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

Gene ID: 84868, updated on 2-Aug-2020

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
109.20200522 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 Functions

What'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 PubChem

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 innate immune response 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
 
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
 

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
    5194..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 109.20200522

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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