U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 6336, updated on 9-Oct-2022

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
110 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38696807..38816217, complement)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38709028..38828431, complement)
105.20220307 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 hs2267 Neighboring gene VISTA enhancer hs2177 Neighboring gene sodium voltage-gated channel alpha subunit 5 Neighboring gene VISTA enhancer hs2268 Neighboring gene VISTA enhancer hs2619 Neighboring gene uncharacterized LOC105377034 Neighboring gene uncharacterized LOC107986042 Neighboring gene sodium voltage-gated channel alpha subunit 11 Neighboring gene RNA, U6 small nuclear 1227, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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 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

Homology

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
 
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
PubMed 
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/Swiss-Prot
    Q9Y5Y9
    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/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: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
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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

    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

    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

    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)