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

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; AllianceGenome:HGNC:18437
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: mouse all
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Genomic context

Location:: 5q33.3

Exon count:: 7

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (157085832..157109044, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (157604811..157627988, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (156512843..156536055, complement)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues 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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

TIM-3/Galectin-9 and CD160 expression in salivary adenoid cystic carcinoma.
Title: TIM-3/Galectin-9 and CD160 expression in salivary adenoid cystic carcinoma.
Pan-cancer analysis of TIM-3 transcriptomic expression reveals high levels in pancreatic cancer and interpatient heterogeneity.
Title: Pan-cancer analysis of TIM-3 transcriptomic expression reveals high levels in pancreatic cancer and interpatient heterogeneity.
Role of TIM-3 in ovarian cancer: the forsaken cop or a new noble.
Title: Role of TIM-3 in ovarian cancer: the forsaken cop or a new noble.
Inhibitory Checkpoint Receptor TIM-3 as a Regulator of the Functional Activity of Dendritic Cells.
Title: Inhibitory Checkpoint Receptor TIM-3 as a Regulator of the Functional Activity of Dendritic Cells.
Impairment of Gal-9 and Tim-3 crosstalk between Tregs and Th17 cells drives tobacco smoke-induced airway inflammation.
Title: Impairment of Gal-9 and Tim-3 crosstalk between Tregs and Th17 cells drives tobacco smoke-induced airway inflammation.
The expression of TIM-3 and Gal-9 on macrophages and Hofbauer cells in the placenta of preeclampsia patients.
Title: The expression of TIM-3 and Gal-9 on macrophages and Hofbauer cells in the placenta of preeclampsia patients.
T-cell Immunoglobulin and Mucin Domain 3 in Circulating Monocytes as a Novel Biomarker for Coronary Artery Disease.
Title: T-cell Immunoglobulin and Mucin Domain 3 in Circulating Monocytes as a Novel Biomarker for Coronary Artery Disease.
TIM-3 Expression in Endometriosis.
Title: TIM-3 Expression in Endometriosis.
Association of tuberculosis risk with genetic polymorphisms of the immune checkpoint genes PDCD1, CTLA-4, and TIM3.
Title: Association of tuberculosis risk with genetic polymorphisms of the immune checkpoint genes PDCD1, CTLA-4, and TIM3.
A potential defensive role of TIM-3 on T lymphocytes in the inflammatory involvement of diabetic kidney disease.
Title: A potential defensive role of TIM-3 on T lymphocytes in the inflammatory involvement of diabetic kidney disease.

Submit: New GeneRIF Correction See all GeneRIFs (424)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

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

EBI GWAS Catalog

Description
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S1431 (e-PCR)
- UniSTS:149627

RH36905 (e-PCR)
- UniSTS:87932

D11S3316 (e-PCR)
- UniSTS:152558

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in adaptive immune response	IEA Inferred from Electronic Annotation more info
involved_in cellular response to lipopolysaccharide	IEA Inferred from Electronic Annotation more info
involved_in defense response to Gram-positive bacterium	IEA Inferred from Electronic Annotation more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in macrophage activation involved in immune response	IEA Inferred from Electronic Annotation more info
involved_in maternal process involved in female pregnancy	IDA Inferred from Direct Assay more info	PubMed
involved_in natural killer cell tolerance induction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in 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
involved_in negative regulation of T cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of T-helper 1 type immune response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of defense response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of granulocyte colony-stimulating factor production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of immunological synapse formation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of interferon-alpha production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of interleukin-2 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of interleukin-3 production	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of interleukin-6 production	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of myeloid dendritic cell activation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of natural killer cell activation	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of type II interferon production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of ERK1 and ERK2 cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of T cell proliferation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of chemokine production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of defense response to bacterium	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of interleukin-1 production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of interleukin-4 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of macrophage activation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of non-canonical NF-kappaB signal transduction	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of type II interferon production	IEA Inferred from Electronic Annotation more info
involved_in regulation of tolerance induction dependent upon immune response	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in toll-like receptor 3 signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in toll-like receptor 7 signaling pathway	IEA Inferred from Electronic Annotation more info
involved_in toll-like receptor 9 signaling pathway	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in anchoring junction	IEA Inferred from Electronic Annotation more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	IEA Inferred from Electronic Annotation more info
located_in immunological synapse	IEA Inferred from Electronic Annotation more info
part_of mediator complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: hepatitis A virus cellular receptor 2

Names: T cell immunoglobulin mucin 3; T-cell immunoglobulin and mucin domain 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)

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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.