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

    Gene ID: 26762, updated on 28-Oct-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_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (157029413..157069407, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (157548433..157588641, complement)
    RS_2024_09 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 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. Kidney injury molecule-1 expression in human kidney transplants with interstitial fibrosis and tubular atrophy. Nogare AL, et al. BMC Nephrol, 2015 Feb 13. PMID 25884518, Free PMC Article
    2. The Application of Kidney Injury Molecule-1 to Determine the Duration Between Shockwave Lithotripsy Sessions. Aydin HR, et al. J Endourol, 2016 Jan. PMID 26407192
    3. Distinct Trafficking of Cell Surface and Endosomal TIM-1 to the Immune Synapse. Echbarthi M, et al. Traffic, 2015 Nov. PMID 26332704, Free PMC Article
    4. Kidney Injury Molecule-1 Enhances Endocytosis of Albumin in Renal Proximal Tubular Cells. Zhao X, et al. J Cell Physiol, 2016 Apr. PMID 26332568, Free PMC Article
    5. A functional polymorphism in the TIM-1 gene is associated with asthma in a Chinese Han population. Liu Q, et al. Int Arch Allergy Immunol, 2007. PMID 17570927

    See all (250) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. T-cell immunoglobulin and mucin 1 (TIM-1) mediates infection of Hantaan virus in Jurkat T cells.
      Title: T-cell immunoglobulin and mucin 1 (TIM-1) mediates infection of Hantaan virus in Jurkat T cells.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    Submit: New GeneRIF Correction See all GeneRIFs (220)

    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_2024_08

    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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