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

    Gene ID: 6324, updated on 17-Jun-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
    NEW
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    Try the new Transcript table

    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)