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

    Gene ID: 26762, updated on 17-Jun-2019

    Summary

    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
    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. Alternative splicing of this gene results in multiple transcript variants. Related pseudogenes have been identified on chromosomes 4, 12 and 19. [provided by RefSeq, Apr 2015]
    Expression
    Biased expression in kidney (RPKM 1.3), colon (RPKM 1.2) and 6 other tissues See more
    Orthologs

    Genomic context

    See HAVCR1 in Genome Data Viewer
    Location:
    5q33.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 5 NC_000005.10 (157028383..157069633, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (156455989..156486130, complement)

    Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene PPP1R2 family member B Neighboring gene T cell immunoglobulin and mucin domain containing 4 Neighboring gene apolipoprotein O pseudogene 1 Neighboring gene hepatitis A virus cellular receptor 2 Neighboring gene mediator complex subunit 7

    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

    NHGRI GWAS Catalog

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

    HIV-1 interactions

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    virus receptor activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    viral entry into host cell IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    integral component of membrane IEA
    Inferred from Electronic Annotation
    more info
     
    motile cilium IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    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)

    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_017001.1 RefSeqGene

      Range
      4841..34547
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001173393.3NP_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
      Q96D42
      UniProtKB/TrEMBL
      B4DPB1
      Related
      ENSP00000427898.1, ENST00000523175.5
      Conserved Domains (1) summary
      pfam07686
      Location:21120
      V-set; Immunoglobulin V-set domain
    2. NM_001308156.2NP_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/Swiss-Prot
      Q96D42
      UniProtKB/TrEMBL
      B4DPB1, E9PFX0
      Related
      ENSP00000428524.1, ENST00000522693.5
      Conserved Domains (1) summary
      pfam07686
      Location:21120
      V-set; Immunoglobulin V-set domain
    3. NM_012206.3NP_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
      Q96D42
      UniProtKB/TrEMBL
      B4DPB1
      Related
      ENSP00000344844.3, ENST00000339252.7
      Conserved Domains (1) summary
      pfam07686
      Location:21120
      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
      157028383..157069633 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      Conserved Domains (1) summary
      pfam07686
      Location:21120
      V-set; Immunoglobulin V-set domain
    2. XM_024446021.1XP_024301789.1  hepatitis A virus cellular receptor 1 isoform X1

      Conserved Domains (1) summary
      pfam07686
      Location:21120
      V-set; Immunoglobulin V-set domain
    3. XM_024446020.1XP_024301788.1  hepatitis A virus cellular receptor 1 isoform X1

      Conserved Domains (1) summary
      pfam07686
      Location:21120
      V-set; Immunoglobulin V-set domain
    4. XM_017009339.2XP_016864828.1  hepatitis A virus cellular receptor 1 isoform X2

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

      Conserved Domains (1) summary
      pfam07686
      Location:21120
      V-set; Immunoglobulin V-set domain
    6. XM_024446019.1XP_024301787.1  hepatitis A virus cellular receptor 1 isoform X1

      Conserved Domains (1) summary
      pfam07686
      Location:21120
      V-set; Immunoglobulin V-set domain
    7. XM_011534515.2XP_011532817.1  hepatitis A virus cellular receptor 1 isoform X4

    8. XM_024446024.1XP_024301792.1  hepatitis A virus cellular receptor 1 isoform X3

      Conserved Domains (1) summary
      pfam07686
      Location:21120
      V-set; Immunoglobulin V-set domain

    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.
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