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

Gene ID: 6336, updated on 21-Jul-2014
Official Symbol
SCN10Aprovided by HGNC
Official Full Name
sodium channel, voltage-gated, type X, alpha subunitprovided by HGNC
Primary source
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]
See SCN10A in Epigenomics, MapViewer
Location:
3p22.2
Exon count :
27
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 3 NC_000003.12 (38697346..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 sodium channel, voltage-gated, type XI, alpha subunit Neighboring gene WD repeat domain 48 Neighboring gene golgi reassembly stacking protein 1, 65kDa

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Associated conditions

Description Tests
Episodic pain syndrome, familial, 2
MedGen: CN182246 OMIM: 615551 GeneReviews: Not available
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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 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 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
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
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
voltage-gated sodium channel activity IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
AV node cell to bundle of His cell communication IMP
Inferred from Mutant Phenotype
more info
 
bundle of His cell to Purkinje myocyte communication IMP
Inferred from Mutant Phenotype
more info
 
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
 
regulation of atrial cardiac muscle cell membrane depolarization IMP
Inferred from Mutant Phenotype
more info
 
regulation of cardiac muscle contraction IMP
Inferred from Mutant Phenotype
more info
 
regulation of heart rate IMP
Inferred from Mutant Phenotype
more info
 
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 
sodium ion transport TAS
Traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
C-fiber IEA
Inferred from Electronic Annotation
more info
 
extracellular vesicular 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
sodium channel protein type 10 subunit alpha
peripheral nerve sodium channel 3
sodium channel protein type X subunit alpha
voltage-gated sodium channel subunit alpha Nav1.8
sodium channel, voltage-gated, type X, 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.

Genomic

  1. NG_031891.1 

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

mRNA and Protein(s)

  1. NM_001293306.1NP_001280235.1  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
    Conserved Domains (4) summary
    cd13433
    Location:14181470
    Blast Score: 303
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11871416
    Blast Score: 468
    Ion_trans; Ion transport protein
    pfam06512
    Location:9041161
    Blast Score: 617
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:448533
    Blast Score: 99
    DUF3451; Domain of unknown function (DUF3451)
  2. NM_001293307.1NP_001280236.1  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
    Conserved Domains (3) summary
    cd13433
    Location:13211373
    Blast Score: 302
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:10901319
    Blast Score: 458
    Ion_trans; Ion transport protein
    pfam06512
    Location:8061064
    Blast Score: 616
    Na_trans_assoc; Sodium ion transport-associated
  3. NM_006514.2NP_006505.2  sodium channel protein type 10 subunit alpha isoform 1

    See proteins identical to NP_006505.2

    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
    Blast Score: 303
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11881417
    Blast Score: 468
    Ion_trans; Ion transport protein
    pfam06512
    Location:9041162
    Blast Score: 617
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:448533
    Blast Score: 99
    DUF3451; Domain of unknown function (DUF3451)

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000003.12 

    Range
    38697346..38794010
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005265371.1XP_005265428.1  

    Conserved Domains (4) summary
    cd13433
    Location:14221474
    Blast Score: 303
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11911420
    Blast Score: 468
    Ion_trans; Ion transport protein
    pfam06512
    Location:9071165
    Blast Score: 617
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:451536
    Blast Score: 99
    DUF3451; Domain of unknown function (DUF3451)

Alternate HuRef

Genomic

  1. AC_000135.1 

    Range
    38781159..38877645
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018914.2 

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

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