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SCN3B sodium voltage-gated channel beta subunit 3 [ Homo sapiens (human) ]

Gene ID: 55800, updated on 2-Nov-2024

Summary

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Official Symbol
SCN3Bprovided by HGNC
Official Full Name
sodium voltage-gated channel beta subunit 3provided by HGNC
Primary source
HGNC:HGNC:20665
See related
Ensembl:ENSG00000166257 MIM:608214; AllianceGenome:HGNC:20665
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
SCNB3; ATFB16; BRGDA7; HSA243396
Summary
Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit and one or more regulatory beta subunits. They are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel beta subunit gene family, and influences the inactivation kinetics of the sodium channel. Two alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
Expression
Biased expression in brain (RPKM 50.6) and adrenal (RPKM 4.9) See more
Orthologs
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Genomic context

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See SCN3B in Genome Data Viewer
Location:
11q24.1
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (123629188..123654624, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (123658164..123683597, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (123499896..123525332, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene GRAM domain containing 1B Neighboring gene uncharacterized LOC124902776 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4015 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4016 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr11:123313949-123314928 Neighboring gene Sharpr-MPRA regulatory region 13459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5684 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4017 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5686 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:123364173-123364689 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:123364690-123365206 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4018 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr11:123407917-123408491 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4019 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:123430192-123430855 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:123430856-123431518 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:123431519-123432182 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:123446989-123447488 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:123446487-123446988 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:123448087-123448624 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:123449825-123450047 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:123450909-123451518 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:123474209-123474708 Neighboring gene splicing factor 3a, subunit 3 pseudogene 2 Neighboring gene uncharacterized LOC124902777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4021 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4020 Neighboring gene uncharacterized LOC105369543 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:123572538-123573038 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:123573039-123573539 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:123599312-123600511 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5687 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4022 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4023 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr11:123612953-123613550 Neighboring gene zinc finger protein 202 Neighboring gene olfactory receptor family 6 subfamily X member 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. Hippocampal Nabeta3 expression in patients with temporal lobe epilepsy. van Gassen KL, et al. Epilepsia, 2009 Apr. PMID 19385982
  2. Tissue distribution and functional expression of the human voltage-gated sodium channel beta3 subunit. Stevens EB, et al. Pflugers Arch, 2001 Jan. PMID 11212211
  3. The voltage-gated Na+ channel beta3 subunit does not mediate trans homophilic cell adhesion or associate with the cell adhesion molecule contactin. McEwen DP, et al. Neurosci Lett, 2009 Oct 25. PMID 19596049, Free PMC Article
  4. Functional dominant-negative mutation of sodium channel subunit gene SCN3B associated with atrial fibrillation in a Chinese GeneID population. Wang P, et al. Biochem Biophys Res Commun, 2010 Jul 16. PMID 20558140, Free PMC Article
  5. Functional modulation of human brain Nav1.3 sodium channels, expressed in mammalian cells, by auxiliary beta 1, beta 2 and beta 3 subunits. Meadows LS, et al. Neuroscience, 2002. PMID 12220575

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Voltage-gated sodium channels beta3 subunit promotes tumorigenesis in hepatocellular carcinoma by facilitating p53 degradation.
    Title: Voltage-gated sodium channels β3 subunit promotes tumorigenesis in hepatocellular carcinoma by facilitating p53 degradation.
  2. rs1783901 may play a potential role of gene regulation and/or epistasis in a complex etiology of vertigo.
    Title: An Analysis of the Association between Epilepsy-Related Genes and Vertigo in the Polish Population.
  3. Contribution of Cardiac Sodium Channel beta-Subunit Variants to Brugada Syndrome.
    Title: Contribution of Cardiac Sodium Channel β-Subunit Variants to Brugada Syndrome.
  4. In a nonreferred nationwide Danish cohort of SIDS cases, up to 5/66 (7.5%) of SIDS cases can be explained by genetic variants in the sodium channel complex genes.
    Title: The role of the sodium current complex in a nonreferred nationwide cohort of sudden infant death syndrome.
  5. SCN1-3B the gene that encode respectively a- and b-subunits of the cardiac fast voltage-gated sodium channel, have been linked to atrial fibrillation.
    Title: Risk factors and genetics of atrial fibrillation.
  6. The Val110Ile mutation of SCN3B is a relatively common cause of SCN5A-negative BrS in Japan, which has a reduced sodium current because of the loss of cell surface expression of Nav1.5.
    Title: Novel SCN3B mutation associated with brugada syndrome affects intracellular trafficking and function of Nav1.5.
  7. the beta3 subunit can mediate trans homophilic-binding via its Ig domain and the beta3-Ig domain can associate heterophilically with the beta1 subunit
    Title: The immunoglobulin domain of the sodium channel β3 subunit contains a surface-localized disulfide bond that is required for homophilic binding.
  8. three mutations in SCN3B were investigated electrophysiologically and all led to loss of function in the sodium current, supporting the hypothesis that decreased sodium current enhances atrial fibrillation susceptibility
    Title: Mutations in sodium channel β-subunit SCN3B are associated with early-onset lone atrial fibrillation.
  9. The researchers found evidence of an association between SCN3B subunit mutations and sudden infant death syndrome pathogenesis.
    Title: Sudden infant death syndrome-associated mutations in the sodium channel beta subunits.
  10. The sodium channel {beta}3-subunit induces multiphasic gating in NaV1.3 and affects fast inactivation via distinct intracellular regions.
    Title: The sodium channel {beta}3-subunit induces multiphasic gating in NaV1.3 and affects fast inactivation via distinct intracellular regions.
Submit: New GeneRIF Correction See all GeneRIFs (16)

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
Brugada syndrome 7
MedGen: C2751088 OMIM: 613120 GeneReviews: Brugada Syndrome
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EBI GWAS Catalog

Description
A genome-wide association study identifies multiple susceptibility loci for chronic lymphocytic leukemia.
EBI GWAS Catalog
Genome-wide association study identifies multiple risk loci for chronic lymphocytic leukemia.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables sodium channel inhibitor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables sodium channel regulator activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables sodium channel regulator activity IMP
Inferred from Mutant Phenotype
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 involved in cardiac muscle cell action potential IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in SA node cell action potential ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in atrial cardiac muscle cell action potential IMP
Inferred from Mutant Phenotype
more info
 PubMed 
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 membrane depolarization IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in membrane depolarization during action potential IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in membrane depolarization during action potential IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in membrane depolarization during cardiac muscle cell action potential IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nervous system development IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of heart rate ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of sodium ion transport IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of sodium ion transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in protein localization to plasma membrane IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of atrial cardiac muscle cell membrane depolarization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of heart rate by cardiac conduction IBA
Inferred from Biological aspect of Ancestor
more info
  
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 IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of ventricular cardiac muscle cell membrane depolarization 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 NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in ventricular cardiac muscle cell action potential IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in ventricular cardiac muscle cell action potential IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in Z disc ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in membrane NAS
Non-traceable Author Statement
more info
 PubMed 
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 TAS
Traceable Author Statement
more info
 PubMed 

General protein information

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Preferred Names
sodium channel regulatory subunit beta-3
Names
sodium channel subunit beta-3
sodium channel, voltage-gated, type III, beta subunit
voltage-gated sodium channel beta-3 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

  1. NG_016283.1 RefSeqGene

    Range
    5001..30421
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_421

mRNA and Protein(s)

  1. NM_001040151.2 → NP_001035241.1  sodium channel regulatory subunit beta-3 precursor

    See identical proteins and their annotated locations for NP_001035241.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform.
    Source sequence(s)
    AP002765
    Consensus CDS
    CCDS8442.1
    UniProtKB/Swiss-Prot
    A5H1I5, Q17RL3, Q9NY72, Q9ULR2
    Related
    ENSP00000299333.3, ENST00000299333.8
    Conserved Domains (2) summary
    pfam07686
    Location:28 → 140
    V-set; Immunoglobulin V-set domain
    cd00096
    Location:31 → 37
    Ig; Ig strand A' [structural motif]

  2. NM_018400.4 → NP_060870.1  sodium channel regulatory subunit beta-3 precursor

    See identical proteins and their annotated locations for NP_060870.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript.
    Source sequence(s)
    AP002765
    Consensus CDS
    CCDS8442.1
    UniProtKB/Swiss-Prot
    A5H1I5, Q17RL3, Q9NY72, Q9ULR2
    Related
    ENSP00000376523.2, ENST00000392770.6
    Conserved Domains (2) summary
    pfam07686
    Location:28 → 140
    V-set; Immunoglobulin V-set domain
    cd00096
    Location:31 → 37
    Ig; Ig strand A' [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    123629188..123654624 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542897.3 → XP_011541199.1  sodium channel regulatory subunit beta-3 isoform X1

    See identical proteins and their annotated locations for XP_011541199.1

    UniProtKB/Swiss-Prot
    A5H1I5, Q17RL3, Q9NY72, Q9ULR2
    Conserved Domains (2) summary
    pfam07686
    Location:28 → 140
    V-set; Immunoglobulin V-set domain
    cd00096
    Location:31 → 37
    Ig; Ig strand A' [structural motif]

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    123658164..123683597 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054369351.1 → XP_054225326.1  sodium channel regulatory subunit beta-3 isoform X1

    UniProtKB/Swiss-Prot
    A5H1I5, Q17RL3, Q9NY72, Q9ULR2
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NY72.1 GenPept UniProtKB/Swiss-Prot:Q9NY72

Gene LinkOut

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