Atlas of Genetics and Cytogenetics in Oncology and Haematology


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SCN1A (sodium voltage-gated channel alpha subunit 1)

Identity

Other namesEIEE6
FEB3
FEB3A
FHM3
GEFSP2
HBSCI
NAC1
Nav1.1
SCN1
SMEI
HGNC (Hugo) SCN1A
LocusID (NCBI) 6323
Atlas_Id 50222
Location 2q24.3  [Link to chromosome band 2q24]
Location_base_pair Starts at 166845670 and ends at 166930149 bp from pter ( according to hg19-Feb_2009)

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)SCN1A   10585
Cards
Entrez_Gene (NCBI)SCN1A  6323  sodium voltage-gated channel alpha subunit 1
AliasesEIEE6; FEB3; FEB3A; FHM3; 
GEFSP2; HBSCI; NAC1; Nav1.1; SCN1; SMEI
GeneCards (Weizmann)SCN1A
Ensembl hg19 (Hinxton)ENSG00000144285 [Gene_View]  chr2:166845670-166930149 [Contig_View]  SCN1A [Vega]
Ensembl hg38 (Hinxton)ENSG00000144285 [Gene_View]  chr2:166845670-166930149 [Contig_View]  SCN1A [Vega]
ICGC DataPortalENSG00000144285
TCGA cBioPortalSCN1A
AceView (NCBI)SCN1A
Genatlas (Paris)SCN1A
WikiGenes6323
SOURCE (Princeton)SCN1A
Genomic and cartography
GoldenPath hg19 (UCSC)SCN1A  -     chr2:166845670-166930149 -  2q24.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)SCN1A  -     2q24.3   [Description]    (hg38-Dec_2013)
EnsemblSCN1A - 2q24.3 [CytoView hg19]  SCN1A - 2q24.3 [CytoView hg38]
Mapping of homologs : NCBISCN1A [Mapview hg19]  SCN1A [Mapview hg38]
OMIM182389   604403   607208   609634   
Gene and transcription
Genbank (Entrez)AB093548 AB093549 AB098335 AF225985 AK094487
RefSeq transcript (Entrez)NM_001165963 NM_001165964 NM_001202435 NM_006920
RefSeq genomic (Entrez)NC_000002 NC_018913 NG_011906 NT_005403 NW_004929305
Consensus coding sequences : CCDS (NCBI)SCN1A
Cluster EST : UnigeneHs.740081 [ NCBI ]
CGAP (NCI)Hs.740081
Alternative Splicing GalleryENSG00000144285
Gene ExpressionSCN1A [ NCBI-GEO ]   SCN1A [ EBI - ARRAY_EXPRESS ]   SCN1A [ SEEK ]   SCN1A [ MEM ]
Gene Expression Viewer (FireBrowse)SCN1A [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6323
GTEX Portal (Tissue expression)SCN1A
Protein : pattern, domain, 3D structure
UniProt/SwissProtP35498 (Uniprot)
NextProtP35498  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP35498
Splice isoforms : SwissVarP35498 (Swissvar)
PhosPhoSitePlusP35498
Domains : Interpro (EBI)Channel_four-helix_dom    Ion_trans_dom    IQ_motif_EF-hand-BS    Na_channel_a1su    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   
Domain families : Smart (EMBL)IQ (SM00015)  
DMDM Disease mutations6323
Blocks (Seattle)SCN1A
SuperfamilyP35498
Human Protein AtlasENSG00000144285
Peptide AtlasP35498
HPRD01669
IPIIPI00018934   IPI00748990   IPI00917812   
Protein Interaction databases
DIP (DOE-UCLA)P35498
IntAct (EBI)P35498
FunCoupENSG00000144285
BioGRIDSCN1A
STRING (EMBL)SCN1A
ZODIACSCN1A
Ontologies - Pathways
QuickGOP35498
Ontology : AmiGOvoltage-gated sodium channel complex  positive regulation of defense response to virus by host  voltage-gated sodium channel activity  voltage-gated sodium channel activity  plasma membrane  sodium ion transport  adult walking behavior  intercalated disc  neuronal action potential propagation  neuronal action potential  Z disc  T-tubule  sodium ion binding  node of Ranvier  regulation of ion transmembrane transport  sodium ion transmembrane transport  neuronal cell body  axon initial segment  neuromuscular process controlling posture  regulation of postsynaptic membrane potential  regulation of postsynaptic membrane potential  regulation of postsynaptic membrane potential  membrane depolarization during action potential  xenophagy  
Ontology : EGO-EBIvoltage-gated sodium channel complex  positive regulation of defense response to virus by host  voltage-gated sodium channel activity  voltage-gated sodium channel activity  plasma membrane  sodium ion transport  adult walking behavior  intercalated disc  neuronal action potential propagation  neuronal action potential  Z disc  T-tubule  sodium ion binding  node of Ranvier  regulation of ion transmembrane transport  sodium ion transmembrane transport  neuronal cell body  axon initial segment  neuromuscular process controlling posture  regulation of postsynaptic membrane potential  regulation of postsynaptic membrane potential  regulation of postsynaptic membrane potential  membrane depolarization during action potential  xenophagy  
Pathways : KEGGDopaminergic synapse   
NDEx Network
Atlas of Cancer Signalling NetworkSCN1A
Wikipedia pathwaysSCN1A
Orthology - Evolution
OrthoDB6323
GeneTree (enSembl)ENSG00000144285
Phylogenetic Trees/Animal Genes : TreeFamSCN1A
Homologs : HomoloGeneSCN1A
Homology/Alignments : Family Browser (UCSC)SCN1A
Gene fusions - Rearrangements
Polymorphisms : SNP, variants
NCBI Variation ViewerSCN1A [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SCN1A
dbVarSCN1A
ClinVarSCN1A
1000_GenomesSCN1A 
Exome Variant ServerSCN1A
ExAC (Exome Aggregation Consortium)SCN1A (select the gene name)
Genetic variants : HAPMAP6323
Genomic Variants (DGV)SCN1A [DGVbeta]
Mutations
ICGC Data PortalSCN1A 
TCGA Data PortalSCN1A 
Broad Tumor PortalSCN1A
OASIS PortalSCN1A [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSCN1A 
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)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
LOVD (Leiden Open Variation Database)Familial Hemiplegic Migraine (FHM) Variation Database
BioMutasearch SCN1A
DgiDB (Drug Gene Interaction Database)SCN1A
DoCM (Curated mutations)SCN1A (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SCN1A (select a term)
intoGenSCN1A
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] 
Diseases
DECIPHER (Syndromes)2:166845670-166930149  ENSG00000144285
CONAN: Copy Number AnalysisSCN1A 
Mutations and Diseases : HGMDSCN1A
OMIM182389    604403    607208    609634   
MedgenSCN1A
Genetic Testing Registry SCN1A
NextProtP35498 [Medical]
TSGene6323
GENETestsSCN1A
Huge Navigator SCN1A [HugePedia]
snp3D : Map Gene to Disease6323
BioCentury BCIQSCN1A
ClinGenSCN1A
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6323
Chemical/Pharm GKB GenePA301
Clinical trialSCN1A
Miscellaneous
canSAR (ICR)SCN1A (select the gene name)
Probes
Litterature
PubMed249 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSCN1A
EVEXSCN1A
GoPubMedSCN1A
iHOPSCN1A
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Aug 9 19:08:58 CEST 2016

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