Atlas of Genetics and Cytogenetics in Oncology and Haematology


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HAVCR2 (hepatitis A virus cellular receptor 2)

Identity

Alias_symbol (synonym)Tim-3
TIM3
FLJ14428
TIMD3
CD366
Other aliasHAVcr-2
KIM-3
TIMD-3
HGNC (Hugo) HAVCR2
LocusID (NCBI) 84868
Atlas_Id 47642
Location 5q33.3  [Link to chromosome band 5q33]
Location_base_pair Starts at 156512843 and ends at 156536248 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
FAM120AOS (9q22.31) / HAVCR2 (5q33.3)

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

 


External links

Nomenclature
HGNC (Hugo)HAVCR2   18437
Cards
Entrez_Gene (NCBI)HAVCR2  84868  hepatitis A virus cellular receptor 2
AliasesCD366; HAVcr-2; KIM-3; TIM3; 
TIMD-3; TIMD3; Tim-3
GeneCards (Weizmann)HAVCR2
Ensembl hg19 (Hinxton)ENSG00000135077 [Gene_View]  chr5:156512843-156536248 [Contig_View]  HAVCR2 [Vega]
Ensembl hg38 (Hinxton)ENSG00000135077 [Gene_View]  chr5:156512843-156536248 [Contig_View]  HAVCR2 [Vega]
ICGC DataPortalENSG00000135077
TCGA cBioPortalHAVCR2
AceView (NCBI)HAVCR2
Genatlas (Paris)HAVCR2
WikiGenes84868
SOURCE (Princeton)HAVCR2
Genetics Home Reference (NIH)HAVCR2
Genomic and cartography
GoldenPath hg19 (UCSC)HAVCR2  -     chr5:156512843-156536248 -  5q33.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)HAVCR2  -     5q33.3   [Description]    (hg38-Dec_2013)
EnsemblHAVCR2 - 5q33.3 [CytoView hg19]  HAVCR2 - 5q33.3 [CytoView hg38]
Mapping of homologs : NCBIHAVCR2 [Mapview hg19]  HAVCR2 [Mapview hg38]
OMIM606652   
Gene and transcription
Genbank (Entrez)AB924452 AF251707 AF450242 AF450243 AK027334
RefSeq transcript (Entrez)NM_032782
RefSeq genomic (Entrez)NC_000005 NC_018916 NG_030444 NT_023133 NW_004929325
Consensus coding sequences : CCDS (NCBI)HAVCR2
Cluster EST : UnigeneHs.710500 [ NCBI ]
CGAP (NCI)Hs.710500
Alternative Splicing GalleryENSG00000135077
Gene ExpressionHAVCR2 [ NCBI-GEO ]   HAVCR2 [ EBI - ARRAY_EXPRESS ]   HAVCR2 [ SEEK ]   HAVCR2 [ MEM ]
Gene Expression Viewer (FireBrowse)HAVCR2 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)84868
GTEX Portal (Tissue expression)HAVCR2
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8TDQ0   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8TDQ0  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8TDQ0
Splice isoforms : SwissVarQ8TDQ0
PhosPhoSitePlusQ8TDQ0
Domaine pattern : Prosite (Expaxy)IG_LIKE (PS50835)   
Domains : Interpro (EBI)Ig-like_dom    Ig-like_fold    Ig_sub    Ig_V-set   
Domain families : Pfam (Sanger)V-set (PF07686)   
Domain families : Pfam (NCBI)pfam07686   
Domain families : Smart (EMBL)IG (SM00409)  
Conserved Domain (NCBI)HAVCR2
DMDM Disease mutations84868
Blocks (Seattle)HAVCR2
PDB (SRS)5DZL    5F71   
PDB (PDBSum)5DZL    5F71   
PDB (IMB)5DZL    5F71   
PDB (RSDB)5DZL    5F71   
Structural Biology KnowledgeBase5DZL    5F71   
SCOP (Structural Classification of Proteins)5DZL    5F71   
CATH (Classification of proteins structures)5DZL    5F71   
SuperfamilyQ8TDQ0
Human Protein AtlasENSG00000135077
Peptide AtlasQ8TDQ0
HPRD16227
IPIIPI00651768   IPI00383032   IPI00974307   IPI00984771   
Protein Interaction databases
DIP (DOE-UCLA)Q8TDQ0
IntAct (EBI)Q8TDQ0
FunCoupENSG00000135077
BioGRIDHAVCR2
STRING (EMBL)HAVCR2
ZODIACHAVCR2
Ontologies - Pathways
QuickGOQ8TDQ0
Ontology : AmiGOimmunological synapse  adaptive immune response  macrophage activation involved in immune response  natural killer cell tolerance induction  regulation of tolerance induction dependent upon immune response  negative regulation of T-helper 1 type immune response  negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target  early endosome  inflammatory response  cell surface  negative regulation of gene expression  integral component of membrane  cell junction  negative regulation of myeloid dendritic cell activation  negative regulation of NF-kappaB transcription factor activity  negative regulation of interferon-alpha production  negative regulation of interferon-gamma production  negative regulation of interleukin-2 production  negative regulation of interleukin-3 production  negative regulation of interleukin-6 production  negative regulation of tumor necrosis factor production  positive regulation of chemokine production  positive regulation of interferon-gamma production  positive regulation of interleukin-1 production  positive regulation of interleukin-4 production  negative regulation of natural killer cell activation  toll-like receptor 3 signaling pathway  toll-like receptor 7 signaling pathway  toll-like receptor 9 signaling pathway  positive regulation of T cell proliferation  negative regulation of T cell proliferation  positive regulation of macrophage activation  innate immune response  metal ion binding  defense response to Gram-positive bacterium  maternal process involved in female pregnancy  extracellular exosome  positive regulation of ERK1 and ERK2 cascade  cellular response to lipopolysaccharide  negative regulation of granulocyte colony-stimulating factor production  negative regulation of defense response to bacterium  positive regulation of defense response to bacterium  positive regulation of NIK/NF-kappaB signaling  positive regulation of tumor necrosis factor secretion  negative regulation of immunological synapse formation  negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell  
Ontology : EGO-EBIimmunological synapse  adaptive immune response  macrophage activation involved in immune response  natural killer cell tolerance induction  regulation of tolerance induction dependent upon immune response  negative regulation of T-helper 1 type immune response  negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target  early endosome  inflammatory response  cell surface  negative regulation of gene expression  integral component of membrane  cell junction  negative regulation of myeloid dendritic cell activation  negative regulation of NF-kappaB transcription factor activity  negative regulation of interferon-alpha production  negative regulation of interferon-gamma production  negative regulation of interleukin-2 production  negative regulation of interleukin-3 production  negative regulation of interleukin-6 production  negative regulation of tumor necrosis factor production  positive regulation of chemokine production  positive regulation of interferon-gamma production  positive regulation of interleukin-1 production  positive regulation of interleukin-4 production  negative regulation of natural killer cell activation  toll-like receptor 3 signaling pathway  toll-like receptor 7 signaling pathway  toll-like receptor 9 signaling pathway  positive regulation of T cell proliferation  negative regulation of T cell proliferation  positive regulation of macrophage activation  innate immune response  metal ion binding  defense response to Gram-positive bacterium  maternal process involved in female pregnancy  extracellular exosome  positive regulation of ERK1 and ERK2 cascade  cellular response to lipopolysaccharide  negative regulation of granulocyte colony-stimulating factor production  negative regulation of defense response to bacterium  positive regulation of defense response to bacterium  positive regulation of NIK/NF-kappaB signaling  positive regulation of tumor necrosis factor secretion  negative regulation of immunological synapse formation  negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell  
NDEx NetworkHAVCR2
Atlas of Cancer Signalling NetworkHAVCR2
Wikipedia pathwaysHAVCR2
Orthology - Evolution
OrthoDB84868
GeneTree (enSembl)ENSG00000135077
Phylogenetic Trees/Animal Genes : TreeFamHAVCR2
HOVERGENQ8TDQ0
HOGENOMQ8TDQ0
Homologs : HomoloGeneHAVCR2
Homology/Alignments : Family Browser (UCSC)HAVCR2
Gene fusions - Rearrangements
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerHAVCR2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)HAVCR2
dbVarHAVCR2
ClinVarHAVCR2
1000_GenomesHAVCR2 
Exome Variant ServerHAVCR2
ExAC (Exome Aggregation Consortium)HAVCR2 (select the gene name)
Genetic variants : HAPMAP84868
Genomic Variants (DGV)HAVCR2 [DGVbeta]
DECIPHER (Syndromes)5:156512843-156536248  ENSG00000135077
CONAN: Copy Number AnalysisHAVCR2 
Mutations
ICGC Data PortalHAVCR2 
TCGA Data PortalHAVCR2 
Broad Tumor PortalHAVCR2
OASIS PortalHAVCR2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICHAVCR2  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDHAVCR2
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
BioMutasearch HAVCR2
DgiDB (Drug Gene Interaction Database)HAVCR2
DoCM (Curated mutations)HAVCR2 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)HAVCR2 (select a term)
intoGenHAVCR2
Cancer3DHAVCR2(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM606652   
Orphanet
MedgenHAVCR2
Genetic Testing Registry HAVCR2
NextProtQ8TDQ0 [Medical]
TSGene84868
GENETestsHAVCR2
Huge Navigator HAVCR2 [HugePedia]
snp3D : Map Gene to Disease84868
BioCentury BCIQHAVCR2
ClinGenHAVCR2
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD84868
Chemical/Pharm GKB GenePA134883425
Clinical trialHAVCR2
Miscellaneous
canSAR (ICR)HAVCR2 (select the gene name)
Probes
Litterature
PubMed176 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineHAVCR2
EVEXHAVCR2
GoPubMedHAVCR2
iHOPHAVCR2
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 13:08:37 CET 2017

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