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VIM (vimentin)

Identity

Other aliasCTRCT30
HEL113
HGNC (Hugo) VIM
LocusID (NCBI) 7431
Atlas_Id 42791
Location 10p13  [Link to chromosome band 10p13]
Location_base_pair Starts at 17270258 and ends at 17279592 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
COL5A2 (2q32.2) / VIM (10p13)ENO3 (17p13.2) / VIM (10p13)FOS (14q24.3) / VIM (10p13)
KRT8 (12q13.13) / VIM (10p13)PRR13 (12q13.13) / VIM (10p13)SPAG9 (17q21.33) / VIM (10p13)
VIM (10p13) / DNM1L (12p11.21)VIM (10p13) / EEA1 (12q22)VIM (10p13) / IQCE (7p22.3)
VIM (10p13) / IQCG (3q29)VIM (10p13) / KRT7 (12q13.13)VIM (10p13) / LAMA4 (6q21)
VIM (10p13) / PLEKHA5 (12p12.3)VIM (10p13) / SIAE (11q24.2)VIM (10p13) / ZNF664 (12q24.31)
VIM 10p13 / DNM1L 12p11.21VIM 10p13 / EEA1 12q22VIM 10p13 / IQCE 7p22.3
VIM 10p13 / LAMA4 6q21VIM 10p13 / PLEKHA5 12p12.3VIM 10p13 / SIAE 11q24.2

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 Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  del(13q) in chronic lymphocytic leukemia


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 14 ]
  Soft Tissues: Aggressive angiomyxoma
Soft Tissues: Alveolar soft part sarcoma with t(X;17)(p11;q25) ASPSCR1/TFE3
Thyroid: Anaplastic (undifferentiated) carcinoma
Soft Tissues: Dermatofibrosarcoma Protuberans
Soft Tissues: Desmoid-type fibromatosis
Bone: Epithelioid hemangioendothelioma
Soft Tissues: Extraskeletal osteosarcoma
Fallopian tube tumors: an overview
Head and Neck: Iris Hamartomas
Lymphangioleiomyomatosis
Liver: Nested stromal epithelial tumor
Lung: Pleuropulmonary blastoma
Kidney: Renal Oncocytoma
Bone: Vascular Tumors


External links

Nomenclature
HGNC (Hugo)VIM   12692
Cards
Entrez_Gene (NCBI)VIM  7431  vimentin
AliasesCTRCT30; HEL113
GeneCards (Weizmann)VIM
Ensembl hg19 (Hinxton)ENSG00000026025 [Gene_View]  chr10:17270258-17279592 [Contig_View]  VIM [Vega]
Ensembl hg38 (Hinxton)ENSG00000026025 [Gene_View]  chr10:17270258-17279592 [Contig_View]  VIM [Vega]
ICGC DataPortalENSG00000026025
TCGA cBioPortalVIM
AceView (NCBI)VIM
Genatlas (Paris)VIM
WikiGenes7431
SOURCE (Princeton)VIM
Genetics Home Reference (NIH)VIM
Genomic and cartography
GoldenPath hg19 (UCSC)VIM  -     chr10:17270258-17279592 +  10p13   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)VIM  -     10p13   [Description]    (hg38-Dec_2013)
EnsemblVIM - 10p13 [CytoView hg19]  VIM - 10p13 [CytoView hg38]
Mapping of homologs : NCBIVIM [Mapview hg19]  VIM [Mapview hg38]
OMIM116300   193060   
Gene and transcription
Genbank (Entrez)AF328728 AK056766 AK091813 AK093924 AK097336
RefSeq transcript (Entrez)NM_003380
RefSeq genomic (Entrez)NC_000010 NC_018921 NG_012413 NT_008705 NW_004929370
Consensus coding sequences : CCDS (NCBI)VIM
Cluster EST : UnigeneHs.691131 [ NCBI ]
CGAP (NCI)Hs.691131
Alternative Splicing GalleryENSG00000026025
Gene ExpressionVIM [ NCBI-GEO ]   VIM [ EBI - ARRAY_EXPRESS ]   VIM [ SEEK ]   VIM [ MEM ]
Gene Expression Viewer (FireBrowse)VIM [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)7431
GTEX Portal (Tissue expression)VIM
Protein : pattern, domain, 3D structure
UniProt/SwissProtP08670   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtP08670  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProP08670
Splice isoforms : SwissVarP08670
PhosPhoSitePlusP08670
Domaine pattern : Prosite (Expaxy)IF (PS00226)   
Domains : Interpro (EBI)IF    Intermed_filament_DNA-bd    Intermediate_filament_CS   
Domain families : Pfam (Sanger)Filament (PF00038)    Filament_head (PF04732)   
Domain families : Pfam (NCBI)pfam00038    pfam04732   
Conserved Domain (NCBI)VIM
DMDM Disease mutations7431
Blocks (Seattle)VIM
PDB (SRS)1GK4    1GK6    1GK7    3G1E    3KLT    3S4R    3SSU    3SWK    3TRT    3UF1    4MCY    4MCZ    4MD0    4MD5    4MDI    4MDJ    4YPC    4YV3   
PDB (PDBSum)1GK4    1GK6    1GK7    3G1E    3KLT    3S4R    3SSU    3SWK    3TRT    3UF1    4MCY    4MCZ    4MD0    4MD5    4MDI    4MDJ    4YPC    4YV3   
PDB (IMB)1GK4    1GK6    1GK7    3G1E    3KLT    3S4R    3SSU    3SWK    3TRT    3UF1    4MCY    4MCZ    4MD0    4MD5    4MDI    4MDJ    4YPC    4YV3   
PDB (RSDB)1GK4    1GK6    1GK7    3G1E    3KLT    3S4R    3SSU    3SWK    3TRT    3UF1    4MCY    4MCZ    4MD0    4MD5    4MDI    4MDJ    4YPC    4YV3   
Structural Biology KnowledgeBase1GK4    1GK6    1GK7    3G1E    3KLT    3S4R    3SSU    3SWK    3TRT    3UF1    4MCY    4MCZ    4MD0    4MD5    4MDI    4MDJ    4YPC    4YV3   
SCOP (Structural Classification of Proteins)1GK4    1GK6    1GK7    3G1E    3KLT    3S4R    3SSU    3SWK    3TRT    3UF1    4MCY    4MCZ    4MD0    4MD5    4MDI    4MDJ    4YPC    4YV3   
CATH (Classification of proteins structures)1GK4    1GK6    1GK7    3G1E    3KLT    3S4R    3SSU    3SWK    3TRT    3UF1    4MCY    4MCZ    4MD0    4MD5    4MDI    4MDJ    4YPC    4YV3   
SuperfamilyP08670
Human Protein AtlasENSG00000026025
Peptide AtlasP08670
HPRD01899
IPIIPI00418471   IPI00975690   IPI00982595   IPI00552689   
Protein Interaction databases
DIP (DOE-UCLA)P08670
IntAct (EBI)P08670
FunCoupENSG00000026025
BioGRIDVIM
STRING (EMBL)VIM
ZODIACVIM
Ontologies - Pathways
QuickGOP08670
Ontology : AmiGOglycoprotein binding  double-stranded RNA binding  structural constituent of cytoskeleton  structural constituent of eye lens  protein binding  cytoplasm  peroxisome  cytosol  cytosol  cytoskeleton  cytoskeleton  intermediate filament  plasma membrane  focal adhesion  movement of cell or subcellular component  protein C-terminus binding  positive regulation of gene expression  negative regulation of neuron projection development  astrocyte development  viral process  muscle filament sliding  cell leading edge  identical protein binding  neuron projection  intermediate filament organization  intermediate filament cytoskeleton  Bergmann glial cell differentiation  SMAD protein signal transduction  extracellular exosome  lens fiber cell development  scaffold protein binding  keratin filament binding  
Ontology : EGO-EBIglycoprotein binding  double-stranded RNA binding  structural constituent of cytoskeleton  structural constituent of eye lens  protein binding  cytoplasm  peroxisome  cytosol  cytosol  cytoskeleton  cytoskeleton  intermediate filament  plasma membrane  focal adhesion  movement of cell or subcellular component  protein C-terminus binding  positive regulation of gene expression  negative regulation of neuron projection development  astrocyte development  viral process  muscle filament sliding  cell leading edge  identical protein binding  neuron projection  intermediate filament organization  intermediate filament cytoskeleton  Bergmann glial cell differentiation  SMAD protein signal transduction  extracellular exosome  lens fiber cell development  scaffold protein binding  keratin filament binding  
Pathways : KEGGEpstein-Barr virus infection    MicroRNAs in cancer   
NDEx NetworkVIM
Atlas of Cancer Signalling NetworkVIM
Wikipedia pathwaysVIM
Orthology - Evolution
OrthoDB7431
GeneTree (enSembl)ENSG00000026025
Phylogenetic Trees/Animal Genes : TreeFamVIM
HOVERGENP08670
HOGENOMP08670
Homologs : HomoloGeneVIM
Homology/Alignments : Family Browser (UCSC)VIM
Gene fusions - Rearrangements
Fusion : MitelmanVIM/DNM1L [10p13/12p11.21]  
Fusion : MitelmanVIM/IQCE [10p13/7p22.3]  [t(7;10)(p22;p13)]  
Fusion : MitelmanVIM/PLEKHA5 [10p13/12p12.3]  [t(10;12)(p13;p12)]  
Fusion : MitelmanVIM/SIAE [10p13/11q24.2]  [t(10;11)(p13;q24)]  
Fusion: TCGAVIM 10p13 DNM1L 12p11.21 KIRC
Fusion: TCGAVIM 10p13 EEA1 12q22 HNSC
Fusion: TCGAVIM 10p13 IQCE 7p22.3 LUAD
Fusion: TCGAVIM 10p13 LAMA4 6q21 SKCM
Fusion: TCGAVIM 10p13 PLEKHA5 12p12.3 SKCM
Fusion: TCGAVIM 10p13 SIAE 11q24.2 KIRC
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVIM [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VIM
dbVarVIM
ClinVarVIM
1000_GenomesVIM 
Exome Variant ServerVIM
ExAC (Exome Aggregation Consortium)VIM (select the gene name)
Genetic variants : HAPMAP7431
Genomic Variants (DGV)VIM [DGVbeta]
DECIPHER (Syndromes)10:17270258-17279592  ENSG00000026025
CONAN: Copy Number AnalysisVIM 
Mutations
ICGC Data PortalVIM 
TCGA Data PortalVIM 
Broad Tumor PortalVIM
OASIS PortalVIM [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVIM  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDVIM
intOGen PortalVIM
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)Eye diseases - LOVD
BioMutasearch VIM
DgiDB (Drug Gene Interaction Database)VIM
DoCM (Curated mutations)VIM (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VIM (select a term)
intoGenVIM
Cancer3DVIM(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM116300    193060   
Orphanet14001   
MedgenVIM
Genetic Testing Registry VIM
NextProtP08670 [Medical]
TSGene7431
GENETestsVIM
Huge Navigator VIM [HugePedia]
snp3D : Map Gene to Disease7431
BioCentury BCIQVIM
ClinGenVIM
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD7431
Chemical/Pharm GKB GenePA37311
Clinical trialVIM
Miscellaneous
canSAR (ICR)VIM (select the gene name)
Probes
Litterature
PubMed424 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVIM
EVEXVIM
GoPubMedVIM
iHOPVIM
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:33:53 CET 2017

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