Atlas of Genetics and Cytogenetics in Oncology and Haematology

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SNTA1 (syntrophin alpha 1)

Identity

Alias_namesSNT1
syntrophin
Alias_symbol (synonym)TACIP1
LQT12
Other aliasdJ1187J4.5
HGNC (Hugo) SNTA1
LocusID (NCBI) 6640
Atlas_Id 52306
Location 20q11.21  [Link to chromosome band 20q11]
Location_base_pair Starts at 33407957 and ends at 33443892 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)
ARVCF (22q11.21) / SNTA1 (20q11.21)ZDHHC20 (13q12.11) / SNTA1 (20q11.21)

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

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  t(17;20)(q24;q11) HELZ/SNTA1

External links

Nomenclature
HGNC (Hugo)SNTA1   11167
LRG (Locus Reference Genomic)LRG_332
Cards
Entrez_Gene (NCBI)SNTA1  6640  syntrophin alpha 1
AliasesLQT12; SNT1; TACIP1; dJ1187J4.5
GeneCards (Weizmann)SNTA1
Ensembl hg19 (Hinxton)ENSG00000101400 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000101400 [Gene_View]  ENSG00000101400 [Sequence]  chr20:33407957-33443892 [Contig_View]  SNTA1 [Vega]
ICGC DataPortalENSG00000101400
TCGA cBioPortalSNTA1
AceView (NCBI)SNTA1
Genatlas (Paris)SNTA1
WikiGenes6640
SOURCE (Princeton)SNTA1
Genetics Home Reference (NIH)SNTA1
Genomic and cartography
GoldenPath hg38 (UCSC)SNTA1  -     chr20:33407957-33443892 -  20q11.21   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)SNTA1  -     20q11.21   [Description]    (hg19-Feb_2009)
EnsemblSNTA1 - 20q11.21 [CytoView hg19]  SNTA1 - 20q11.21 [CytoView hg38]
Mapping of homologs : NCBISNTA1 [Mapview hg19]  SNTA1 [Mapview hg38]
OMIM601017   612955   
Gene and transcription
Genbank (Entrez)AK095942 AK291994 AK301800 AU118614 BC026215
RefSeq transcript (Entrez)NM_003098
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)SNTA1
Cluster EST : UnigeneHs.31121 [ NCBI ]
CGAP (NCI)Hs.31121
Alternative Splicing GalleryENSG00000101400
Gene ExpressionSNTA1 [ NCBI-GEO ]   SNTA1 [ EBI - ARRAY_EXPRESS ]   SNTA1 [ SEEK ]   SNTA1 [ MEM ]
Gene Expression Viewer (FireBrowse)SNTA1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)6640
GTEX Portal (Tissue expression)SNTA1
Human Protein AtlasENSG00000101400-SNTA1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ13424   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ13424  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ13424
Splice isoforms : SwissVarQ13424
PhosPhoSitePlusQ13424
Domaine pattern : Prosite (Expaxy)PDZ (PS50106)    PH_DOMAIN (PS50003)   
Domains : Interpro (EBI)PDZ    PDZ_sf    PH-like_dom_sf    PH_domain    SNTA1    Syntrophin   
Domain families : Pfam (Sanger)PDZ (PF00595)    PH (PF00169)   
Domain families : Pfam (NCBI)pfam00595    pfam00169   
Domain families : Smart (EMBL)PDZ (SM00228)  PH (SM00233)  
Conserved Domain (NCBI)SNTA1
DMDM Disease mutations6640
Blocks (Seattle)SNTA1
SuperfamilyQ13424
Human Protein Atlas [tissue]ENSG00000101400-SNTA1 [tissue]
Peptide AtlasQ13424
HPRD03009
IPIIPI00164528   IPI00910896   
Protein Interaction databases
DIP (DOE-UCLA)Q13424
IntAct (EBI)Q13424
FunCoupENSG00000101400
BioGRIDSNTA1
STRING (EMBL)SNTA1
ZODIACSNTA1
Ontologies - Pathways
QuickGOQ13424
Ontology : AmiGOregulation of heart rate  actin binding  structural molecule activity  protein binding  calmodulin binding  cytoplasm  cytoskeleton  muscle contraction  dystrophin-associated glycoprotein complex  syntrophin complex  lateral plasma membrane  sodium channel regulator activity  cell junction  PDZ domain binding  neuromuscular junction  protein-containing complex  sarcolemma  ion channel binding  synapse  nitric-oxide synthase binding  ATPase binding  regulation of ventricular cardiac muscle cell membrane repolarization  ventricular cardiac muscle cell action potential  negative regulation of peptidyl-cysteine S-nitrosylation  regulation of sodium ion transmembrane transport  
Ontology : EGO-EBIregulation of heart rate  actin binding  structural molecule activity  protein binding  calmodulin binding  cytoplasm  cytoskeleton  muscle contraction  dystrophin-associated glycoprotein complex  syntrophin complex  lateral plasma membrane  sodium channel regulator activity  cell junction  PDZ domain binding  neuromuscular junction  protein-containing complex  sarcolemma  ion channel binding  synapse  nitric-oxide synthase binding  ATPase binding  regulation of ventricular cardiac muscle cell membrane repolarization  ventricular cardiac muscle cell action potential  negative regulation of peptidyl-cysteine S-nitrosylation  regulation of sodium ion transmembrane transport  
NDEx NetworkSNTA1
Atlas of Cancer Signalling NetworkSNTA1
Wikipedia pathwaysSNTA1
Orthology - Evolution
OrthoDB6640
GeneTree (enSembl)ENSG00000101400
Phylogenetic Trees/Animal Genes : TreeFamSNTA1
HOGENOMQ13424
Homologs : HomoloGeneSNTA1
Homology/Alignments : Family Browser (UCSC)SNTA1
Gene fusions - Rearrangements
Fusion : QuiverSNTA1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerSNTA1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)SNTA1
dbVarSNTA1
ClinVarSNTA1
1000_GenomesSNTA1 
Exome Variant ServerSNTA1
ExAC (Exome Aggregation Consortium)ENSG00000101400
GNOMAD BrowserENSG00000101400
Varsome BrowserSNTA1
Genetic variants : HAPMAP6640
Genomic Variants (DGV)SNTA1 [DGVbeta]
DECIPHERSNTA1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisSNTA1 
Mutations
ICGC Data PortalSNTA1 
TCGA Data PortalSNTA1 
Broad Tumor PortalSNTA1
OASIS PortalSNTA1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICSNTA1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDSNTA1
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)Zhejiang University Center for Genetic and Genomic Medicine (ZJU-CGGM)
BioMutasearch SNTA1
DgiDB (Drug Gene Interaction Database)SNTA1
DoCM (Curated mutations)SNTA1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)SNTA1 (select a term)
intoGenSNTA1
Cancer3DSNTA1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601017    612955   
Orphanet14727   
DisGeNETSNTA1
MedgenSNTA1
Genetic Testing Registry SNTA1
NextProtQ13424 [Medical]
TSGene6640
GENETestsSNTA1
Target ValidationSNTA1
Huge Navigator SNTA1 [HugePedia]
snp3D : Map Gene to Disease6640
BioCentury BCIQSNTA1
ClinGenSNTA1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD6640
Chemical/Pharm GKB GenePA36007
Clinical trialSNTA1
Miscellaneous
canSAR (ICR)SNTA1 (select the gene name)
DataMed IndexSNTA1
Probes
Litterature
PubMed63 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineSNTA1
EVEXSNTA1
GoPubMedSNTA1
iHOPSNTA1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Jan 17 18:39:29 CET 2019
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