Atlas of Genetics and Cytogenetics in Oncology and Haematology

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VCL (vinculin)

Identity

Other aliasCMD1W
CMH15
HEL114
MV
MVCL
HGNC (Hugo) VCL
LocusID (NCBI) 7414
Atlas_Id 42785
Location 10q22.2  [Link to chromosome band 10q22]
Location_base_pair Starts at 73998114 and ends at 74120156 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)
C10orf11 (10q22.2) / VCL (10q22.2)KIF1C (17p13.2) / VCL (10q22.2)PPP1R10 (6p21.33) / VCL (10q22.2)
SLC44A2 (19p13.2) / VCL (10q22.2)VCL (10q22.2) / ABCC8 (11p15.1)VCL (10q22.2) / ADK (10q22.2)
VCL (10q22.2) / ALK (2p23.2)VCL (10q22.2) / FGFR2 (10q26.13)VCL (10q22.2) / NTRK2 (9q21.33)
VCL (10q22.2) / SEC24C (10q22.2)VCL (10q22.2) / SFTPD (10q22.3)VCL (10q22.2) / VCL (10q22.2)
VCL (10q22.2) / ZSWIM8 (10q22.2)VCL 10q22.2 / ALK 2p23.2C10orf11 10q22.2 / VCL 10q22.2
VCL 10q22.2 / FGFR2 10q26.13VCL 10q22.2 KIAA0913VCL 10q22.2 / SEC24C 10q22.2
VCL 10q22.2 / SFTPD 10q22.3

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) [ 7 ]
  Kidney: ALK-rearranged renal cell carcinoma
t(9;10)(q21;q22) VCL/NTRK2
VCL/SEC24C (10q22)
VCL/SFTPD (10q22)
VCL/ZSWIM8 (10q22)
t(10;10)(q22;q26) VCL/FGFR2
t(10;11)(q22;p15) VCL/ABCC8

External links

Nomenclature
HGNC (Hugo)VCL   12665
LRG (Locus Reference Genomic)LRG_383
Cards
Entrez_Gene (NCBI)VCL  7414  vinculin
AliasesCMD1W; CMH15; HEL114; MV; 
MVCL
GeneCards (Weizmann)VCL
Ensembl hg19 (Hinxton)ENSG00000035403 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000035403 [Gene_View]  ENSG00000035403 [Sequence]  chr10:73998114-74120156 [Contig_View]  VCL [Vega]
ICGC DataPortalENSG00000035403
TCGA cBioPortalVCL
AceView (NCBI)VCL
Genatlas (Paris)VCL
WikiGenes7414
SOURCE (Princeton)VCL
Genetics Home Reference (NIH)VCL
Genomic and cartography
GoldenPath hg38 (UCSC)VCL  -     chr10:73998114-74120156 +  10q22.2   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VCL  -     10q22.2   [Description]    (hg19-Feb_2009)
GoldenPathVCL - 10q22.2 [CytoView hg19]  VCL - 10q22.2 [CytoView hg38]
ImmunoBaseENSG00000035403
Mapping of homologs : NCBIVCL [Mapview hg19]  VCL [Mapview hg38]
OMIM193065   611407   613255   
Gene and transcription
Genbank (Entrez)AA368699 AI290052 AK126978 AK296509 AK300280
RefSeq transcript (Entrez)NM_003373 NM_014000
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)VCL
Cluster EST : UnigeneHs.643896 [ NCBI ]
CGAP (NCI)Hs.643896
Alternative Splicing GalleryENSG00000035403
Gene ExpressionVCL [ NCBI-GEO ]   VCL [ EBI - ARRAY_EXPRESS ]   VCL [ SEEK ]   VCL [ MEM ]
Gene Expression Viewer (FireBrowse)VCL [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7414
GTEX Portal (Tissue expression)VCL
Human Protein AtlasENSG00000035403-VCL [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtP18206   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP18206  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP18206
Splice isoforms : SwissVarP18206
PhosPhoSitePlusP18206
Domaine pattern : Prosite (Expaxy)VINCULIN_1 (PS00663)    VINCULIN_2 (PS00664)   
Domains : Interpro (EBI)Alpha-catenin/vinculin-like_sf    Vinculin    Vinculin/catenin    Vinculin_CS   
Domain families : Pfam (Sanger)Vinculin (PF01044)   
Domain families : Pfam (NCBI)pfam01044   
Conserved Domain (NCBI)VCL
DMDM Disease mutations7414
Blocks (Seattle)VCL
PDB (RSDB)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3JBK    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP    4LN2    4LNP    4PR9    5L0C    5L0D    5L0F    5L0G    5L0H    5L0I    5L0J    5O2Q    6FUY   
PDB Europe1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3JBK    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP    4LN2    4LNP    4PR9    5L0C    5L0D    5L0F    5L0G    5L0H    5L0I    5L0J    5O2Q    6FUY   
PDB (PDBSum)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3JBK    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP    4LN2    4LNP    4PR9    5L0C    5L0D    5L0F    5L0G    5L0H    5L0I    5L0J    5O2Q    6FUY   
PDB (IMB)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3JBK    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP    4LN2    4LNP    4PR9    5L0C    5L0D    5L0F    5L0G    5L0H    5L0I    5L0J    5O2Q    6FUY   
Structural Biology KnowledgeBase1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3JBK    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP    4LN2    4LNP    4PR9    5L0C    5L0D    5L0F    5L0G    5L0H    5L0I    5L0J    5O2Q    6FUY   
SCOP (Structural Classification of Proteins)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3JBK    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP    4LN2    4LNP    4PR9    5L0C    5L0D    5L0F    5L0G    5L0H    5L0I    5L0J    5O2Q    6FUY   
CATH (Classification of proteins structures)1RKC    1RKE    1SYQ    1TR2    1YDI    2GWW    2HSQ    2IBF    3H2U    3H2V    3JBK    3MYI    3RF3    3S90    3TJ5    3TJ6    3VF0    4DJ9    4EHP    4LN2    4LNP    4PR9    5L0C    5L0D    5L0F    5L0G    5L0H    5L0I    5L0J    5O2Q    6FUY   
SuperfamilyP18206
Human Protein Atlas [tissue]ENSG00000035403-VCL [tissue]
Peptide AtlasP18206
HPRD01900
IPIIPI00307162   IPI00291175   IPI00384973   IPI00909711   IPI01011952   IPI00910496   IPI01014113   
Protein Interaction databases
DIP (DOE-UCLA)P18206
IntAct (EBI)P18206
FunCoupENSG00000035403
BioGRIDVCL
STRING (EMBL)VCL
ZODIACVCL
Ontologies - Pathways
QuickGOP18206
Ontology : AmiGOmorphogenesis of an epithelium  podosome  dystroglycan binding  platelet degranulation  actin binding  actin binding  structural molecule activity  protein binding  extracellular region  cytosol  cytoskeleton  cell-cell junction  adherens junction  cell-cell adherens junction  fascia adherens  focal adhesion  focal adhesion  focal adhesion  muscle contraction  cell adhesion  cell-matrix adhesion  beta-catenin binding  lamellipodium assembly  cell-substrate junction  negative regulation of cell migration  ubiquitin protein ligase binding  protein-containing complex  adherens junction assembly  protein localization to cell surface  secretory granule lumen  specific granule lumen  sarcolemma  costamere  costamere  apical junction assembly  neutrophil degranulation  alpha-catenin binding  cadherin binding  cadherin binding  axon extension  extracellular exosome  platelet aggregation  epithelial cell-cell adhesion  extracellular vesicle  ficolin-1-rich granule lumen  
Ontology : EGO-EBImorphogenesis of an epithelium  podosome  dystroglycan binding  platelet degranulation  actin binding  actin binding  structural molecule activity  protein binding  extracellular region  cytosol  cytoskeleton  cell-cell junction  adherens junction  cell-cell adherens junction  fascia adherens  focal adhesion  focal adhesion  focal adhesion  muscle contraction  cell adhesion  cell-matrix adhesion  beta-catenin binding  lamellipodium assembly  cell-substrate junction  negative regulation of cell migration  ubiquitin protein ligase binding  protein-containing complex  adherens junction assembly  protein localization to cell surface  secretory granule lumen  specific granule lumen  sarcolemma  costamere  costamere  apical junction assembly  neutrophil degranulation  alpha-catenin binding  cadherin binding  cadherin binding  axon extension  extracellular exosome  platelet aggregation  epithelial cell-cell adhesion  extracellular vesicle  ficolin-1-rich granule lumen  
Pathways : KEGGFocal adhesion    Adherens junction    Leukocyte transendothelial migration    Regulation of actin cytoskeleton    Bacterial invasion of epithelial cells    Shigellosis    Amoebiasis   
NDEx NetworkVCL
Atlas of Cancer Signalling NetworkVCL
Wikipedia pathwaysVCL
Orthology - Evolution
OrthoDB7414
GeneTree (enSembl)ENSG00000035403
Phylogenetic Trees/Animal Genes : TreeFamVCL
HOGENOMP18206
Homologs : HomoloGeneVCL
Homology/Alignments : Family Browser (UCSC)VCL
Gene fusions - Rearrangements
Fusion : MitelmanC10orf11/VCL [10q22.2/10q22.2]  [t(10;10)(q22;q22)]  
Fusion : MitelmanVCL/ABCC8 [10q22.2/11p15.1]  [t(10;11)(q22;p15)]  
Fusion : MitelmanVCL/ALK [10q22.2/2p23.2]  [t(2;10)(p23;q22)]  
Fusion : MitelmanVCL/FGFR2 [10q22.2/10q26.13]  [t(10;10)(q22;q26)]  
Fusion : MitelmanVCL/NTRK2 [10q22.2/9q21.33]  [t(9;10)(q21;q22)]  
Fusion : MitelmanVCL/SEC24C [10q22.2/10q22.2]  [t(10;10)(q22;q22)]  
Fusion : MitelmanVCL/SFTPD [10q22.2/10q22.3]  [t(10;10)(q22;q22)]  
Fusion : MitelmanVCL/ZSWIM8 [10q22.2/10q22.2]  [t(10;10)(q22;q22)]  
Fusion PortalC10orf11 10q22.2 VCL 10q22.2 LUAD
Fusion PortalVCL 10q22.2 FGFR2 10q26.13 THCA
Fusion PortalVCL 10q22.2 KIAA0913 OV
Fusion PortalVCL 10q22.2 SEC24C 10q22.2 HNSC
Fusion PortalVCL 10q22.2 SFTPD 10q22.3 LUSC
Fusion : QuiverVCL
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVCL [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VCL
dbVarVCL
ClinVarVCL
1000_GenomesVCL 
Exome Variant ServerVCL
ExAC (Exome Aggregation Consortium)ENSG00000035403
GNOMAD BrowserENSG00000035403
Varsome BrowserVCL
Genetic variants : HAPMAP7414
Genomic Variants (DGV)VCL [DGVbeta]
DECIPHERVCL [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVCL 
Mutations
ICGC Data PortalVCL 
TCGA Data PortalVCL 
Broad Tumor PortalVCL
OASIS PortalVCL [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVCL  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDVCL
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)
LOVD (Leiden Open Variation Database)MSeqDR-LSDB Mitochondrial Disease Locus Specific Database
BioMutasearch VCL
DgiDB (Drug Gene Interaction Database)VCL
DoCM (Curated mutations)VCL (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VCL (select a term)
intoGenVCL
Cancer3DVCL(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM193065    611407    613255   
Orphanet635   
DisGeNETVCL
MedgenVCL
Genetic Testing Registry VCL
NextProtP18206 [Medical]
TSGene7414
GENETestsVCL
Target ValidationVCL
Huge Navigator VCL [HugePedia]
snp3D : Map Gene to Disease7414
BioCentury BCIQVCL
ClinGenVCL
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD7414
Chemical/Pharm GKB GenePA37288
Clinical trialVCL
Miscellaneous
canSAR (ICR)VCL (select the gene name)
DataMed IndexVCL
Probes
Litterature
PubMed191 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVCL
EVEXVCL
GoPubMedVCL
iHOPVCL
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Fri Jun 7 18:21:40 CEST 2019
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