Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SCN5A (sodium voltage-gated channel alpha subunit 5)

Identity

Alias_namesCMD1E
sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)
sodium channel, voltage-gated, type V, alpha subunit
sodium channel, voltage gated, type V alpha subunit
Alias_symbol (synonym)Nav1.5
LQT3
HB1
HBBD
PFHB1
IVF
HB2
HH1
SSS1
CDCD2
CMPD2
ICCD
Other aliasVF1
HGNC (Hugo) SCN5A
LocusID (NCBI) 6331
Atlas_Id 45877
Location 3p22.2  [Link to chromosome band 3p22]
Location_base_pair Starts at 38548062 and ends at 38649672 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)
Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


External links

Nomenclature
HGNC (Hugo)SCN5A   10593
LRG (Locus Reference Genomic)LRG_289
Cards
Entrez_Gene (NCBI)SCN5A  6331  sodium voltage-gated channel alpha subunit 5
AliasesCDCD2; CMD1E; CMPD2; HB1; 
HB2; HBBD; HH1; ICCD; IVF; LQT3; Nav1.5; PFHB1; SSS1; VF1
GeneCards (Weizmann)SCN5A
Ensembl hg19 (Hinxton)ENSG00000183873 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000183873 [Gene_View]  chr3:38548062-38649672 [Contig_View]  SCN5A [Vega]
ICGC DataPortalENSG00000183873
TCGA cBioPortalSCN5A
AceView (NCBI)SCN5A
Genatlas (Paris)SCN5A
WikiGenes6331
SOURCE (Princeton)SCN5A
Genetics Home Reference (NIH)SCN5A
Genomic and cartography
GoldenPath hg38 (UCSC)SCN5A  -     chr3:38548062-38649672 -  3p22.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SCN5A  -     3p22.2   [Description]    (hg19-Feb_2009)
EnsemblSCN5A - 3p22.2 [CytoView hg19]  SCN5A - 3p22.2 [CytoView hg38]
Mapping of homologs : NCBISCN5A [Mapview hg19]  SCN5A [Mapview hg38]
OMIM113900   272120   600163   601144   601154   603829   603830   608567   614022   
Gene and transcription
Genbank (Entrez)###############################################################################################################################################################################################################################################################
RefSeq transcript (Entrez)NM_000335 NM_001099404 NM_001099405 NM_001160160 NM_001160161 NM_198056
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SCN5A
Cluster EST : UnigeneHs.517898 [ NCBI ]
CGAP (NCI)Hs.517898
Alternative Splicing GalleryENSG00000183873
Gene ExpressionSCN5A [ NCBI-GEO ]   SCN5A [ EBI - ARRAY_EXPRESS ]   SCN5A [ SEEK ]   SCN5A [ MEM ]
Gene Expression Viewer (FireBrowse)SCN5A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6331
GTEX Portal (Tissue expression)SCN5A
Human Protein AtlasENSG00000183873-SCN5A [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ14524   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ14524  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ14524
Splice isoforms : SwissVarQ14524
PhosPhoSitePlusQ14524
Domains : Interpro (EBI)Channel_four-helix_dom    Ion_trans_dom    Na_channel_a5su    Na_channel_asu    Na_trans_assoc    Na_trans_cytopl   
Domain families : Pfam (Sanger)Ion_trans (PF00520)    Na_trans_assoc (PF06512)    Na_trans_cytopl (PF11933)   
Domain families : Pfam (NCBI)pfam00520    pfam06512    pfam11933   
Conserved Domain (NCBI)SCN5A
DMDM Disease mutations6331
Blocks (Seattle)SCN5A
PDB (SRS)2KBI    2L53    4DCK    4DJC    4JQ0    4OVN   
PDB (PDBSum)2KBI    2L53    4DCK    4DJC    4JQ0    4OVN   
PDB (IMB)2KBI    2L53    4DCK    4DJC    4JQ0    4OVN   
PDB (RSDB)2KBI    2L53    4DCK    4DJC    4JQ0    4OVN   
Structural Biology KnowledgeBase2KBI    2L53    4DCK    4DJC    4JQ0    4OVN   
SCOP (Structural Classification of Proteins)2KBI    2L53    4DCK    4DJC    4JQ0    4OVN   
CATH (Classification of proteins structures)2KBI    2L53    4DCK    4DJC    4JQ0    4OVN   
SuperfamilyQ14524
Human Protein Atlas [tissue]ENSG00000183873-SCN5A [tissue]
Peptide AtlasQ14524
HPRD02543
IPIIPI00377006   IPI00791220   IPI00896549   IPI00031422   IPI00930104   IPI01013301   IPI00930084   IPI01011127   IPI00103378   IPI01008809   IPI00927490   IPI01008869   IPI00930507   IPI00926465   
Protein Interaction databases
DIP (DOE-UCLA)Q14524
IntAct (EBI)Q14524
FunCoupENSG00000183873
BioGRIDSCN5A
STRING (EMBL)SCN5A
ZODIACSCN5A
Ontologies - Pathways
QuickGOQ14524
Ontology : AmiGOvoltage-gated sodium channel complex  voltage-gated sodium channel complex  regulation of heart rate  cardiac ventricle development  brainstem development  voltage-gated sodium channel activity  voltage-gated sodium channel activity  protein binding  calmodulin binding  intracellular  endoplasmic reticulum  plasma membrane  plasma membrane  plasma membrane  caveola  caveola  sodium ion transport  cell surface  positive regulation of sodium ion transport  intercalated disc  intercalated disc  response to denervation involved in regulation of muscle adaptation  integral component of membrane  lateral plasma membrane  fibroblast growth factor binding  neuronal action potential  enzyme binding  protein kinase binding  protein domain specific binding  telencephalon development  cerebellum development  Z disc  T-tubule  ankyrin binding  ubiquitin protein ligase binding  sodium ion transmembrane transport  sodium ion transmembrane transport  sarcolemma  odontogenesis of dentin-containing tooth  ion channel binding  positive regulation of action potential  positive regulation of epithelial cell proliferation  nitric-oxide synthase binding  membrane depolarization  cardiac muscle contraction  regulation of postsynaptic membrane potential  regulation of ventricular cardiac muscle cell membrane repolarization  regulation of atrial cardiac muscle cell membrane depolarization  regulation of atrial cardiac muscle cell membrane repolarization  regulation of ventricular cardiac muscle cell membrane depolarization  cardiac conduction  cellular response to calcium ion  cardiac muscle cell action potential involved in contraction  regulation of cardiac muscle cell contraction  ventricular cardiac muscle cell action potential  voltage-gated sodium channel activity involved in cardiac muscle cell action potential  voltage-gated sodium channel activity involved in cardiac muscle cell action potential  membrane depolarization during action potential  membrane depolarization during cardiac muscle cell action potential  atrial cardiac muscle cell action potential  SA node cell action potential  AV node cell action potential  bundle of His cell action potential  membrane depolarization during AV node cell action potential  membrane depolarization during SA node cell action potential  membrane depolarization during Purkinje myocyte cell action potential  membrane depolarization during bundle of His cell action potential  voltage-gated sodium channel activity involved in AV node cell action potential  voltage-gated sodium channel activity involved in bundle of His cell action potential  voltage-gated sodium channel activity involved in Purkinje myocyte action potential  voltage-gated sodium channel activity involved in SA node cell action potential  AV node cell to bundle of His cell communication  regulation of heart rate by cardiac conduction  scaffold protein binding  membrane depolarization during atrial cardiac muscle cell action potential  regulation of sodium ion transmembrane transport  
Ontology : EGO-EBIvoltage-gated sodium channel complex  voltage-gated sodium channel complex  regulation of heart rate  cardiac ventricle development  brainstem development  voltage-gated sodium channel activity  voltage-gated sodium channel activity  protein binding  calmodulin binding  intracellular  endoplasmic reticulum  plasma membrane  plasma membrane  plasma membrane  caveola  caveola  sodium ion transport  cell surface  positive regulation of sodium ion transport  intercalated disc  intercalated disc  response to denervation involved in regulation of muscle adaptation  integral component of membrane  lateral plasma membrane  fibroblast growth factor binding  neuronal action potential  enzyme binding  protein kinase binding  protein domain specific binding  telencephalon development  cerebellum development  Z disc  T-tubule  ankyrin binding  ubiquitin protein ligase binding  sodium ion transmembrane transport  sodium ion transmembrane transport  sarcolemma  odontogenesis of dentin-containing tooth  ion channel binding  positive regulation of action potential  positive regulation of epithelial cell proliferation  nitric-oxide synthase binding  membrane depolarization  cardiac muscle contraction  regulation of postsynaptic membrane potential  regulation of ventricular cardiac muscle cell membrane repolarization  regulation of atrial cardiac muscle cell membrane depolarization  regulation of atrial cardiac muscle cell membrane repolarization  regulation of ventricular cardiac muscle cell membrane depolarization  cardiac conduction  cellular response to calcium ion  cardiac muscle cell action potential involved in contraction  regulation of cardiac muscle cell contraction  ventricular cardiac muscle cell action potential  voltage-gated sodium channel activity involved in cardiac muscle cell action potential  voltage-gated sodium channel activity involved in cardiac muscle cell action potential  membrane depolarization during action potential  membrane depolarization during cardiac muscle cell action potential  atrial cardiac muscle cell action potential  SA node cell action potential  AV node cell action potential  bundle of His cell action potential  membrane depolarization during AV node cell action potential  membrane depolarization during SA node cell action potential  membrane depolarization during Purkinje myocyte cell action potential  membrane depolarization during bundle of His cell action potential  voltage-gated sodium channel activity involved in AV node cell action potential  voltage-gated sodium channel activity involved in bundle of His cell action potential  voltage-gated sodium channel activity involved in Purkinje myocyte action potential  voltage-gated sodium channel activity involved in SA node cell action potential  AV node cell to bundle of His cell communication  regulation of heart rate by cardiac conduction  scaffold protein binding  membrane depolarization during atrial cardiac muscle cell action potential  regulation of sodium ion transmembrane transport  
Pathways : KEGGAdrenergic signaling in cardiomyocytes   
NDEx NetworkSCN5A
Atlas of Cancer Signalling NetworkSCN5A
Wikipedia pathwaysSCN5A
Orthology - Evolution
OrthoDB6331
GeneTree (enSembl)ENSG00000183873
Phylogenetic Trees/Animal Genes : TreeFamSCN5A
HOVERGENQ14524
HOGENOMQ14524
Homologs : HomoloGeneSCN5A
Homology/Alignments : Family Browser (UCSC)SCN5A
Gene fusions - Rearrangements
Tumor Fusion PortalSCN5A
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSCN5A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SCN5A
dbVarSCN5A
ClinVarSCN5A
1000_GenomesSCN5A 
Exome Variant ServerSCN5A
ExAC (Exome Aggregation Consortium)ENSG00000183873
GNOMAD BrowserENSG00000183873
Genetic variants : HAPMAP6331
Genomic Variants (DGV)SCN5A [DGVbeta]
DECIPHERSCN5A [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSCN5A 
Mutations
ICGC Data PortalSCN5A 
TCGA Data PortalSCN5A 
Broad Tumor PortalSCN5A
OASIS PortalSCN5A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSCN5A  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSCN5A
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
LOVD (Leiden Open Variation Database)Mendelian genes
LOVD (Leiden Open Variation Database)Zhejiang University Center for Genetic and Genomic Medicine (ZJU-CGGM)
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch SCN5A
DgiDB (Drug Gene Interaction Database)SCN5A
DoCM (Curated mutations)SCN5A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SCN5A (select a term)
intoGenSCN5A
Cancer3DSCN5A(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM113900    272120    600163    601144    601154    603829    603830    608567    614022   
Orphanet17628    635    982    965    19072    8022    8592    14727   
DisGeNETSCN5A
MedgenSCN5A
Genetic Testing Registry SCN5A
NextProtQ14524 [Medical]
TSGene6331
GENETestsSCN5A
Target ValidationSCN5A
Huge Navigator SCN5A [HugePedia]
snp3D : Map Gene to Disease6331
BioCentury BCIQSCN5A
ClinGenSCN5A (curated)
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6331
Chemical/Pharm GKB GenePA304
Clinical trialSCN5A
Miscellaneous
canSAR (ICR)SCN5A (select the gene name)
Probes
Litterature
PubMed499 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSCN5A
EVEXSCN5A
GoPubMedSCN5A
iHOPSCN5A
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Nov 21 14:33:42 CET 2017

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