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Aliases for SCN3B Gene

Aliases for SCN3B Gene

  • Sodium Voltage-Gated Channel Beta Subunit 3 2 3 5
  • Sodium Channel, Voltage-Gated, Type III, Beta Subunit 2 3
  • Sodium Channel, Voltage Gated, Type III Beta Subunit 2
  • Sodium Channel, Voltage-Gated, Type III, Beta 2
  • Voltage-Gated Sodium Channel Beta-3 Subunit 3
  • Sodium Channel Subunit Beta-3 3
  • HSA243396 3
  • KIAA1158 4
  • ATFB16 3
  • BRGDA7 3
  • SCNB3 3

External Ids for SCN3B Gene

Previous GeneCards Identifiers for SCN3B Gene

  • GC11M125013
  • GC11M123533
  • GC11M123037
  • GC11M123039
  • GC11M123005
  • GC11M119441
  • GC11M123500

Summaries for SCN3B Gene

Entrez Gene Summary for SCN3B Gene

  • 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]

GeneCards Summary for SCN3B Gene

SCN3B (Sodium Voltage-Gated Channel Beta Subunit 3) is a Protein Coding gene. Diseases associated with SCN3B include Brugada Syndrome 7 and Brugada Syndrome. Among its related pathways are Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways and Direct p53 effectors. Gene Ontology (GO) annotations related to this gene include ion channel binding and voltage-gated sodium channel activity. An important paralog of this gene is SCN1B.

UniProtKB/Swiss-Prot for SCN3B Gene

  • Modulates channel gating kinetics. Causes unique persistent sodium currents. Inactivates the sodium channel opening more slowly than the subunit beta-1. Its association with NFASC may target the sodium channels to the nodes of Ranvier of developing axons and retain these channels at the nodes in mature myelinated axons (By similarity).

Tocris Summary for SCN3B Gene

  • Voltage-gated sodium channels (NaV) are responsible for action potential initiation and propagation in excitable cells, including nerve, muscle, and neuroendocrine cell types. They are also expressed at low levels in non-excitable cells, where their physiological role is unclear.

Gene Wiki entry for SCN3B Gene

Additional gene information for SCN3B Gene

No data available for CIViC summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for SCN3B Gene

Genomics for SCN3B Gene

GeneHancer (GH) Regulatory Elements for SCN3B Gene

Promoters and enhancers for SCN3B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J123653 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650.7 +0.3 264 2.6 ZFP64 ARID4B SIN3A FEZF1 ZNF48 GLIS2 ZNF213 ZNF143 ATF7 KLF13 LOC105369543 SCN3B
GH11J123543 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 9.6 +109.7 109668 5 PKNOX1 KLF1 JUN INSM2 EBF1 IRF4 ZNF366 EED FOS IKZF2 SCN3B UBASH3B GC11P123564 GC11M123460 GRAMD1B
GH11J123576 Enhancer 1.1 Ensembl ENCODE dbSUPER 10.4 +78.1 78098 0.7 HDGF CTCF FOXA2 MAX IRF4 RAD21 EED ZNF143 BCLAF1 CREM GC11M123572 GC11M123574 GC11M123576 GRAMD1B SCN3B
GH11J123535 Enhancer 1 Ensembl ENCODE dbSUPER 9.1 +118.1 118067 2.8 STAT1 NANOG USF2 ATF2 SP1 ZNF366 STAT3 TRIM28 NR2C2 SCN3B GC11P123564 GC11M123460 GRAMD1B
GH11J123628 Enhancer 0.7 ENCODE 11.4 +25.9 25872 1.1 HDAC1 TEAD4 TAL1 FOSL1 TCF12 EGR1 POLR2A VEZF1 CBFA2T2 RCOR1 SCN3B GC11P123628 LOC105369543
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around SCN3B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the SCN3B gene promoter:
  • p53
  • NRSF form 1
  • NRSF form 2
  • LHX3b
  • Lhx3a
  • HTF
  • RP58

Genomic Locations for SCN3B Gene

Genomic Locations for SCN3B Gene
chr11:123,629,187-123,655,244
(GRCh38/hg38)
Size:
26,058 bases
Orientation:
Minus strand
chr11:123,499,895-123,525,952
(GRCh37/hg19)
Size:
26,058 bases
Orientation:
Minus strand

Genomic View for SCN3B Gene

Genes around SCN3B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SCN3B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SCN3B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SCN3B Gene

Proteins for SCN3B Gene

  • Protein details for SCN3B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NY72-SCN3B_HUMAN
    Recommended name:
    Sodium channel subunit beta-3
    Protein Accession:
    Q9NY72
    Secondary Accessions:
    • A5H1I5
    • Q17RL3
    • Q9ULR2

    Protein attributes for SCN3B Gene

    Size:
    215 amino acids
    Molecular mass:
    24702 Da
    Quaternary structure:
    • The voltage-sensitive sodium channel consists of an ion conducting pore forming alpha-subunit regulated by one or more beta-1, beta-2, beta-3 and/or beta-4 subunits. Beta-1 and beta-3 are non-covalently associated with alpha, while beta-2 and beta-4 are covalently linked by disulfide bonds (By similarity).
    SequenceCaution:
    • Sequence=BAA86472.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for SCN3B Gene

neXtProt entry for SCN3B Gene

Post-translational modifications for SCN3B Gene

  • Glycosylation at isoforms=121, isoforms=113, posLast=109109, and posLast=9595
  • Modification sites at PhosphoSitePlus

Other Protein References for SCN3B Gene

No data available for DME Specific Peptides for SCN3B Gene

Domains & Families for SCN3B Gene

Gene Families for SCN3B Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • FDA approved drug targets
  • Predicted membrane proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for SCN3B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NY72

UniProtKB/Swiss-Prot:

SCN3B_HUMAN :
  • Belongs to the sodium channel auxiliary subunit SCN3B (TC 8.A.17) family.
Family:
  • Belongs to the sodium channel auxiliary subunit SCN3B (TC 8.A.17) family.
genes like me logo Genes that share domains with SCN3B: view

Function for SCN3B Gene

Molecular function for SCN3B Gene

UniProtKB/Swiss-Prot Function:
Modulates channel gating kinetics. Causes unique persistent sodium currents. Inactivates the sodium channel opening more slowly than the subunit beta-1. Its association with NFASC may target the sodium channels to the nodes of Ranvier of developing axons and retain these channels at the nodes in mature myelinated axons (By similarity).

Phenotypes From GWAS Catalog for SCN3B Gene

Gene Ontology (GO) - Molecular Function for SCN3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005244 voltage-gated ion channel activity IEA --
GO:0005248 voltage-gated sodium channel activity NAS 10688874
GO:0005272 sodium channel activity IEA --
GO:0017080 sodium channel regulator activity IMP 20042427
GO:0044325 ion channel binding IPI 20042427
genes like me logo Genes that share ontologies with SCN3B: view
genes like me logo Genes that share phenotypes with SCN3B: view

Human Phenotype Ontology for SCN3B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SCN3B Gene

MGI Knock Outs for SCN3B:
  • Scn3b Scn3b<tm1Clhh>
  • Scn3b Scn3b<tm1a(KOMP)Wtsi>

Animal Model Products

  • Taconic Biosciences Mouse Models for SCN3B

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCN3B

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SCN3B Gene

Localization for SCN3B Gene

Subcellular locations from UniProtKB/Swiss-Prot for SCN3B Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SCN3B gene
Compartment Confidence
plasma membrane 5
nucleus 2
cytosol 2
extracellular 1
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Intermediate filaments (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SCN3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001518 voltage-gated sodium channel complex TAS 21895525
GO:0005886 plasma membrane IDA --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane NAS 10688874
GO:0030018 Z disc ISS --
genes like me logo Genes that share ontologies with SCN3B: view

Pathways & Interactions for SCN3B Gene

genes like me logo Genes that share pathways with SCN3B: view

Gene Ontology (GO) - Biological Process for SCN3B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006811 ion transport IEA --
GO:0006814 sodium ion transport NAS 10688874
GO:0007399 nervous system development IEA --
GO:0010460 positive regulation of heart rate ISS --
GO:0010765 positive regulation of sodium ion transport IMP 21051419
genes like me logo Genes that share ontologies with SCN3B: view

No data available for SIGNOR curated interactions for SCN3B Gene

Drugs & Compounds for SCN3B Gene

(6) Drugs for SCN3B Gene - From: DrugBank, DGIdb, HMDB, and Tocris

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Zonisamide Approved, Investigational Pharma blocker, Target, inhibitor Antiepileptic with anticonvulsant and mechanistic effect 69
Brivaracetam Approved, Investigational Pharma Target, inhibitor ligand for SV2A, selective and high-affinity 0
Dichlorobenzyl alcohol Approved Pharma Target, antagonist 0
Valproic Acid Approved, Investigational Pharma Target, inhibitor HDAC1 inhibitor, Histone deacetylase (HDAC)inhibitors 333
Carbamazepine Approved, Investigational Pharma Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 134

(2) Additional Compounds for SCN3B Gene - From: HMDB and Tocris

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
sodium
  • Na(+)
  • Na+
  • SODIUM ion
7440-23-5
Amiloride hydrochloride
2016-88-8

(3) Tocris Compounds for SCN3B Gene

Compound Action Cas Number
Amiloride hydrochloride Na+ channel blocker; also I2 imidazoline ligand 2016-88-8
Carbamazepine Inhibitor of neuronal voltage-gated Na+ channels; anticonvulsant 298-46-4
Vinpocetine Na+ channel blocker 42971-09-5
genes like me logo Genes that share compounds with SCN3B: view

Transcripts for SCN3B Gene

mRNA/cDNA for SCN3B Gene

Unigene Clusters for SCN3B Gene

Sodium channel, voltage-gated, type III, beta subunit:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SCN3B

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SCN3B Gene

No ASD Table

Relevant External Links for SCN3B Gene

GeneLoc Exon Structure for
SCN3B
ECgene alternative splicing isoforms for
SCN3B

Expression for SCN3B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for SCN3B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SCN3B Gene

This gene is overexpressed in Brain - Anterior cingulate cortex (BA24) (x7.5), Brain - Frontal Cortex (BA9) (x6.8), Brain - Cortex (x6.6), Brain - Hippocampus (x6.2), and Brain - Amygdala (x4.2).

Protein differential expression in normal tissues from HIPED for SCN3B Gene

This gene is overexpressed in Fetal Brain (56.3) and Frontal cortex (11.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SCN3B Gene



Protein tissue co-expression partners for SCN3B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of SCN3B Gene:

SCN3B

SOURCE GeneReport for Unigene cluster for SCN3B Gene:

Hs.4865

mRNA Expression by UniProt/SwissProt for SCN3B Gene:

Q9NY72-SCN3B_HUMAN
Tissue specificity: Expressed in the atrium.

Evidence on tissue expression from TISSUES for SCN3B Gene

  • Nervous system(4.9)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SCN3B Gene

Germ Layers:
  • ectoderm
  • mesoderm
Systems:
  • cardiovascular
  • nervous
Regions:
Head and neck:
  • brain
  • ear
  • head
Thorax:
  • heart
  • heart valve
General:
  • blood
  • blood vessel
  • coagulation system
  • red blood cell
genes like me logo Genes that share expression patterns with SCN3B: view

Orthologs for SCN3B Gene

This gene was present in the common ancestor of chordates.

Orthologs for SCN3B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia SCN3B 34 33
  • 99.38 (n)
OneToOne
dog
(Canis familiaris)
Mammalia SCN3B 34 33
  • 92.09 (n)
OneToOne
cow
(Bos Taurus)
Mammalia SCN3B 34 33
  • 92.09 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia SCN3B 34
  • 91 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Scn3b 16 34 33
  • 89.46 (n)
rat
(Rattus norvegicus)
Mammalia Scn3b 33
  • 89.15 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia SCN3B 34
  • 88 (a)
OneToOne
chicken
(Gallus gallus)
Aves SCN3B 34 33
  • 73.18 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia SCN3B 34
  • 71 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia scn3b 33
  • 65.12 (n)
zebrafish
(Danio rerio)
Actinopterygii scn3b 34 33
  • 59.38 (n)
OneToOne
Species where no ortholog for SCN3B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for SCN3B Gene

ENSEMBL:
Gene Tree for SCN3B (if available)
TreeFam:
Gene Tree for SCN3B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SCN3B: view image

Paralogs for SCN3B Gene

Paralogs for SCN3B Gene

(1) SIMAP similar genes for SCN3B Gene using alignment to 3 proteins:

  • SCN3B_HUMAN
  • E9PJP6_HUMAN
  • E9PQS8_HUMAN
genes like me logo Genes that share paralogs with SCN3B: view

Variants for SCN3B Gene

Sequence variations from dbSNP and Humsavar for SCN3B Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs10400374 likely-benign, Brugada syndrome 123,632,053(-) C/T 3_prime_UTR_variant, intron_variant
rs111341342 uncertain-significance, Brugada syndrome 123,654,140(-) G/C 5_prime_UTR_variant, intron_variant
rs114709124 uncertain-significance, Brugada syndrome 123,629,276(-) T/C 3_prime_UTR_variant
rs115252019 likely-benign, Brugada syndrome 123,632,907(-) G/T 3_prime_UTR_variant, intron_variant
rs115752338 benign, likely-benign, not specified, Brugada syndrome 7, Cardiovascular phenotype, Brugada syndrome 123,645,608(-) G/A/T coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for SCN3B Gene

Variant ID Type Subtype PubMed ID
esv3627959 CNV loss 21293372
nsv556484 CNV loss 21841781
esv2759868 CNV loss 17122850
dgv419e212 CNV loss 25503493

Variation tolerance for SCN3B Gene

Residual Variation Intolerance Score: 35.3% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.45; 9.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SCN3B Gene

Human Gene Mutation Database (HGMD)
SCN3B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SCN3B

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SCN3B Gene

Disorders for SCN3B Gene

MalaCards: The human disease database

(6) MalaCards diseases for SCN3B Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
brugada syndrome 7
  • brgda7
brugada syndrome
  • right bundle branch block, st segment elevation, and sudden death syndrome
familial atrial fibrillation
  • atrial fibrillation, familial, 1
atrial fibrillation
  • a-fib
right bundle branch block
  • right bundle branch block with left posterior fascicular block
- elite association - COSMIC cancer census association via MalaCards
Search SCN3B in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

SCN3B_HUMAN
  • Brugada syndrome 7 (BRGDA7) [MIM:613120]: A tachyarrhythmia characterized by right bundle branch block and ST segment elevation on an electrocardiogram (ECG). It can cause the ventricles to beat so fast that the blood is prevented from circulating efficiently in the body. When this situation occurs, the individual will faint and may die in a few minutes if the heart is not reset. {ECO:0000269 PubMed:20031595}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Atrial fibrillation, familial, 16 (ATFB16) [MIM:613120]: A familial form of atrial fibrillation, a common sustained cardiac rhythm disturbance. Atrial fibrillation is characterized by disorganized atrial electrical activity and ineffective atrial contraction promoting blood stasis in the atria and reduces ventricular filling. It can result in palpitations, syncope, thromboembolic stroke, and congestive heart failure. {ECO:0000269 PubMed:20558140, ECO:0000269 PubMed:21051419}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SCN3B

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with SCN3B: view

No data available for Genatlas for SCN3B Gene

Publications for SCN3B Gene

  1. Functional dominant-negative mutation of sodium channel subunit gene SCN3B associated with atrial fibrillation in a Chinese GeneID population. (PMID: 20558140) Wang P … Wang QK (Biochemical and biophysical research communications 2010) 3 4 44 58
  2. beta 3: an additional auxiliary subunit of the voltage-sensitive sodium channel that modulates channel gating with distinct kinetics. (PMID: 10688874) Morgan K … Jackson AP (Proceedings of the National Academy of Sciences of the United States of America 2000) 2 3 4 58
  3. Mutations in sodium channel β-subunit SCN3B are associated with early-onset lone atrial fibrillation. (PMID: 21051419) Olesen MS … Svendsen JH (Cardiovascular research 2011) 3 4 58
  4. Loss-of-function mutation of the SCN3B-encoded sodium channel {beta}3 subunit associated with a case of idiopathic ventricular fibrillation. (PMID: 20042427) Valdivia CR … Makielski JC (Cardiovascular research 2010) 3 4 58
  5. Mutations in sodium channel β1- and β2-subunits associated with atrial fibrillation. (PMID: 19808477) Watanabe H … Roden DM (Circulation. Arrhythmia and electrophysiology 2009) 3 44 58

Products for SCN3B Gene

Sources for SCN3B Gene

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