SCN7A sodium voltage-gated channel alpha subunit 7 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SCN7Aprovided by HGNC
Official Full Name: sodium voltage-gated channel alpha subunit 7provided by HGNC
Primary source: HGNC:HGNC:10594
See related: Ensembl:ENSG00000136546 MIM:182392; AllianceGenome:HGNC:10594
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: NaG; SCN6A; Nav2.1; Nav2.2
Summary: This gene encodes one of the many voltage-gated sodium channel proteins. For proper functioning of neurons and muscles during action potentials, voltage-gated sodium channels direct sodium ion diffusion for membrane depolarization. This sodium channel protein has some atypical characteristics; the similarity between the human and mouse proteins is lower compared to other orthologous sodium channel pairs. Also, the S4 segments, which sense voltage changes, have fewer positive charged residues that in other sodium channels; domain 4 has fewer arginine and lysine residues compared to other sodium channel proteins. Several alternatively spliced transcript variants exist, but the full-length natures of all of them remain unknown. [provided by RefSeq, Dec 2011]
Expression: Broad expression in ovary (RPKM 21.8), lung (RPKM 14.7) and 15 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 2q24.3

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	2	NC_000002.12 (166403573..166494249, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	2	NC_060926.1 (166861052..166951694, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	2	NC_000002.11 (167260083..167350759, complement)

Chromosome 2 - NC_000002.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

Genomic analyses reveal SCN7A is associated with the prognosis of esophageal squamous cell carcinoma.
Title: Genomic analyses reveal SCN7A is associated with the prognosis of esophageal squamous cell carcinoma.
Identification of SCN7A as the key gene associated with tumor mutation burden in gastric cancer.
Title: Identification of SCN7A as the key gene associated with tumor mutation burden in gastric cancer.
The authors demonstrated that the sodium channel Nax functions as a sodium sensor. With increased extracellular sodium, Nax up-regulates prostasin, which results in activation of the sodium channel ENaC.
Title: Sodium channel Nax is a regulator in epithelial sodium homeostasis.
SNP rs7565062 of SCN7A was significantly associated with essential hypertension in a Northern Han Chinese population
Title: The association between the polymorphisms in a sodium channel gene SCN7A and essential hypertension: a case-control study in the Northern Han Chinese.
Observational study of gene-disease association. (HuGE Navigator)
Title: Genetic variations associated with echocardiographic left ventricular traits in hypertensive blacks.

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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

EBI GWAS Catalog

Description
Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis. 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

A007J23 (e-PCR)
- UniSTS:1793

WI-9171 (e-PCR)
- UniSTS:8247

G59750 (e-PCR)
- UniSTS:137046

SHGC-82665 (e-PCR)
- UniSTS:100740

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables osmolarity-sensing monoatomic cation channel activity	ISS Inferred from Sequence or Structural Similarity more info
enables sodium channel activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transmembrane transporter binding	IEA Inferred from Electronic Annotation more info
enables voltage-gated sodium channel activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cardiac muscle cell action potential involved in contraction	IBA Inferred from Biological aspect of Ancestor more info
involved_in cellular homeostasis	IEA Inferred from Electronic Annotation more info
involved_in osmosensory signaling pathway	ISS Inferred from Sequence or Structural Similarity more info
involved_in response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in sodium ion homeostasis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in glial cell projection	IEA Inferred from Electronic Annotation more info
is_active_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
part_of voltage-gated sodium channel complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: sodium channel protein type 7 subunit alpha

Names: atypical sodium channel Nav2.1; nax channel; putative voltage-gated sodium channel subunit alpha Nax; sodium channel protein cardiac and skeletal muscle subunit alpha; sodium channel protein type VII subunit alpha; sodium channel, voltage-gated, type VI, alpha polypeptide; sodium channel, voltage-gated, type VII, alpha subunit; voltage-dependent sodium channel alpha subunit

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_031928.2 RefSeqGene

Range

5000..95676

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_002976.4 → NP_002967.2 sodium channel protein type 7 subunit alpha

See identical proteins and their annotated locations for NP_002967.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the protein-coding transcript.

Source sequence(s)

AC074101, AC092583

Consensus CDS

CCDS46442.1

UniProtKB/Swiss-Prot

Q01118

Related

ENSP00000496114.1, ENST00000643258.1

Conserved Domains (3) summary

cd13433
Location:1194 → 1246

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

pfam00520
Location:951 → 1198

Ion_trans; Ion transport protein

pfam06512
Location:743 → 927

Na_trans_assoc; Sodium ion transport-associated

RNA

NR_045628.1 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate exon and is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC074101, AC092583, BC062699, BC141864, CK903677

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_000002.12 Reference GRCh38.p14 Primary Assembly

Range

166403573..166494249 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006712680.3 → XP_006712743.1 sodium channel protein type 7 subunit alpha isoform X1

See identical proteins and their annotated locations for XP_006712743.1

UniProtKB/Swiss-Prot

Q01118

Related

ENSP00000403846.2, ENST00000441411.2

Conserved Domains (3) summary

cd13433
Location:1194 → 1246

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

pfam00520
Location:951 → 1198

Ion_trans; Ion transport protein

pfam06512
Location:743 → 927

Na_trans_assoc; Sodium ion transport-associated
XM_011511615.3 → XP_011509917.1 sodium channel protein type 7 subunit alpha isoform X1

See identical proteins and their annotated locations for XP_011509917.1

UniProtKB/Swiss-Prot

Q01118

Conserved Domains (3) summary

cd13433
Location:1194 → 1246

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

pfam00520
Location:951 → 1198

Ion_trans; Ion transport protein

pfam06512
Location:743 → 927

Na_trans_assoc; Sodium ion transport-associated
XM_017004667.2 → XP_016860156.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118

Conserved Domains (3) summary

cd13433
Location:1194 → 1246

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

pfam00520
Location:951 → 1198

Ion_trans; Ion transport protein

pfam06512
Location:743 → 927

Na_trans_assoc; Sodium ion transport-associated
XM_006712682.4 → XP_006712745.1 sodium channel protein type 7 subunit alpha isoform X1

See identical proteins and their annotated locations for XP_006712745.1

UniProtKB/Swiss-Prot

Q01118

Conserved Domains (3) summary

cd13433
Location:1194 → 1246

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

pfam00520
Location:951 → 1198

Ion_trans; Ion transport protein

pfam06512
Location:743 → 927

Na_trans_assoc; Sodium ion transport-associated
XM_047445398.1 → XP_047301354.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118
XM_047445397.1 → XP_047301353.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118
XM_047445396.1 → XP_047301352.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118

Alternate T2T-CHM13v2.0

Genomic

NC_060926.1 Alternate T2T-CHM13v2.0

Range

166861052..166951694 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054343313.1 → XP_054199288.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118
XM_054343319.1 → XP_054199294.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118
XM_054343316.1 → XP_054199291.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118
XM_054343314.1 → XP_054199289.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118
XM_054343318.1 → XP_054199293.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118
XM_054343317.1 → XP_054199292.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118
XM_054343315.1 → XP_054199290.1 sodium channel protein type 7 subunit alpha isoform X1

UniProtKB/Swiss-Prot

Q01118