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    CD58 CD58 molecule [ Homo sapiens (human) ]

    Gene ID: 965, updated on 12-May-2019

    Summary

    Official Symbol
    CD58provided by HGNC
    Official Full Name
    CD58 moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:1688
    See related
    Ensembl:ENSG00000116815 MIM:153420
    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
    ag3; LFA3; LFA-3
    Summary
    This gene encodes a member of the immunoglobulin superfamily. The encoded protein is a ligand of the T lymphocyte CD2 protein, and functions in adhesion and activation of T lymphocytes. The protein is localized to the plasma membrane. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2009]
    Expression
    Low expression observed in reference dataset See more
    Orthologs

    Genomic context

    See CD58 in Genome Data Viewer
    Location:
    1p13.1
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    109 current GRCh38.p12 (GCF_000001405.38) 1 NC_000001.11 (116500390..116571093, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (117057156..117113715, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATP1A1 antisense RNA 1 Neighboring gene RNA, U6 small nuclear 817, pseudogene Neighboring gene long intergenic non-protein coding RNA 1762 Neighboring gene HNF1 motif-containing MPRA enhancer 99 Neighboring gene uncharacterized LOC112268235 Neighboring gene uncharacterized LOC105378925 Neighboring gene nucleosome assembly protein 1 like 4 pseudogene 1 Neighboring gene microRNA 548ac Neighboring gene uncharacterized LOC105378924 Neighboring gene immunoglobulin superfamily member 3 Neighboring gene microRNA 320b-1

    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
    Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.
    NHGRI GWA Catalog
    Genome-wide association study identifies new multiple sclerosis susceptibility loci on chromosomes 12 and 20.
    NHGRI GWA Catalog
    Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci.
    NHGRI GWA Catalog
    Meta-analysis of genome scans and replication identify CD6, IRF8 and TNFRSF1A as new multiple sclerosis susceptibility loci.
    NHGRI GWA Catalog
    Modeling the cumulative genetic risk for multiple sclerosis from genome-wide association data.
    NHGRI GWA Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Molecular interactions of CD2 with LFA-3 and CD28 with B7-1 in conjunction with TCR occupancy prevent T cells from programmed apoptosis mediated by binding of CD4 to HIV-1 gp120, resulting in increased levels of IL-2 and IL-4 secretion from the T cells PubMed
    env Antibodies to LFA-3 block the early stages of HIV-1 infection by cell-free virus following HIV-1 gp120 binding to CD4 PubMed
    Nef nef B lymphocytes exposed to supernatants from HIV-1 Nef-expressing macrophages have upregulated expression of receptors CD22, CD54, and CD58 PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Cell adhesion molecules (CAMs), organism-specific biosystem (from KEGG)
      Cell adhesion molecules (CAMs), organism-specific biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell adhesion molecules (CAMs), conserved biosystem (from KEGG)
      Cell adhesion molecules (CAMs), conserved biosystemCell adhesion molecules are (glyco)proteins expressed on the cell surface and play a critical role in a wide array of biologic processes that include hemostasis, the immune response, inflammation, em...
    • Cell surface interactions at the vascular wall, organism-specific biosystem (from REACTOME)
      Cell surface interactions at the vascular wall, organism-specific biosystemLeukocyte extravasation is a rigorously controlled process that guides white cell movement from the vascular lumen to sites of tissue inflammation. The powerful adhesive interactions that are require...
    • Epstein-Barr virus infection, organism-specific biosystem (from KEGG)
      Epstein-Barr virus infection, organism-specific biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
    • Epstein-Barr virus infection, conserved biosystem (from KEGG)
      Epstein-Barr virus infection, conserved biosystemEpstein-Barr virus (EBV) is a ubiquitous human herpesvirus that is associated with oncogenesis. EBV infection to primary human B lymphocytes leads to induction of EBV-specific HLA-restricted cytotoxi...
    • Hemostasis, organism-specific biosystem (from REACTOME)
      Hemostasis, organism-specific biosystemHemostasis is a physiological response that culminates in the arrest of bleeding from an injured vessel. Under normal conditions the vascular endothelium supports vasodilation, inhibits platelet adhe...
    • Immune System, organism-specific biosystem (from REACTOME)
      Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
    • Innate Immune System, organism-specific biosystem (from REACTOME)
      Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
    • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
      Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ23181, FLJ43722

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    signaling receptor binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    signaling receptor binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    cell-cell adhesion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cellular response to interferon-gamma IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cellular response to tumor necrosis factor IDA
    Inferred from Direct Assay
    more info
    PubMed 
    heterotypic cell-cell adhesion IDA
    Inferred from Direct Assay
    more info
    PubMed 
    leukocyte migration TAS
    Traceable Author Statement
    more info
     
    neutrophil degranulation TAS
    Traceable Author Statement
    more info
     
    positive regulation of interleukin-8 secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    cell surface IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cell surface IDA
    Inferred from Direct Assay
    more info
    PubMed 
    extracellular exosome HDA PubMed 
    ficolin-1-rich granule membrane TAS
    Traceable Author Statement
    more info
     
    integral component of plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    membrane HDA PubMed 
    plasma membrane TAS
    Traceable Author Statement
    more info
     
    secretory granule membrane TAS
    Traceable Author Statement
    more info
     

    General protein information

    Preferred Names
    lymphocyte function-associated antigen 3
    Names
    CD58 antigen, (lymphocyte function-associated antigen 3)
    surface glycoprotein LFA-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.

    mRNA and Protein(s)

    1. NM_001144822.1NP_001138294.1  lymphocyte function-associated antigen 3 isoform 2

      See identical proteins and their annotated locations for NP_001138294.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) includes an alternate segment in the 3' coding region compared to variant 1 that causes a frameshift. The resulting protein (isoform 2) has a distinct C-terminus, compared to isoform 1. This variant (2) also contains a unique 3' UTR compared to variant 1.
      Source sequence(s)
      AK291980, AL355794
      Consensus CDS
      CCDS44199.1
      UniProtKB/Swiss-Prot
      P19256
      Related
      ENSP00000409080.2, ENST00000457047.6
      Conserved Domains (1) summary
      cd05741
      Location:39120
      Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins
    2. NM_001779.3NP_001770.1  lymphocyte function-associated antigen 3 isoform 1

      See identical proteins and their annotated locations for NP_001770.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shortest transcript and encodes the longer isoform (1).
      Source sequence(s)
      AL355794, CA312671, Y00636
      Consensus CDS
      CCDS888.1
      UniProtKB/Swiss-Prot
      P19256
      Related
      ENSP00000358501.5, ENST00000369489.10
      Conserved Domains (1) summary
      cd05741
      Location:39120
      Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins

    RNA

    1. NR_026665.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site in an internal exon, compared to variant 1. This variant is represented as non-coding because the use of the supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AL355794, CD365881, X06296

    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.p12 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p12 Primary Assembly

      Range
      116500390..116571093 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002869.2XP_016858358.1  lymphocyte function-associated antigen 3 isoform X1

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