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    HAVCR2 hepatitis A virus cellular receptor 2 [ Homo sapiens (human) ]

    Gene ID: 84868, updated on 17-Jun-2019

    Summary

    Official Symbol
    HAVCR2provided by HGNC
    Official Full Name
    hepatitis A virus cellular receptor 2provided by HGNC
    Primary source
    HGNC:HGNC:18437
    See related
    Ensembl:ENSG00000135077 MIM:606652
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    TIM3; CD366; KIM-3; SPTCL; TIMD3; Tim-3; TIMD-3; HAVcr-2
    Summary
    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]
    Expression
    Broad expression in lymph node (RPKM 12.1), spleen (RPKM 10.5) and 23 other tissues See more
    Orthologs

    Genomic context

    See HAVCR2 in Genome Data Viewer
    Location:
    5q33.3
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (157085832..157109044, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (156512843..156536248, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene T cell immunoglobulin and mucin domain containing 4 Neighboring gene apolipoprotein O pseudogene 1 Neighboring gene hepatitis A virus cellular receptor 1 Neighboring gene mediator complex subunit 7 Neighboring gene family with sequence similarity 71 member B

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Subcutaneous panniculitis-like T-cell lymphoma
    MedGen: C0522624 OMIM: 618398 GeneReviews: Not available
    not available

    NHGRI GWAS Catalog

    Description
    Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
    NHGRI GWA Catalog

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Shedding of sHAVCR2 from in vitro stimulated CD8+ T cells from HIV-infected patients (acute, early and chronic antiretroviral naive) is increased relative to complimentary cells from uninfected, antiretroviral-treated and elite controller patients PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Treatment of PBMCs taken from treatment-naive HIV chronically infected individuals with a HIV-1 Gag peptide pool in the presence of ADAM10 inhibitor upregulates the levels of Tim-3 and IFN-gamma in CD8+ T cells PubMed
    gag The enhancement of Tim-3 and PD-1 expression by common gamma-chain IL-2 can inhibit the function of T cells re-stimulated by HIV-1 Gag and TCR PubMed
    capsid gag TIM-3 inhibits the release of HIV-1 in terms of reduced levels of CA and RT activity in virus particles, and induces the accumulation of cell-associated CA PubMed
    reverse transcriptase gag-pol Knockdown of TIM-3 by shRNA enhances relative HIV-1 RT activity in HIV-1 infected monocyte-derived macrophages PubMed
    gag-pol TIM-3 inhibits the release of HIV-1 in terms of reduced levels of CA and RT activity in virus particles, and induces the accumulation of cell-associated CA PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Cytokine Signaling in Immune system, organism-specific biosystem (from REACTOME)
      Cytokine Signaling in Immune system, organism-specific biosystemCytokines are small proteins that regulate and mediate immunity, inflammation, and hematopoiesis. They are secreted in response to immune stimuli, and usually act briefly, locally, at very low concen...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Interleukin-2 signaling, organism-specific biosystem (from REACTOME)
      Interleukin-2 signaling, organism-specific biosystemInterleukin-2 (IL-2) is a cytokine that is produced by T cells in response to antigen stimulation. Originally, IL-2 was discovered because of its potent growth factor activity on activated T cells in...
    • Signaling by Interleukins, organism-specific biosystem (from REACTOME)
      Signaling by Interleukins, organism-specific biosystemInterleukins are low molecular weight proteins that bind to cell surface receptors and act in an autocrine and/or paracrine fashion. They were first identified as factors produced by leukocytes but a...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Potential readthrough

    Included gene: MED7

    Homology

    Clone Names

    • FLJ14428

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    adaptive immune response IEA
    Inferred from Electronic Annotation
    more info
     
    cellular response to lipopolysaccharide IEA
    Inferred from Electronic Annotation
    more info
     
    defense response to Gram-positive bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    innate immune response IEA
    Inferred from Electronic Annotation
    more info
     
    macrophage activation involved in immune response IEA
    Inferred from Electronic Annotation
    more info
     
    maternal process involved in female pregnancy IDA
    Inferred from Direct Assay
    more info
    PubMed 
    natural killer cell tolerance induction IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of NF-kappaB transcription factor activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of T cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of T-helper 1 type immune response IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of defense response to bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of gene expression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of granulocyte colony-stimulating factor production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of immunological synapse formation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of interferon-alpha production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of interferon-gamma production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of interleukin-2 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of interleukin-3 production IDA
    Inferred from Direct Assay
    more info
    PubMed 
    negative regulation of interleukin-6 production IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of myeloid dendritic cell activation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of natural killer cell activation IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target IEA
    Inferred from Electronic Annotation
    more info
     
    negative regulation of tumor necrosis factor production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of ERK1 and ERK2 cascade IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of NIK/NF-kappaB signaling IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of T cell proliferation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of chemokine production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of defense response to bacterium IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interferon-gamma production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-1 production IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of interleukin-4 production IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of macrophage activation IEA
    Inferred from Electronic Annotation
    more info
     
    positive regulation of tumor necrosis factor secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of tolerance induction dependent upon immune response IEA
    Inferred from Electronic Annotation
    more info
     
    regulation of transcription by RNA polymerase II IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    toll-like receptor 3 signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    toll-like receptor 7 signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    toll-like receptor 9 signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    cell junction IEA
    Inferred from Electronic Annotation
    more info
     
    cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    early endosome IEA
    Inferred from Electronic Annotation
    more info
     
    immunological synapse IEA
    Inferred from Electronic Annotation
    more info
     
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    mediator complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 

    General protein information

    Preferred Names
    hepatitis A virus cellular receptor 2
    Names
    T cell immunoglobulin mucin 3
    T-cell immunoglobulin and mucin domain-containing protein 3
    T-cell immunoglobulin mucin family member 3
    T-cell immunoglobulin mucin receptor 3
    T-cell membrane protein 3
    kidney injury molecule-3

    NCBI Reference Sequences (RefSeq)

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_030444.1 RefSeqGene

      Range
      5001..28406
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_032782.5NP_116171.3  hepatitis A virus cellular receptor 2 precursor

      See identical proteins and their annotated locations for NP_116171.3

      Status: REVIEWED

      Source sequence(s)
      AC011377, AF251707, AF450243, BP291914
      Consensus CDS
      CCDS4333.1
      UniProtKB/Swiss-Prot
      Q8TDQ0
      Related
      ENSP00000312002.4, ENST00000307851.9
      Conserved Domains (2) summary
      smart00410
      Location:26126
      IG_like; Immunoglobulin like
      pfam07686
      Location:28122
      V-set; Immunoglobulin V-set domain

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000005.10 Reference GRCh38.p13 Primary Assembly

      Range
      157085832..157109044 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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