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

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: mouse all
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Genomic context

Location:: 3p22.2

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (38696807..38816217, complement)
RS_2023_10	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_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Heterologous expression of the human wild-type and variant NaV 1.8 (A1073V) in rat sensory neurons.
Title: Heterologous expression of the human wild-type and variant Na(V) 1.8 (A1073V) in rat sensory neurons.
Molecular and Functional Relevance of NaV1.8-Induced Atrial Arrhythmogenic Triggers in a Human SCN10A Knock-Out Stem Cell Model.
Title: Molecular and Functional Relevance of Na(V)1.8-Induced Atrial Arrhythmogenic Triggers in a Human SCN10A Knock-Out Stem Cell Model.
Patient-specific induced pluripotent stem cell properties implicate Ca[2+]-homeostasis in clinical arrhythmia associated with combined heterozygous RYR2 and SCN10A variants.
Title: Patient-specific induced pluripotent stem cell properties implicate Ca(2+)-homeostasis in clinical arrhythmia associated with combined heterozygous RYR2 and SCN10A variants.
Biallelic Loss of Function Mutation in Sodium Channel Gene SCN10A in an Autism Spectrum Disorder Trio from Pakistan.
Title: Biallelic Loss of Function Mutation in Sodium Channel Gene SCN10A in an Autism Spectrum Disorder Trio from Pakistan.
Clinical Implications of SCN10A Loss-of-Function Variants in 169 610 Exomes Representing the General Population.
Title: Clinical Implications of SCN10A Loss-of-Function Variants in 169 610 Exomes Representing the General Population.
Common variants in SCN10A gene associated with Brugada syndrome.
Title: Common variants in SCN10A gene associated with Brugada syndrome.
Contributions of NaV1.8 and NaV1.9 to excitability in human induced pluripotent stem-cell derived somatosensory neurons.
Title: Contributions of Na(V)1.8 and Na(V)1.9 to excitability in human induced pluripotent stem-cell derived somatosensory neurons.
Detrimental proarrhythmogenic interaction of Ca(2+)/calmodulin-dependent protein kinase II and NaV1.8 in heart failure.
Title: Detrimental proarrhythmogenic interaction of Ca(2+)/calmodulin-dependent protein kinase II and Na(V)1.8 in heart failure.
Disordered breathing in a Pitt-Hopkins syndrome model involves Phox2b-expressing parafacial neurons and aberrant Nav1.8 expression.
Title: Disordered breathing in a Pitt-Hopkins syndrome model involves Phox2b-expressing parafacial neurons and aberrant Nav1.8 expression.
Family-based exome sequencing identifies rare coding variants in age-related macular degeneration.
Title: Family-based exome sequencing identifies rare coding variants in age-related macular degeneration.

Submit: New GeneRIF Correction See all GeneRIFs (72)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S1100 (e-PCR)
- UniSTS:146836

SCN10A_3461 (e-PCR)
- UniSTS:462510

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables transmembrane transporter binding	IPI Inferred from Physical Interaction more info	PubMed
enables voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IEA Inferred from Electronic Annotation more info
enables voltage-gated sodium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables voltage-gated sodium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated sodium channel activity	IMP Inferred from Mutant Phenotype more info	PubMed

Process	Evidence Code	Pubs
involved_in AV node cell action potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in bundle of His cell action potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cardiac muscle cell action potential involved in contraction	IBA Inferred from Biological aspect of Ancestor more info
involved_in membrane depolarization during action potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in odontogenesis of dentin-containing tooth	IEA Inferred from Electronic Annotation more info
involved_in regulation of atrial cardiac muscle cell membrane depolarization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of cardiac muscle contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of heart rate	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of monoatomic ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of presynaptic membrane potential	IEA Inferred from Electronic Annotation more info
involved_in sensory perception	TAS Traceable Author Statement more info	PubMed
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in sodium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed

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 more info	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

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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)

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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

NG_031891.3 RefSeqGene

Range

5000..124410

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001293306.2 → NP_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:1418 → 1470

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1150 → 1426

Ion_trans; Ion transport protein

pfam06512
Location:904 → 1146

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:488 → 615

Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
NM_001293307.2 → NP_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:1321 → 1373

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1053 → 1329

Ion_trans; Ion transport protein

pfam06512
Location:806 → 1049

Na_trans_assoc; Sodium ion transport-associated
NM_006514.4 → NP_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:1419 → 1471

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1151 → 1427

Ion_trans; Ion transport protein

pfam06512
Location:904 → 1147

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:452 → 615

Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000003.12 Reference GRCh38.p14 Primary Assembly

Range

38696807..38816217 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A2R8Y6J6

Conserved Domains (4) summary

cd13433
Location:1324 → 1376

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1074 → 1332

Ion_trans; Ion transport protein

pfam06512
Location:809 → 1052

Na_trans_assoc; Sodium ion transport-associated

pfam16905
Location:1647 → 1704

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_011533993.3 → XP_011532295.1 sodium channel protein type 10 subunit alpha isoform X2

UniProtKB/TrEMBL

A0A2R8Y6J6

Conserved Domains (5) summary

cd13433
Location:1421 → 1473

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1171 → 1429

Ion_trans; Ion transport protein

pfam06512
Location:907 → 1149

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:466 → 537

Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

pfam16905
Location:1744 → 1801

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_005265371.4 → XP_005265428.1 sodium channel protein type 10 subunit alpha isoform X1

UniProtKB/TrEMBL

A0A2R8Y6J6

Conserved Domains (5) summary

cd13433
Location:1422 → 1474

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1172 → 1430

Ion_trans; Ion transport protein

pfam06512
Location:907 → 1150

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:466 → 537

Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

pfam16905
Location:1745 → 1802

GPHH; Voltage-dependent L-type calcium channel, IQ-associated

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

38709028..38828431 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054347488.1 → XP_054203463.1 sodium channel protein type 10 subunit alpha isoform X3
XM_054347487.1 → XP_054203462.1 sodium channel protein type 10 subunit alpha isoform X2
XM_054347486.1 → XP_054203461.1 sodium channel protein type 10 subunit alpha isoform X1