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HAVCR1 hepatitis A virus cellular receptor 1 [ Homo sapiens (human) ]

Gene ID: 26762, updated on 3-Apr-2024

Summary

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Official Symbol
HAVCR1provided by HGNC
Official Full Name
hepatitis A virus cellular receptor 1provided by HGNC
Primary source
HGNC:HGNC:17866
See related
Ensembl:ENSG00000113249 MIM:606518; AllianceGenome:HGNC:17866
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
TIM; KIM1; TIM1; CD365; HAVCR; KIM-1; TIM-1; TIMD1; TIMD-1; HAVCR-1
Summary
The protein encoded by this gene is a membrane receptor for both human hepatitis A virus (HHAV) and TIMD4. The encoded protein may be involved in the moderation of asthma and allergic diseases. The reference genome represents an allele that retains a MTTVP amino acid segment that confers protection against atopy in HHAV seropositive individuals. The protein is a receptor for multiple other viruses, including Ebola virus, Marburg virus, Dengue virus, and Zika virus and is a possible entry factor for SARS-CoV-2 and other coronaviruses. [provided by RefSeq, Sep 2021]
Annotation information
Note: This gene has been reviewed for its involvement in coronavirus biology, and is involved in SARS-CoV-2 infection.
Expression
Biased expression in kidney (RPKM 1.3), colon (RPKM 1.2) and 6 other tissues See more
Orthologs
all
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Genomic context

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See HAVCR1 in Genome Data Viewer
Location:
5q33.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (157029413..157069407, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (157548433..157588641, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (156456424..156486127, complement)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PPP1R2 family member B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:156339619-156340818 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:156340819-156341764 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23495 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23496 Neighboring gene T cell immunoglobulin and mucin domain containing 4 Neighboring gene apolipoprotein O pseudogene 1 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:156441149-156441653 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:156441654-156442157 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:156477155-156477714 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr5:156499176-156500375 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23497 Neighboring gene hepatitis A virus cellular receptor 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23498 Neighboring gene mediator complex subunit 7

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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

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Related articles in PubMed

  1. Single Nucleotide Variants of the Human TIM-1 IgV Domain with Reduced Ability to Promote Viral Entry into Cells. Hattori T, et al. Viruses, 2022 Sep 26. PMID 36298679, Free PMC Article
  2. In-silico analysis of interacting pathways through KIM-1 protein interaction in diabetic nephropathy. Abid F, et al. BMC Nephrol, 2022 Jul 18. PMID 35843953, Free PMC Article
  3. TIM-1 promotes proliferation and metastasis, and inhibits apoptosis, in cervical cancer through the PI3K/AKT/p53 pathway. Chen L, et al. BMC Cancer, 2022 Apr 7. PMID 35392845, Free PMC Article
  4. The Phosphatidylserine Receptor TIM-1 Enhances Authentic Chikungunya Virus Cell Entry. Kirui J, et al. Cells, 2021 Jul 20. PMID 34359995, Free PMC Article
  5. T-Cell Expression and Release of Kidney Injury Molecule-1 in Response to Glucose Variations Initiates Kidney Injury in Early Diabetes. Forbes JM, et al. Diabetes, 2021 Aug. PMID 34285121, Free PMC Article

See all (246) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Potential Alternative Receptors for SARS-CoV-2-Induced Kidney Damage: TLR-4, KIM-1/TIM-1, and CD147.
    Title: Potential Alternative Receptors for SARS-CoV-2-Induced Kidney Damage: TLR-4, KIM-1/TIM-1, and CD147.
  2. Urinary neutrophil gelatinase-associated lipocalin (uNGAL) and kidney injury molecule-1 (uKIM-1) as markers of active lupus nephritis.
    Title: Urinary neutrophil gelatinase-associated lipocalin (uNGAL) and kidney injury molecule-1 (uKIM-1) as markers of active lupus nephritis.
  3. KIM-1, IL-18, and NGAL, in the Machine Learning Prediction of Kidney Injury among Children Undergoing Hematopoietic Stem Cell Transplantation-A Pilot Study.
    Title: KIM-1, IL-18, and NGAL, in the Machine Learning Prediction of Kidney Injury among Children Undergoing Hematopoietic Stem Cell Transplantation-A Pilot Study.
  4. Clinical significance of elevated soluble T-cell immunoglobulin and mucin domain 1 and soluble P-selectin in individuals with obstructive sleep apnea-hypopnea syndrome.
    Title: Clinical significance of elevated soluble T-cell immunoglobulin and mucin domain 1 and soluble P-selectin in individuals with obstructive sleep apnea-hypopnea syndrome.
  5. Correlations of cardiac function with vascular endothelial function, renal function and KIM-1 in patients with dilated cardiomyopathy-induced heart failure.
    Title: Correlations of cardiac function with vascular endothelial function, renal function and KIM-1 in patients with dilated cardiomyopathy-induced heart failure.
  6. Single Nucleotide Variants of the Human TIM-1 IgV Domain with Reduced Ability to Promote Viral Entry into Cells.
    Title: Single Nucleotide Variants of the Human TIM-1 IgV Domain with Reduced Ability to Promote Viral Entry into Cells.
  7. miR-142 Targets TIM-1 in Human Endothelial Cells: Potential Implications for Stroke, COVID-19, Zika, Ebola, Dengue, and Other Viral Infections.
    Title: miR-142 Targets TIM-1 in Human Endothelial Cells: Potential Implications for Stroke, COVID-19, Zika, Ebola, Dengue, and Other Viral Infections.
  8. Altered expression of Tim family molecules and an imbalanced ratio of Tim-3 to Tim-1 expression in patients with type 1 diabetes.
    Title: Altered expression of Tim family molecules and an imbalanced ratio of Tim-3 to Tim-1 expression in patients with type 1 diabetes.
  9. In-silico analysis of interacting pathways through KIM-1 protein interaction in diabetic nephropathy.
    Title: In-silico analysis of interacting pathways through KIM-1 protein interaction in diabetic nephropathy.
  10. Altered Tim-1 and IL-10 Expression in Regulatory B Cell Subsets in Type 1 Diabetes.
    Title: Altered Tim-1 and IL-10 Expression in Regulatory B Cell Subsets in Type 1 Diabetes.
Submit: New GeneRIF Correction See all GeneRIFs (219)

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

EBI GWAS Catalog

Description
Biological, clinical and population relevance of 95 loci for blood lipids.
EBI GWAS Catalog
Common variants at 30 loci contribute to polygenic dyslipidemia.
EBI GWAS Catalog
Genomic study in Mexicans identifies a new locus for triglycerides and refines European lipid loci.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

HIV-1 interactions

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Protein interactions

Protein Gene Interaction Pubs
Envelope transmembrane glycoprotein gp41 env Immunoprecipitation using an antibody against TIM-1 can pull down HIV-1 gp41 in cells, indicating that TIM-1 interacts with gp41 in vivo PubMed
Pr55(Gag) gag TIM-1 induces accumulation of HIV-1 Gag-GFP at the plasma membrane of 293 T cells and inhibits release of HIV-1 Gag-GFP virus-like particles PubMed
capsid gag TIM-1 mutants N114A, D115A, and ND114/115AA exhibit a significantly decreased ability to inhibit HIV-1 release in terms of CA levels compared with wild-type TIM-1 in 293T cells PubMed
gag TIM-1 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 TIM-1 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

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables phosphatidylserine binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables virus receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables virus receptor activity IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in phagocytosis, engulfment IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in positive regulation of mast cell activation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in symbiont entry into host cell IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in motile cilium IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
hepatitis A virus cellular receptor 1
Names
T cell immunoglobin domain and mucin domain protein 1
T-cell immunoglobulin mucin family member 1
T-cell immunoglobulin mucin receptor 1
T-cell membrane protein 1
kidney injury molecule 1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

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_017001.2 RefSeqGene

    Range
    15291..44994
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001173393.3 → NP_001166864.1  hepatitis A virus cellular receptor 1 isoform a precursor

    See identical proteins and their annotated locations for NP_001166864.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Both variants 1 and 3 encode isoform a.
    Source sequence(s)
    AC026777, AF043724, AK298259, BC013325
    Consensus CDS
    CCDS43392.1
    UniProtKB/Swiss-Prot
    O43656, Q96D42
    UniProtKB/TrEMBL
    F1CME6
    Related
    ENSP00000427898.1, ENST00000523175.6
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

  2. NM_001308156.2 → NP_001295085.1  hepatitis A virus cellular receptor 1 isoform b precursor

    See identical proteins and their annotated locations for NP_001295085.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, and lacks an alternate exon that results in a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct C-terminus and is longer than isoform a.
    Source sequence(s)
    AC026777, AK298259, BC013325
    Consensus CDS
    CCDS78076.1
    UniProtKB/TrEMBL
    E9PFX0
    Related
    ENSP00000428524.1, ENST00000522693.5
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

  3. NM_012206.3 → NP_036338.2  hepatitis A virus cellular receptor 1 isoform a precursor

    See identical proteins and their annotated locations for NP_036338.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the shorter isoform (a). Both variants 1 and 3 encode isoform a.
    Source sequence(s)
    AK298259, AW604297, BC013325, BG752287
    Consensus CDS
    CCDS43392.1
    UniProtKB/Swiss-Prot
    O43656, Q96D42
    UniProtKB/TrEMBL
    F1CME6
    Related
    ENSP00000344844.3, ENST00000339252.8
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    157029413..157069407 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_024446023.2 → XP_024301791.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    E9PFX0
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

  2. XM_047417097.1 → XP_047273053.1  hepatitis A virus cellular receptor 1 isoform X3

    UniProtKB/Swiss-Prot
    O43656, Q96D42
    Related
    ENSP00000514125.1, ENST00000699093.1

  3. XM_024446021.2 → XP_024301789.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    E9PFX0
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

  4. XM_024446020.2 → XP_024301788.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    E9PFX0
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

  5. XM_024446022.2 → XP_024301790.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    E9PFX0
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

  6. XM_047417096.1 → XP_047273052.1  hepatitis A virus cellular receptor 1 isoform X3

    UniProtKB/Swiss-Prot
    O43656, Q96D42

  7. XM_017009339.3 → XP_016864828.1  hepatitis A virus cellular receptor 1 isoform X2

  8. XM_047417098.1 → XP_047273054.1  hepatitis A virus cellular receptor 1 isoform X4

  9. XM_024446019.2 → XP_024301787.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    E9PFX0
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

  10. XM_024446024.2 → XP_024301792.1  hepatitis A virus cellular receptor 1 isoform X3

    UniProtKB/Swiss-Prot
    O43656, Q96D42
    UniProtKB/TrEMBL
    F1CME6
    Conserved Domains (1) summary
    pfam07686
    Location:21 → 120
    V-set; Immunoglobulin V-set domain

  11. XM_011534515.3 → XP_011532817.1  hepatitis A virus cellular receptor 1 isoform X5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    157548433..157588641 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054352369.1 → XP_054208344.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    B4DPB1

  2. XM_054352372.1 → XP_054208347.1  hepatitis A virus cellular receptor 1 isoform X3

    UniProtKB/TrEMBL
    F1CME7

  3. XM_054352368.1 → XP_054208343.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    B4DPB1

  4. XM_054352367.1 → XP_054208342.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    B4DPB1

  5. XM_054352365.1 → XP_054208340.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    B4DPB1

  6. XM_054352373.1 → XP_054208348.1  hepatitis A virus cellular receptor 1 isoform X3

    UniProtKB/TrEMBL
    F1CME7

  7. XM_054352370.1 → XP_054208345.1  hepatitis A virus cellular receptor 1 isoform X2

  8. XM_054352374.1 → XP_054208349.1  hepatitis A virus cellular receptor 1 isoform X4

  9. XM_054352366.1 → XP_054208341.1  hepatitis A virus cellular receptor 1 isoform X1

    UniProtKB/TrEMBL
    B4DPB1

  10. XM_054352371.1 → XP_054208346.1  hepatitis A virus cellular receptor 1 isoform X3

    UniProtKB/TrEMBL
    F1CME7

  11. XM_054352375.1 → XP_054208350.1  hepatitis A virus cellular receptor 1 isoform X6

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001099414.1: Suppressed sequence

    Description
    NM_001099414.1: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96D42.3 GenPept UniProtKB/Swiss-Prot:Q96D42

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