SCN4B sodium voltage-gated channel beta subunit 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SCN4Bprovided by HGNC
Official Full Name: sodium voltage-gated channel beta subunit 4provided by HGNC
Primary source: HGNC:HGNC:10592
See related: Ensembl:ENSG00000177098 MIM:608256; AllianceGenome:HGNC:10592
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: LQT10; ATFB17; Navbeta4
Summary: The protein encoded by this gene is one of several sodium channel beta subunits. These subunits interact with voltage-gated alpha subunits to change sodium channel kinetics. The encoded transmembrane protein forms interchain disulfide bonds with SCN2A. Defects in this gene are a cause of long QT syndrome type 10 (LQT10). Three protein-coding and one non-coding transcript variant have been found for this gene.[provided by RefSeq, Mar 2009]
Expression: Broad expression in fat (RPKM 19.5), brain (RPKM 8.6) and 18 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q23.3

Exon count:: 5

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (118133377..118152823, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (118149764..118169227, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (118004092..118023538, complement)

Chromosome 11 - NC_000011.10 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?

Anti-NSCLC role of SCN4B by negative regulation of the cGMP-PKG pathway: Integrated utilization of bioinformatics analysis and in vitro assay validation.
Title: Anti-NSCLC role of SCN4B by negative regulation of the cGMP-PKG pathway: Integrated utilization of bioinformatics analysis and in vitro assay validation.
SCN4B inhibits the progression of lung adenocarcinoma and is associated with better prognosis.
Title: SCN4B inhibits the progression of lung adenocarcinoma and is associated with better prognosis.
The Voltage-Gated Sodium Channel Beta4 Subunit Maintains Epithelial Phenotype in Mammary Cells.
Title: The Voltage-Gated Sodium Channel Beta4 Subunit Maintains Epithelial Phenotype in Mammary Cells.
Silencing of microRNA-3175 represses cell proliferation and invasion in prostate cancer by targeting the potential tumor-suppressor SCN4B.
Title: Silencing of microRNA-3175 represses cell proliferation and invasion in prostate cancer by targeting the potential tumor-suppressor SCN4B.
These data suggest that rare variant p.Gly8Ser of SCN4B confers a significant risk of AF, and SCN4B is a candidate susceptibility gene for AF.
Title: Significant association of rare variant p.Gly8Ser in cardiac sodium channel β4-subunit SCN4B with atrial fibrillation.
Data identified one rare nonsynonymous heterozygous variant, p.Gly8Ser, in SCN4B that was significantly associated with a risk of ventricular tachycardia (VT) in two independent populations.
Title: Identification of rare variants in cardiac sodium channel β4-subunit gene SCN4B associated with ventricular tachycardia.
this study reports the cryo-electron microscopy structure of the human Nav1.4-beta1 complex at 3.2-A resolution.
Title: Structure of the human voltage-gated sodium channel Na(v)1.4 in complex with β1.
SCN4B overexpression reduces cancer cell invasiveness and tumour progression.
Title: SCN4B acts as a metastasis-suppressor gene preventing hyperactivation of cell migration in breast cancer.
Preserved SCN4B expression is an independent indicator of favorable recurrence-free survival in classical papillary thyroid cancer.
Title: Preserved SCN4B expression is an independent indicator of favorable recurrence-free survival in classical papillary thyroid cancer.
Data suggest that extracellular domains of SCN4B directly interact with each other in parallel homodimers that involve an intermolecular disulfide bond between unpaired Cys residues (Cys58) in loop connecting strands B and C and intermolecular hydrophobic and hydrogen-bonding interactions of N-terminal segments (Ser30-Val35); SCN4B homodimers appear to play role in cell-cell adhesion.
Title: Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel β4 subunit explain its role in cell-cell adhesion.

Submit: New GeneRIF Correction See all GeneRIFs (24)

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
Long QT syndrome 10 MedGen: C2678484 OMIM: 611819 GeneReviews: Long QT Syndrome Overview	Compare labs

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

RH98735 (e-PCR)
- UniSTS:88577

WI-19664 (e-PCR)
- UniSTS:5016

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium channel regulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables sodium channel regulator activity	IDA Inferred from Direct Assay more info	PubMed
enables transmembrane transporter binding	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane transporter binding	IPI Inferred from Physical Interaction more info	PubMed
enables voltage-gated sodium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated sodium channel activity involved in cardiac muscle cell action potential	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 cardiac conduction	IBA Inferred from Biological aspect of Ancestor more info
involved_in cardiac muscle cell action potential involved in contraction	IBA Inferred from Biological aspect of Ancestor more info
involved_in cardiac muscle cell action potential involved in contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cardiac muscle contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in membrane depolarization during cardiac muscle cell action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in membrane depolarization during cardiac muscle cell action potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuronal action potential	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of sodium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of heart rate by cardiac conduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of sodium ion transmembrane transporter activity	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of ventricular cardiac muscle cell membrane repolarization	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of ventricular cardiac muscle cell membrane repolarization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion transmembrane transport	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transport	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in intercalated disc	ISS Inferred from Sequence or Structural Similarity more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
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
part_of voltage-gated sodium channel complex	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: sodium channel subunit beta-4

Names: sodium channel, voltage-gated, type IV, beta 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_011710.1 RefSeqGene

Range

5001..24539

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_330

mRNA and Protein(s)

NM_001142348.2 → NP_001135820.1 sodium channel subunit beta-4 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks multiple in-frame exons in the 5' coding region, compared to variant 1. This variant encodes isoform 2 which has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AY149967, BC035017, DA109496, DB101246, DB237478

Consensus CDS

CCDS44744.1

UniProtKB/Swiss-Prot

Q8IWT1

Related

ENSP00000436343.1, ENST00000529878.1
NM_001142349.2 → NP_001135821.1 sodium channel subunit beta-4 isoform 3

See identical proteins and their annotated locations for NP_001135821.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and 5' coding region, compared to variant 1. These differences cause translation initiation at an in-frame downstream ATG and an isoform (3) which has a shorter N-terminus, compared to isoform 1. Translation initiation from the start codon 197 nucleotides upstream would subject the transcript to nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AY149967, BC035017, DA111034, DA211092, DB101246

UniProtKB/Swiss-Prot

Q8IWT1

Related

ENST00000415030.6

Conserved Domains (2) summary

cd00096
Location:2 → 10

Ig; Ig strand E [structural motif]

cl11960
Location:2 → 41

Ig; Immunoglobulin domain
NM_174934.4 → NP_777594.1 sodium channel subunit beta-4 isoform 1 precursor

See identical proteins and their annotated locations for NP_777594.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AY149967, BC035017, DB101246, DB237478

Consensus CDS

CCDS8389.1

UniProtKB/Swiss-Prot

E9PPT5, Q6PIG5, Q8IWT1

UniProtKB/TrEMBL

B0YJ93

Related

ENSP00000322460.4, ENST00000324727.9

Conserved Domains (2) summary

cd00096
Location:31 → 35

Ig; Ig strand A [structural motif]

cl11960
Location:31 → 151

Ig; Immunoglobulin domain

RNA

NR_024527.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR and 5' coding region, compared to variant 1. This variant is represented as non-coding because it lacks an in-frame coding region that contains the translation start codon, compared to variant 1.

Source sequence(s)

AY149967, BC035017, DA111034, DA247019, DB101246