Atlas of Genetics and Cytogenetics in Oncology and Haematology


Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

X Y 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 NA

VARS2 (valyl-tRNA synthetase 2, mitochondrial)

Identity

Alias_namesmitochondrial
VARS2L
VARSL
Alias_symbol (synonym)DKFZP434L1435
KIAA1885
G7a
Other aliasCOXPD20
VALRS
HGNC (Hugo) VARS2
LocusID (NCBI) 57176
Atlas_Id 43073
Location 6p21.33  [Link to chromosome band 6p21]
Location_base_pair Starts at 30914208 and ends at 30926458 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)
CD63 (12q13.2) / VARS2 (6p21.33)TRERF1 (6p21.1) / VARS2 (6p21.33)TRERF1 6p21.1 / VARS2 6p21.33

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(6;6)(p21;p21) TRERF1/VARS2


External links

Nomenclature
HGNC (Hugo)VARS2   21642
Cards
Entrez_Gene (NCBI)VARS2  57176  valyl-tRNA synthetase 2, mitochondrial
AliasesCOXPD20; VALRS; VARS2L; VARSL
GeneCards (Weizmann)VARS2
Ensembl hg19 (Hinxton)ENSG00000137411 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000137411 [Gene_View]  ENSG00000137411 [Sequence]  chr6:30914208-30926458 [Contig_View]  VARS2 [Vega]
ICGC DataPortalENSG00000137411
TCGA cBioPortalVARS2
AceView (NCBI)VARS2
Genatlas (Paris)VARS2
WikiGenes57176
SOURCE (Princeton)VARS2
Genetics Home Reference (NIH)VARS2
Genomic and cartography
GoldenPath hg38 (UCSC)VARS2  -     chr6:30914208-30926458 +  6p21.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)VARS2  -     6p21.33   [Description]    (hg19-Feb_2009)
EnsemblVARS2 - 6p21.33 [CytoView hg19]  VARS2 - 6p21.33 [CytoView hg38]
Mapping of homologs : NCBIVARS2 [Mapview hg19]  VARS2 [Mapview hg38]
OMIM612802   615917   
Gene and transcription
Genbank (Entrez)AB067472 AK000511 AK025618 AK026063 AK094483
RefSeq transcript (Entrez)NM_001167733 NM_001167734 NM_020442
RefSeq genomic (Entrez)NC_000006 NC_018917 NG_034224 NT_113891 NT_167245 NT_167246 NT_167247 NT_167248
Consensus coding sequences : CCDS (NCBI)VARS2
Cluster EST : UnigeneHs.597526 [ NCBI ]
CGAP (NCI)Hs.597526
Alternative Splicing GalleryENSG00000137411
Gene ExpressionVARS2 [ NCBI-GEO ]   VARS2 [ EBI - ARRAY_EXPRESS ]   VARS2 [ SEEK ]   VARS2 [ MEM ]
Gene Expression Viewer (FireBrowse)VARS2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)57176
GTEX Portal (Tissue expression)VARS2
Human Protein AtlasENSG00000137411-VARS2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ5ST30   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ5ST30  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ5ST30
Splice isoforms : SwissVarQ5ST30
Catalytic activity : Enzyme6.1.1.9 [ Enzyme-Expasy ]   6.1.1.96.1.1.9 [ IntEnz-EBI ]   6.1.1.9 [ BRENDA ]   6.1.1.9 [ KEGG ]   
PhosPhoSitePlusQ5ST30
Domaine pattern : Prosite (Expaxy)AA_TRNA_LIGASE_I (PS00178)   
Domains : Interpro (EBI)aa-tRNA-synth_I_CS    aa-tRNA-synth_Ia    Anticodon_Ia_Val    M/V/L/I-tRNA-synth_anticd-bd    Rossmann-like_a/b/a_fold    tRNAsynth_Ia_anticodon-bd    Val/Leu/Ile-tRNA-synth_edit    Valyl-tRNA_ligase   
Domain families : Pfam (Sanger)Anticodon_1 (PF08264)    tRNA-synt_1 (PF00133)   
Domain families : Pfam (NCBI)pfam08264    pfam00133   
Conserved Domain (NCBI)VARS2
DMDM Disease mutations57176
Blocks (Seattle)VARS2
SuperfamilyQ5ST30
Human Protein Atlas [tissue]ENSG00000137411-VARS2 [tissue]
Peptide AtlasQ5ST30
HPRD11670
IPIIPI00644468   IPI00895822   IPI00873561   IPI00640597   IPI00965955   IPI00792104   IPI00647631   
Protein Interaction databases
DIP (DOE-UCLA)Q5ST30
IntAct (EBI)Q5ST30
FunCoupENSG00000137411
BioGRIDVARS2
STRING (EMBL)VARS2
ZODIACVARS2
Ontologies - Pathways
QuickGOQ5ST30
Ontology : AmiGOaminoacyl-tRNA editing activity  valine-tRNA ligase activity  ATP binding  mitochondrion  cytosol  valyl-tRNA aminoacylation  aminoacyl-tRNA metabolism involved in translational fidelity  
Ontology : EGO-EBIaminoacyl-tRNA editing activity  valine-tRNA ligase activity  ATP binding  mitochondrion  cytosol  valyl-tRNA aminoacylation  aminoacyl-tRNA metabolism involved in translational fidelity  
NDEx NetworkVARS2
Atlas of Cancer Signalling NetworkVARS2
Wikipedia pathwaysVARS2
Orthology - Evolution
OrthoDB57176
GeneTree (enSembl)ENSG00000137411
Phylogenetic Trees/Animal Genes : TreeFamVARS2
HOVERGENQ5ST30
HOGENOMQ5ST30
Homologs : HomoloGeneVARS2
Homology/Alignments : Family Browser (UCSC)VARS2
Gene fusions - Rearrangements
Fusion : MitelmanTRERF1/VARS2 [6p21.1/6p21.33]  [t(6;6)(p21;p21)]  
Fusion PortalTRERF1 6p21.1 VARS2 6p21.33 BRCA
Fusion : QuiverVARS2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerVARS2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)VARS2
dbVarVARS2
ClinVarVARS2
1000_GenomesVARS2 
Exome Variant ServerVARS2
ExAC (Exome Aggregation Consortium)ENSG00000137411
GNOMAD BrowserENSG00000137411
Genetic variants : HAPMAP57176
Genomic Variants (DGV)VARS2 [DGVbeta]
DECIPHERVARS2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisVARS2 
Mutations
ICGC Data PortalVARS2 
TCGA Data PortalVARS2 
Broad Tumor PortalVARS2
OASIS PortalVARS2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICVARS2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDVARS2
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
BioMutasearch VARS2
DgiDB (Drug Gene Interaction Database)VARS2
DoCM (Curated mutations)VARS2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)VARS2 (select a term)
intoGenVARS2
Cancer3DVARS2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM612802    615917   
Orphanet23121   
DisGeNETVARS2
MedgenVARS2
Genetic Testing Registry VARS2
NextProtQ5ST30 [Medical]
TSGene57176
GENETestsVARS2
Target ValidationVARS2
Huge Navigator VARS2 [HugePedia]
snp3D : Map Gene to Disease57176
BioCentury BCIQVARS2
ClinGenVARS2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD57176
Chemical/Pharm GKB GenePA164742816
Clinical trialVARS2
Miscellaneous
canSAR (ICR)VARS2 (select the gene name)
Probes
Litterature
PubMed20 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineVARS2
EVEXVARS2
GoPubMedVARS2
iHOPVARS2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

Search in all EBI   NCBI

© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Fri Jun 22 16:57:03 CEST 2018

Home   Genes   Leukemias   Solid Tumors   Cancer-Prone   Deep Insight   Case Reports   Journals  Portal   Teaching   

For comments and suggestions or contributions, please contact us

jlhuret@AtlasGeneticsOncology.org.