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SCN10A sodium channel, voltage gated, type X alpha subunit [ Homo sapiens (human) ]

Gene ID: 6336, updated on 4-Jul-2015
Official Symbol
SCN10Aprovided by HGNC
Official Full Name
sodium channel, voltage gated, type X alpha subunitprovided by HGNC
Primary source
HGNC:HGNC:10582
See related
Ensembl:ENSG00000185313; HPRD:09188; 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]
Orthologs
See SCN10A in Epigenomics, MapViewer
Location:
3p22.2
Exon count:
27
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 3 NC_000003.12 (38696891..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 channel, voltage gated, type V alpha subunit Neighboring gene uncharacterized LOC105377034 Neighboring gene sodium channel, voltage gated, type XI alpha subunit Neighboring gene uncharacterized LOC105377643

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...
  • 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...
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 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
C-fiber IEA
Inferred from Electronic Annotation
more info
 
clathrin complex IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
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 (4) summary
    cd13433
    Location:14181470
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11871416
    Ion_trans; Ion transport protein
    pfam06512
    Location:9041161
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:448533
    DUF3451; Domain of unknown function (DUF3451)
  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 (3) summary
    cd13433
    Location:13211373
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:10901319
    Ion_trans; Ion transport protein
    pfam06512
    Location:8061064
    Na_trans_assoc; Sodium ion transport-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, OTTHUMP00000045936, ENST00000449082, OTTHUMT00000109745
    Conserved Domains (4) summary
    cd13433
    Location:14191471
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11881417
    Ion_trans; Ion transport protein
    pfam06512
    Location:9041162
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:448533
    DUF3451; Domain of unknown function (DUF3451)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 107

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p2 Primary Assembly

    Range
    38696891..38794010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011533994.1XP_011532296.1  

    Conserved Domains (3) summary
    cd13433
    Location:13241376
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:10931322
    Ion_trans; Ion transport protein
    pfam06512
    Location:8091067
    Na_trans_assoc; Sodium ion transport-associated
  2. XM_011533993.1XP_011532295.1  

    Conserved Domains (4) summary
    cd13433
    Location:14211473
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11901419
    Ion_trans; Ion transport protein
    pfam06512
    Location:9071164
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:451536
    DUF3451; Domain of unknown function (DUF3451)
  3. XM_005265371.2XP_005265428.1  

    Conserved Domains (4) summary
    cd13433
    Location:14221474
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11911420
    Ion_trans; Ion transport protein
    pfam06512
    Location:9071165
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:451536
    DUF3451; Domain of unknown function (DUF3451)

Alternate CHM1_1.1

Genomic

  1. NC_018914.2 Alternate CHM1_1.1

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