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

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: mouse all
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Genomic context

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_000019.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Impact of rs1805127 and rs55742440 Variants on Atrial Remodeling in Hypertrophic Cardiomyopathy Patients with Atrial Fibrillation: A Romanian Cohort Study.
Title: Impact of rs1805127 and rs55742440 Variants on Atrial Remodeling in Hypertrophic Cardiomyopathy Patients with Atrial Fibrillation: A Romanian Cohort Study.
Association of sodium voltage-gated channel genes polymorphisms with epilepsy risk and prognosis in the Saudi population.
Title: Association of sodium voltage-gated channel genes polymorphisms with epilepsy risk and prognosis in the Saudi population.
Neonatal Scn1b-null mice have sinoatrial node dysfunction, altered atrial structure, and atrial fibrillation.
Title: Neonatal Scn1b-null mice have sinoatrial node dysfunction, altered atrial structure, and atrial fibrillation.
Homozygous SCN1B variants causing early infantile epileptic encephalopathy 52 affect voltage-gated sodium channel function.
Title: Homozygous SCN1B variants causing early infantile epileptic encephalopathy 52 affect voltage-gated sodium channel function.
Sodium channel beta1 subunits are post-translationally modified by tyrosine phosphorylation, S-palmitoylation, and regulated intramembrane proteolysis.
Title: Sodium channel β1 subunits are post-translationally modified by tyrosine phosphorylation, S-palmitoylation, and regulated intramembrane proteolysis.
The sequencing analyses of the SCN1B gene revealed the presence of a new pathogenic variation c.374C>T (p.R125L) in family A and a putative disease-associated haplotype in five families. Using multiple alignments, the c.374G>T changed a highly conserved arginine to a leucine p.R125L located in the extracellular domain of the protein.
Title: Clinical and genetic aspect of 30 tunisian families with febrile seizures.
The S248R and R250T mutations of SCN1Bbeta gene caused gain-of-function of Ito by associated with Kv4.3, which maybe underlie the early repolarization syndrome (ERS) phenotype of the probands.
Title: SCN1Bβ mutations that affect their association with Kv4.3 underlie early repolarization syndrome.
this study reports the cryo-electron microscopy structures of the human Nav1.7-beta1-beta2 complex bound to two combinations of pore blockers and gating modifier toxins (GMTs), tetrodotoxin with protoxin-II and saxitoxin with huwentoxin-IV, both determined at overall resolutions of 3.2 angstroms.
Title: Structures of human Na(v)1.7 channel in complex with auxiliary subunits and animal toxins.
our results show that the role of beta1 subunit on the maturation and expression of the entire NaCh complex is of paramount importance to understand the pathological conditions resulted from a defective interaction between the NaCh constituents.
Title: A mutation of SCN1B associated with GEFS+ causes functional and maturation defects of the voltage-dependent sodium channel.
Genetic analysis was suggestive of SCN1B gene mutation associated with Dravet syndrome
Title: Dravet syndrome with SCN1B gene mutation: A rare entity.

Submit: New GeneRIF Correction See all GeneRIFs (52)

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
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 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

GDB:434009 (e-PCR)
- UniSTS:157203

Scn1b (e-PCR), detects polymorphism
- UniSTS:516637

Scn1b (e-PCR), detects polymorphism
- UniSTS:472869

G32458 (e-PCR)
- UniSTS:117043

PMC15797P1 (e-PCR)
- UniSTS:271432

STS-L16242 (e-PCR)
- UniSTS:56151

STS-R56235 (e-PCR)
- UniSTS:19558

U85786 (e-PCR)
- UniSTS:159622

SCN1B_3452 (e-PCR)
- UniSTS:462511

A009D43 (e-PCR)
- UniSTS:83186

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 inhibitor activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
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 voltage-gated sodium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated sodium channel activity involved in Purkinje myocyte action potential	IMP Inferred from Mutant Phenotype 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 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

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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)

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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_013359.1 RefSeqGene

Range

4783..14762

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_420

mRNA and Protein(s)

NM_001037.5 → NP_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:23 → 147

V-set; Immunoglobulin V-set domain

cd00096
Location:26 → 32

Ig; Ig strand A' [structural motif]
NM_001321605.2 → NP_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:8 → 114

V-set; Immunoglobulin V-set domain

cd00096
Location:35 → 41

Ig; Ig strand C' [structural motif]
NM_199037.5 → NP_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:23 → 123

V-set; Immunoglobulin V-set domain