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SCN1B sodium voltage-gated channel beta subunit 1 [ Homo sapiens (human) ]

Gene ID: 6324, updated on 7-Apr-2024

Summary

Official Symbol
SCN1Bprovided by HGNC
Official Full Name
sodium voltage-gated channel beta subunit 1provided by HGNC
Primary source
HGNC:HGNC:10586
See related
Ensembl:ENSG00000105711 MIM:600235; AllianceGenome:HGNC:10586
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
DEE52; ATFB13; BRGDA5; EIEE52; GEFSP1
Summary
Voltage-gated sodium channels are heteromeric proteins that function in the generation and propagation of action potentials in muscle and neuronal cells. They are composed of one alpha and two beta subunits, where the alpha subunit provides channel activity and the beta-1 subunit modulates the kinetics of channel inactivation. This gene encodes a sodium channel beta-1 subunit. Mutations in this gene result in generalized epilepsy with febrile seizures plus, Brugada syndrome 5, and defects in cardiac conduction. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Oct 2009]
Expression
Broad expression in heart (RPKM 5.3), brain (RPKM 5.1) and 21 other tissues See more
Orthologs
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Genomic context

See SCN1B in Genome Data Viewer
Location:
19q13.11
Exon count:
7
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35030470..35040449)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (37575088..37585067)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (35521374..35531353)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124904700 Neighboring gene H3K27ac hESC enhancer GRCh37_chr19:35488612-35489287 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10512 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10513 Neighboring gene GRAM domain containing 1A Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35495135-35495680 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35495681-35496225 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14453 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10514 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:35521843-35521951 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:35531257-35532096 Neighboring gene hepsin Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:35556563-35557324 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:35558779-35559464 Neighboring gene HPN antisense RNA 1 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:35559465-35560150 Neighboring gene MPRA-validated peak3446 silencer Neighboring gene sushi, nidogen and EGF like domains 1 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
Atrial fibrillation, familial, 13
MedGen: C3809311 OMIM: 615377 GeneReviews: Not available
Compare labs
Brugada syndrome 5
MedGen: C2748541 OMIM: 612838 GeneReviews: Brugada Syndrome
Compare labs
Developmental and epileptic encephalopathy, 52
MedGen: C4479236 OMIM: 617350 GeneReviews: Not available
Compare labs
Generalized epilepsy with febrile seizures plus, type 1
MedGen: C1858672 OMIM: 604233 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Haploinsufficency

No evidence available (Last evaluated 2019-09-04)

ClinGen Genome Curation Page
Triplosensitivity

No evidence available (Last evaluated 2019-09-04)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
Discovery and fine mapping of serum protein loci through transethnic meta-analysis.
EBI GWAS Catalog

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in cardiac conduction ISS
Inferred from Sequence or Structural Similarity
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 cell adhesion IEA
Inferred from Electronic Annotation
more info
 
involved_in corticospinal neuron axon guidance ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in locomotion ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in membrane depolarization IDA
Inferred from Direct Assay
more info
PubMed 
involved_in membrane depolarization during Purkinje myocyte cell action potential IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in membrane depolarization during cardiac muscle cell action potential ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in neuronal action potential propagation ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in positive regulation of neuron projection development 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 voltage-gated sodium channel activity IDA
Inferred from Direct Assay
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 sodium ion transmembrane transporter activity IDA
Inferred from Direct Assay
more info
PubMed 
involved_in regulation of ventricular cardiac muscle cell membrane repolarization ISS
Inferred from Sequence or Structural Similarity
more info
PubMed 
involved_in sodium ion transmembrane transport IDA
Inferred from Direct Assay
more info
PubMed 
Component Evidence Code Pubs
located_in T-tubule ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
 
located_in intercalated disc ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in node of Ranvier ISS
Inferred from Sequence or Structural Similarity
more info
 
located_in perikaryon IEA
Inferred from Electronic Annotation
more info
 
located_in plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
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

Preferred Names
sodium channel subunit beta-1
Names
sodium channel, voltage gated, type I beta subunit
sodium channel, voltage-gated, type I, beta

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_013359.1 RefSeqGene

    Range
    4783..14762
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_420

mRNA and Protein(s)

  1. NM_001037.5NP_001028.1  sodium channel subunit beta-1 isoform a precursor

    See identical proteins and their annotated locations for NP_001028.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (a) represents the longer transcript but encodes the shorter isoform (a).
    Source sequence(s)
    AC020907, BC067122
    Consensus CDS
    CCDS12441.1
    UniProtKB/Swiss-Prot
    Q07699, Q5TZZ4, Q6TN97
    UniProtKB/TrEMBL
    Q8WU42
    Related
    ENSP00000262631.3, ENST00000262631.11
    Conserved Domains (2) summary
    pfam07686
    Location:23147
    V-set; Immunoglobulin V-set domain
    cd00096
    Location:2632
    Ig; Ig strand A' [structural motif]
  2. NM_001321605.2NP_001308534.1  sodium channel subunit beta-1 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (c) encodes an isoform (c) that lacks a predicted signal peptide compared to isoforms a and b.
    Source sequence(s)
    AC020907, BC067122, DA062026
    Consensus CDS
    CCDS86744.1
    UniProtKB/TrEMBL
    A0A1W2PR05, Q8WU42
    Related
    ENSP00000492247.1, ENST00000596348.2
    Conserved Domains (2) summary
    pfam07686
    Location:8114
    V-set; Immunoglobulin V-set domain
    cd00096
    Location:3541
    Ig; Ig strand C' [structural motif]
  3. NM_199037.5NP_950238.1  sodium channel subunit beta-1 isoform b precursor

    See identical proteins and their annotated locations for NP_950238.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (b) differs in the 3' UTR and coding region compared to variant a. The resulting isoform (b) is longer and has a distinct C-terminus compared to isoform a.
    Source sequence(s)
    AC020907, AY391842, BC067122
    Consensus CDS
    CCDS46047.1
    UniProtKB/TrEMBL
    A0A1W2PS68
    Related
    ENSP00000396915.2, ENST00000415950.5
    Conserved Domains (1) summary
    pfam07686
    Location:23123
    V-set; Immunoglobulin V-set domain

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

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    35030470..35040449
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    37575088..37585067
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)