HAVCR2 Gene (Protein Coding)

Hepatitis A Virus Cellular Receptor 2

GC05M157063
GIFtS:
43
The protein encoded by this gene belongs to the immunoglobulin superfamily, and TIM family of proteins. CD4-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas, Th2 cells are i... See more...

Aliases for HAVCR2 Gene

Aliases for HAVCR2 Gene

  • Hepatitis A Virus Cellular Receptor 2 2 3 4 5
  • TIMD3 2 3 4
  • TIM3 2 3 4
  • T-Cell Immunoglobulin And Mucin Domain-Containing Protein 3 3 4
  • T-Cell Immunoglobulin Mucin Family Member 3 2 3
  • T-Cell Immunoglobulin Mucin Receptor 3 3 4
  • T-Cell Membrane Protein 3 3 4
  • HAVcr-2 3 4
  • TIMD-3 3 4
  • CD366 2 3
  • Tim-3 2 3
  • T Cell Immunoglobulin Mucin 3 3
  • Kidney Injury Molecule-3 3
  • CD366 Antigen 4
  • FLJ14428 2
  • HAVCR2 5
  • KIM-3 3
  • SPTCL 3
  • TIM-3 4

External Ids for HAVCR2 Gene

Previous GeneCards Identifiers for HAVCR2 Gene

  • GC05M156448
  • GC05M156493
  • GC05M156445
  • GC05M151601
  • GC05M156512

Summaries for HAVCR2 Gene

Entrez Gene Summary for HAVCR2 Gene

  • The protein encoded by this gene belongs to the immunoglobulin superfamily, and TIM family of proteins. CD4-positive T helper lymphocytes can be divided into types 1 (Th1) and 2 (Th2) on the basis of their cytokine secretion patterns. Th1 cells are involved in cell-mediated immunity to intracellular pathogens and delayed-type hypersensitivity reactions, whereas, Th2 cells are involved in the control of extracellular helminthic infections and the promotion of atopic and allergic diseases. This protein is a Th1-specific cell surface protein that regulates macrophage activation, and inhibits Th1-mediated auto- and alloimmune responses, and promotes immunological tolerance. [provided by RefSeq, Sep 2011]

CIViC Summary for HAVCR2 Gene

GeneCards Summary for HAVCR2 Gene

HAVCR2 (Hepatitis A Virus Cellular Receptor 2) is a Protein Coding gene. Diseases associated with HAVCR2 include T-Cell Lymphoma, Subcutaneous Panniculitis-Like and Panniculitis. Among its related pathways are RET signaling and Innate Immune System. An important paralog of this gene is HAVCR1.

UniProtKB/Swiss-Prot Summary for HAVCR2 Gene

  • Cell surface receptor implicated in modulating innate and adaptive immune responses. Generally accepted to have an inhibiting function. Reports on stimulating functions suggest that the activity may be influenced by the cellular context and/or the respective ligand (PubMed:24825777). Regulates macrophage activation (PubMed:11823861). Inhibits T-helper type 1 lymphocyte (Th1)-mediated auto- and alloimmune responses and promotes immunological tolerance (PubMed:14556005). In CD8+ cells attenuates TCR-induced signaling, specifically by blocking NF-kappaB and NFAT promoter activities resulting in the loss of IL-2 secretion. The function may implicate its association with LCK proposed to impair phosphorylation of TCR subunits, and/or LGALS9-dependent recruitment of PTPRC to the immunological synapse (PubMed:24337741, PubMed:26492563). In contrast, shown to activate TCR-induced signaling in T-cells probably implicating ZAP70, LCP2, LCK and FYN (By similarity). Expressed on Treg cells can inhibit Th17 cell responses (PubMed:24838857). Receptor for LGALS9 (PubMed:16286920, PubMed:24337741). Binding to LGALS9 is believed to result in suppression of T-cell responses; the resulting apoptosis of antigen-specific cells may implicate HAVCR2 phosphorylation and disruption of its association with BAG6. Binding to LGALS9 is proposed to be involved in innate immune response to intracellular pathogens. Expressed on Th1 cells interacts with LGALS9 expressed on Mycobacterium tuberculosis-infected macrophages to stimulate antibactericidal activity including IL-1 beta secretion and to restrict intracellular bacterial growth (By similarity). However, the function as receptor for LGALS9 has been challenged (PubMed:23555261). Also reported to enhance CD8+ T-cell responses to an acute infection such as by Listeria monocytogenes (By similarity). Receptor for phosphatidylserine (PtSer); PtSer-binding is calcium-dependent. May recognize PtSer on apoptotic cells leading to their phagocytosis. Mediates the engulfment of apoptotic cells by dendritic cells. Expressed on T-cells, promotes conjugation but not engulfment of apoptotic cells. Expressed on dendritic cells (DCs) positively regulates innate immune response and in synergy with Toll-like receptors promotes secretion of TNF-alpha. In tumor-imfiltrating DCs suppresses nucleic acid-mediated innate immune repsonse by interaction with HMGB1 and interfering with nucleic acid-sensing and trafficking of nucleid acids to endosomes (By similarity). Expressed on natural killer (NK) cells acts as a coreceptor to enhance IFN-gamma production in response to LGALS9 (PubMed:22323453). In contrast, shown to suppress NK cell-mediated cytotoxicity (PubMed:22383801). Negatively regulates NK cell function in LPS-induced endotoxic shock (By similarity).

Gene Wiki entry for HAVCR2 Gene

Additional gene information for HAVCR2 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for HAVCR2 Gene

Genomics for HAVCR2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for HAVCR2 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH05J157141 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 +0.1 69 3.2 SP1 CREB1 GATAD2A PRDM10 REST IKZF1 KDM1A POLR2A RCOR2 BACH1 HAVCR2 ITK THG1L HAVCR1 piR-49545 MED7
GH05J157105 Promoter/Enhancer 1.6 EPDnew Ensembl ENCODE dbSUPER 611.3 +34.6 34636 5.1 IKZF2 POLR2A EED DPF2 RELB RUNX3 GATAD2B HDGF IKZF1 NR2F1 HAVCR2 ITK MED7 TIMD4 HAVCR1 ENSG00000254246 RF00017-5043 HSALNG0046103
GH05J157265 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 12.2 -127.3 -127328 10 ZNF629 ZNF512 POLR2A ZNF7 BACH1 JUND FOXA1 LARP7 ZNF143 PRDM1 CYFIP2 lnc-ITK-2 ENSG00000251405 HAVCR2 THG1L ITK MED7 NIPAL4 ADAM19 ENSG00000248544
GH05J157112 Enhancer 0.5 FANTOM5 dbSUPER 52.1 +29.6 29598 0.3 HLF HAVCR2 ITK MED7 HAVCR1 ADAM19 NIPAL4 ENSG00000254246 RF00017-5043 HSALNG0046103
GH05J157099 Enhancer 1.1 FANTOM5 ENCODE dbSUPER 24.2 +42.4 42448 1.4 CEBPA CEBPB SP1 EGR1 JUN FOS KDM1A JUND FOSL1 MAX HAVCR2 HAVCR1 NIPAL4 ADAM19 ENSG00000254246 lnc-ITK-5
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around HAVCR2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for HAVCR2

Top Transcription factor binding sites by QIAGEN in the HAVCR2 gene promoter:
  • AP-2rep
  • C/EBPbeta
  • FOXI1
  • FOXJ2
  • FOXJ2 (long isoform)
  • GATA-2
  • HFH-1
  • HFH-3
  • Roaz
  • XBP-1

Genomic Locations for HAVCR2 Gene

Genomic Locations for HAVCR2 Gene
chr5:157,085,832-157,142,869
(GRCh38/hg38)
Size:
57,038 bases
Orientation:
Minus strand
chr5:156,512,843-156,569,880
(GRCh37/hg19)
Size:
57,038 bases
Orientation:
Minus strand

Genomic View for HAVCR2 Gene

Genes around HAVCR2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HAVCR2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HAVCR2 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HAVCR2 Gene

Proteins for HAVCR2 Gene

Products:

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  • Protein details for HAVCR2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8TDQ0-HAVR2_HUMAN
    Recommended name:
    Hepatitis A virus cellular receptor 2
    Protein Accession:
    Q8TDQ0
    Secondary Accessions:
    • B2RAY2
    • Q8WW60
    • Q96K94

    Protein attributes for HAVCR2 Gene

    Size:
    301 amino acids
    Molecular mass:
    33394 Da
    Quaternary structure:
    • Interacts with HMGB1; impairs HMGB1 binding to B-DNA and likely HMGB1-mediated innate immune response (By similarity). Interacts with BAG6 (By similarity). Interacts (phosphorylated) with PIK3R1 and PIK3R2. Interacts (not dependent on its phosphorylation status) with FYN (By similarity). Interacts (in basal state T-cells) with VAV1; AKT1/2, LCP2, ZAP70, SYK, PIK3R1, FYN, SH3BP2 and SH2D2A. Interacts (in activated T-cells) with LCK and PLCG (PubMed:26492563, PubMed:24337741).

    Three dimensional structures from OCA and Proteopedia for HAVCR2 Gene

    Alternative splice isoforms for HAVCR2 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HAVCR2 Gene

Protein Expression for HAVCR2 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for HAVCR2 Gene

  • O-glycosylated with core 1 or possibly core 8 glycans.
  • Phosphorylated on tyrosine residues; modestly increased after TCR/CD28 stimulation. Can be phosphorylated in the cytoplasmatic domain by FYN (By similarity). Phosphorylation at Tyr-265 is increased by stimulation with ligand LGALS9.
  • Glycosylation at Thr145 and Asn172
  • Modification sites at PhosphoSitePlus
  • Glycosylation from GlyConnect
    • HAVR2_HUMAN (712)

Other Protein References for HAVCR2 Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

  • Abcam antibodies for HAVCR2

Protein Products

  • Abcam proteins for HAVCR2

No data available for DME Specific Peptides for HAVCR2 Gene

Domains & Families for HAVCR2 Gene

Gene Families for HAVCR2 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins
  • Predicted membrane proteins

Protein Domains for HAVCR2 Gene

InterPro:
Blocks:
  • Immunoglobulin subtype
ProtoNet:

Suggested Antigen Peptide Sequences for HAVCR2 Gene

GenScript: Design optimal peptide antigens:
  • TIM-3 (HAVR2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8TDQ0

UniProtKB/Swiss-Prot:

HAVR2_HUMAN :
  • Belongs to the immunoglobulin superfamily. TIM family.
Family:
  • Belongs to the immunoglobulin superfamily. TIM family.
genes like me logo Genes that share domains with HAVCR2: view

Function for HAVCR2 Gene

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Molecular function for HAVCR2 Gene

UniProtKB/Swiss-Prot Function:
Cell surface receptor implicated in modulating innate and adaptive immune responses. Generally accepted to have an inhibiting function. Reports on stimulating functions suggest that the activity may be influenced by the cellular context and/or the respective ligand (PubMed:24825777). Regulates macrophage activation (PubMed:11823861). Inhibits T-helper type 1 lymphocyte (Th1)-mediated auto- and alloimmune responses and promotes immunological tolerance (PubMed:14556005). In CD8+ cells attenuates TCR-induced signaling, specifically by blocking NF-kappaB and NFAT promoter activities resulting in the loss of IL-2 secretion. The function may implicate its association with LCK proposed to impair phosphorylation of TCR subunits, and/or LGALS9-dependent recruitment of PTPRC to the immunological synapse (PubMed:24337741, PubMed:26492563). In contrast, shown to activate TCR-induced signaling in T-cells probably implicating ZAP70, LCP2, LCK and FYN (By similarity). Expressed on Treg cells can inhibit Th17 cell responses (PubMed:24838857). Receptor for LGALS9 (PubMed:16286920, PubMed:24337741). Binding to LGALS9 is believed to result in suppression of T-cell responses; the resulting apoptosis of antigen-specific cells may implicate HAVCR2 phosphorylation and disruption of its association with BAG6. Binding to LGALS9 is proposed to be involved in innate immune response to intracellular pathogens. Expressed on Th1 cells interacts with LGALS9 expressed on Mycobacterium tuberculosis-infected macrophages to stimulate antibactericidal activity including IL-1 beta secretion and to restrict intracellular bacterial growth (By similarity). However, the function as receptor for LGALS9 has been challenged (PubMed:23555261). Also reported to enhance CD8+ T-cell responses to an acute infection such as by Listeria monocytogenes (By similarity). Receptor for phosphatidylserine (PtSer); PtSer-binding is calcium-dependent. May recognize PtSer on apoptotic cells leading to their phagocytosis. Mediates the engulfment of apoptotic cells by dendritic cells. Expressed on T-cells, promotes conjugation but not engulfment of apoptotic cells. Expressed on dendritic cells (DCs) positively regulates innate immune response and in synergy with Toll-like receptors promotes secretion of TNF-alpha. In tumor-imfiltrating DCs suppresses nucleic acid-mediated innate immune repsonse by interaction with HMGB1 and interfering with nucleic acid-sensing and trafficking of nucleid acids to endosomes (By similarity). Expressed on natural killer (NK) cells acts as a coreceptor to enhance IFN-gamma production in response to LGALS9 (PubMed:22323453). In contrast, shown to suppress NK cell-mediated cytotoxicity (PubMed:22383801). Negatively regulates NK cell function in LPS-induced endotoxic shock (By similarity).

Phenotypes From GWAS Catalog for HAVCR2 Gene

Gene Ontology (GO) - Molecular Function for HAVCR2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25363763
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with HAVCR2: view
genes like me logo Genes that share phenotypes with HAVCR2: view

Human Phenotype Ontology for HAVCR2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for HAVCR2 Gene

MGI Knock Outs for HAVCR2:

Animal Model Products

  • Taconic Biosciences Mouse Models for HAVCR2

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HAVCR2

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for HAVCR2 Gene

Localization for HAVCR2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for HAVCR2 Gene

Membrane. Single-pass type I membrane protein. Cell junction. Cell membrane. Note=Localizes to the immunological synapse between CD8+ T-cells and target cells. {ECO:0000269 PubMed:24337741}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HAVCR2 gene
Compartment Confidence
plasma membrane 4
nucleus 4
extracellular 3
cytoskeleton 3
endosome 3
mitochondrion 2
endoplasmic reticulum 2
cytosol 2
lysosome 2
peroxisome 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for HAVCR2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001772 immunological synapse IEA --
GO:0005769 early endosome IEA --
GO:0005886 plasma membrane IEA --
GO:0009986 cell surface IEA,IDA 25363763
GO:0016020 membrane IEA --
genes like me logo Genes that share ontologies with HAVCR2: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for HAVCR2 Gene

Pathways & Interactions for HAVCR2 Gene

genes like me logo Genes that share pathways with HAVCR2: view

Pathways by source for HAVCR2 Gene

1 Cell Signaling Technology pathway for HAVCR2 Gene

Gene Ontology (GO) - Biological Process for HAVCR2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001819 positive regulation of cytokine production IEA --
GO:0002250 adaptive immune response IEA --
GO:0002281 macrophage activation involved in immune response IEA --
GO:0002376 immune system process IEA --
GO:0002519 natural killer cell tolerance induction IMP 25578313
genes like me logo Genes that share ontologies with HAVCR2: view

No data available for SIGNOR curated interactions for HAVCR2 Gene

Drugs & Compounds for HAVCR2 Gene

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  1. Drug
No Compound Related Data Available

Transcripts for HAVCR2 Gene

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  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for HAVCR2 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
6 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for HAVCR2

Alternative Splicing Database (ASD) splice patterns (SP) for HAVCR2 Gene

ExUns: 1 ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7
SP1: - -
SP2: - - -
SP3:
SP4:

Relevant External Links for HAVCR2 Gene

GeneLoc Exon Structure for
HAVCR2

Expression for HAVCR2 Gene

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mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for HAVCR2 Gene

mRNA expression in normal human tissues for HAVCR2 Gene
mRNA expression by BioGPS for HAVCR2 GenemRNA expression by GTEx for HAVCR2 Gene

mRNA differential expression in normal tissues according to GTEx for HAVCR2 Gene

This gene is overexpressed in Whole Blood (x8.4) and Kidney - Cortex (x4.0).

Protein differential expression in normal tissues from HIPED for HAVCR2 Gene

This gene is overexpressed in Urine (59.1) and Pancreas (9.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for HAVCR2 Gene



Protein tissue co-expression partners for HAVCR2 Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for HAVCR2

SOURCE GeneReport for Unigene cluster for HAVCR2 Gene:

Hs.710500

mRNA Expression by UniProt/SwissProt for HAVCR2 Gene:

Q8TDQ0-HAVR2_HUMAN
Tissue specificity: Expressed in T-helper type 1 (Th1) lymphocytes. Expressed on regulatory T (Treg) cells after TCR stimulation. Expressed in dendritic cells and natural killer (NK) cells. Expressed in epithelial tissues. Expression is increased on CD4+ and CD8+ T-cells in chronic hepatitis C virus (HCV) infection. In progressive HIV-1 infection, expression is up-regulated on HIV-1-specific CD8 T-cells.

Evidence on tissue expression from TISSUES for HAVCR2 Gene

  • Blood(4.8)
  • Lung(4.5)
  • Pancreas(4.4)
  • Spleen(3.5)
  • Lymph node(3.4)
  • Kidney(3)
  • Bone marrow(2.8)
  • Intestine(2.7)
  • Nervous system(2.7)
  • Liver(2.7)
  • Heart(2.6)
  • Skin(2.1)
genes like me logo Genes that share expression patterns with HAVCR2: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for HAVCR2 Gene

Orthologs for HAVCR2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for HAVCR2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia HAVCR2 30 31
  • 98.45 (n)
 OneToOne
Dog
(Canis familiaris)
 Mammalia HAVCR2 30 31
  • 81.83 (n)
 OneToOne
Cow
(Bos Taurus)
 Mammalia HAVCR2 30
  • 79.26 (n)
Rat
(Rattus norvegicus)
 Mammalia Havcr2 30
  • 76.43 (n)
Mouse
(Mus musculus)
 Mammalia Havcr2 30 17 31
  • 74.64 (n)
 OneToOne
Oppossum
(Monodelphis domestica)
 Mammalia HAVCR2 31
  • 34 (a)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 33 (a)
 OneToMany
-- 31
  • 25 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves HAVCR1 31
  • 25 (a)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 2 (a)
 ManyToMany
Zebrafish
(Danio rerio)
 Actinopterygii timd4 31
  • 25 (a)
 OneToMany
Species where no ortholog for HAVCR2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Tropical Clawed Frog (Silurana tropicalis)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for HAVCR2 Gene

ENSEMBL:
Gene Tree for HAVCR2 (if available)
TreeFam:
Gene Tree for HAVCR2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for HAVCR2: view image

Paralogs for HAVCR2 Gene

Paralogs for HAVCR2 Gene

(1) SIMAP similar genes for HAVCR2 Gene using alignment to 3 proteins:

  • HAVR2_HUMAN
  • E5RFR4_HUMAN
  • E5RHN3_HUMAN
genes like me logo Genes that share paralogs with HAVCR2: view

Variants for HAVCR2 Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for HAVCR2 Gene

SNP ID Clinical significance and condition Chr 05 pos Variation AA Info Type
752709 Benign: not provided 157,087,304(-) T/C INTRON_VARIANT
782945 Benign: not provided 157,087,178(-) G/A MISSENSE_VARIANT
rs147827860 Risk Factor: Subcutaneous panniculitis-like T-cell lymphoma. T-cell lymphoma, subcutaneous panniculitis-like (SPTCL) [MIM:618398] 157,106,719(-) G/Ap.Thr101Ile MISSENSE_VARIANT
rs184868814 Risk Factor: Subcutaneous panniculitis-like T-cell lymphoma. T-cell lymphoma, subcutaneous panniculitis-like (SPTCL) [MIM:618398] 157,106,776(-) T/Cp.Tyr82Cys MISSENSE_VARIANT
rs35960726 Risk Factor: Subcutaneous panniculitis-like T-cell lymphoma. T-cell lymphoma, subcutaneous panniculitis-like (SPTCL) [MIM:618398] 157,106,730(-) T/Cp.Ile97Met MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for HAVCR2 Gene

Structural Variations from Database of Genomic Variants (DGV) for HAVCR2 Gene

Variant ID Type Subtype PubMed ID
esv3575892 CNV gain 25503493
nsv1109742 CNV deletion 24896259

Variation tolerance for HAVCR2 Gene

Residual Variation Intolerance Score: 85.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.01; 37.09% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for HAVCR2 Gene

Human Gene Mutation Database (HGMD)
HAVCR2
SNPedia medical, phenotypic, and genealogical associations of SNPs for
HAVCR2

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HAVCR2 Gene

Disorders for HAVCR2 Gene

MalaCards: The human disease database

(24) MalaCards diseases for HAVCR2 Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
t-cell lymphoma, subcutaneous panniculitis-like
  • sptcl
panniculitis
hepatitis a
  • viral hepatitis a
hepatitis
  • hepatitis a
t-cell non-hodgkin lymphoma
  • t-cell nhl
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

HAVR2_HUMAN
  • Note=May be involved in T-cell exhaustion associated with chronic viral infections such as with human immunodeficiency virus (HIV) and hepatitic C virus (HCV). {ECO:0000269 PubMed:19001139, ECO:0000269 PubMed:19587053}.
  • T-cell lymphoma, subcutaneous panniculitis-like (SPTCL) [MIM:618398]: An uncommon form of T-cell non-Hodgkin lymphoma, in which cytotoxic CD8+ T-cells infiltrate subcutaneous adipose tissue, and rimming adipocytes in a lace-like pattern. Affected individuals typically present with multiple subcutaneous nodules, systemic B-cell symptoms, and, in a subset of cases, autoimmune disorders, most commonly systemic lupus erythematosus. A subset of patients develop hemophagocytic lymphohistiocytosis. SPTCL transmission pattern is consistent with autosomal recessive inheritance with incomplete penetrance. {ECO:0000269 PubMed:30374066, ECO:0000269 PubMed:30792187, ECO:0000269 Ref.2}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.

Additional Disease Information for HAVCR2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with HAVCR2: view

No data available for Genatlas for HAVCR2 Gene

Publications for HAVCR2 Gene

  1. Th1-specific cell surface protein Tim-3 regulates macrophage activation and severity of an autoimmune disease. (PMID: 11823861) Monney L … Kuchroo VK (Nature 2002) 2 3 4 23
  2. The role of T-cell immunoglobulin- and mucin-domain-containing molecule-3 polymorphisms in idiopathic thrombocytopenic purpura. (PMID: 19332093) Du WT … Yang RC (Human immunology 2009) 3 23 41
  3. Family-based association study of Tim-1 and Tim-3 gene polymorphisms with childhood asthma in Chinese trios. (PMID: 19494522) Wu QW … Hu LH (International archives of allergy and immunology 2009) 3 23 41
  4. Lack of association of TIM3 polymorphisms and allergic phenotypes. (PMID: 19566956) Zhang J … Sandford AJ (BMC medical genetics 2009) 3 23 41
  5. Significant association between TIM1 promoter polymorphisms and protection against cerebral malaria in Thailand. (PMID: 18294362) Nuchnoi P … Patarapotikul J (Annals of human genetics 2008) 3 23 41

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