancer GRCh37_chr3:39020389-39020890 Neighboring gene RNA, U6 small nuclear 1227, pseudogene

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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 Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

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

    EBI 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.
    EBI GWAS Catalog
    Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction.
    EBI GWAS Catalog
    Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.
    EBI GWAS Catalog
    Genetic determinants of P wave duration and PR segment.
    EBI GWAS Catalog
    Genetic variation in SCN10A influences cardiac conduction.
    EBI GWAS Catalog
    Genome- and phenome-wide analyses of cardiac conduction identifies markers of arrhythmia risk.
    EBI GWAS Catalog
    Genome-wide association studies of the PR interval in African Americans.
    EBI GWAS Catalog
    Genome-wide association study of electrocardiographic parameters identifies a new association for PR interval and confirms previously reported associations.
    EBI GWAS Catalog
    Genome-wide association study of PR interval.
    EBI GWAS Catalog
    Identification of genomic predictors of atrioventricular conduction: using electronic medical records as a tool for genome science.
    EBI GWAS Catalog
    Identification of three novel genetic variations associated with electrocardiographic traits (QRS duration and PR interval) in East Asians.
    EBI GWAS 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.
    EBI GWAS Catalog
    Novel loci associated with PR interval in a genome-wide association study of 10 African American cohorts.
    EBI GWAS Catalog
    Several common variants modulate heart rate, PR interval and QRS duration.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    part_of clathrin complex IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in glutamatergic synapse IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in presynaptic membrane IEA
    Inferred from Electronic Annotation
    more info
     
    part_of voltage-gated sodium channel complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of voltage-gated sodium channel complex IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    sodium channel protein type 10 subunit alpha
    Names
    peripheral nerve sodium channel 3
    sensory neuron sodium channel
    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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_031891.3 RefSeqGene

      Range
      5000..124410
      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
      Consensus CDS
      CCDS87064.1
      UniProtKB/TrEMBL
      A0A2R8Y6J6
      Related
      ENSP00000495595.1, ENST00000643924.1
      Conserved Domains (4) summary
      cd13433
      Location:14181470
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11501426
      Ion_trans; Ion transport protein
      pfam06512
      Location:9041146
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:488615
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    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/TrEMBL
      A0A2R8Y6J6
      Conserved Domains (3) summary
      cd13433
      Location:13211373
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:10531329
      Ion_trans; Ion transport protein
      pfam06512
      Location:8061049
      Na_trans_assoc; Sodium ion transport-associated
    3. NM_006514.4NP_006505.4  sodium channel protein type 10 subunit alpha isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AC116038, AC137625
      Consensus CDS
      CCDS33736.1
      UniProtKB/Swiss-Prot
      A6NDQ1, Q9Y5Y9
      UniProtKB/TrEMBL
      A0A2R8Y6J6
      Related
      ENSP00000390600.2, ENST00000449082.3
      Conserved Domains (4) summary
      cd13433
      Location:14191471
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11511427
      Ion_trans; Ion transport protein
      pfam06512
      Location:9041147
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:452615
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      38696807..38816217 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011533994.3XP_011532296.1  sodium channel protein type 10 subunit alpha isoform X3

      UniProtKB/TrEMBL
      A0A2R8Y6J6
      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_011533993.3XP_011532295.1  sodium channel protein type 10 subunit alpha isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y6J6
      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_005265371.4XP_005265428.1  sodium channel protein type 10 subunit alpha isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y6J6
      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 T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      38709028..38828431 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054347488.1XP_054203463.1  sodium channel protein type 10 subunit alpha isoform X3

      UniProtKB/TrEMBL
      A0A2R8Y6J6
    2. XM_054347487.1XP_054203462.1  sodium channel protein type 10 subunit alpha isoform X2

      UniProtKB/TrEMBL
      A0A2R8Y6J6
    3. XM_054347486.1XP_054203461.1  sodium channel protein type 10 subunit alpha isoform X1

      UniProtKB/TrEMBL
      A0A2R8Y6J6