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    CD48 CD48 molecule [ Homo sapiens (human) ]

    Gene ID: 962, updated on 2-Nov-2024

    Summary

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    Official Symbol
    CD48provided by HGNC
    Official Full Name
    CD48 moleculeprovided by HGNC
    Primary source
    HGNC:HGNC:1683
    See related
    Ensembl:ENSG00000117091 MIM:109530; AllianceGenome:HGNC:1683
    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
    BCM1; BLAST; hCD48; mCD48; BLAST1; SLAMF2; MEM-102
    Summary
    This gene encodes a member of the CD2 subfamily of immunoglobulin-like receptors which includes SLAM (signaling lymphocyte activation molecules) proteins. The encoded protein is found on the surface of lymphocytes and other immune cells, dendritic cells and endothelial cells, and participates in activation and differentiation pathways in these cells. The encoded protein does not have a transmembrane domain, however, but is held at the cell surface by a GPI anchor via a C-terminal domain which maybe cleaved to yield a soluble form of the receptor. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
    Expression
    Biased expression in lymph node (RPKM 70.5), spleen (RPKM 47.2) and 9 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CD48 in Genome Data Viewer
    Location:
    1q23.3
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160678746..160711822, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159815851..159848940, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160648536..160681612, complement)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene signaling lymphocytic activation molecule family member 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1940 Neighboring gene uncharacterized LOC107985220 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:160621837-160622647 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160622648-160623458 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1942 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160635284-160635845 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1943 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:160644012-160644628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1944 Neighboring gene endogenous retrovirus group K member 18 Env polyprotein Neighboring gene SET pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1945 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1946 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1947 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160695816-160696558 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr1:160696559-160697302 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1951 Neighboring gene uncharacterized LOC124904440 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1952 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1463 Neighboring gene SLAM family member 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1953 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1464 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1955 Neighboring gene uncharacterized LOC105371470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1956 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:160751105-160751606 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1958 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:160759219-160759411

    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. CD48 suppresses proliferation and migration as an immune-related prognostic signature in the cervical cancer immune microenvironment. Ma Y, et al. Carcinogenesis, 2024 Feb 12. PMID 37279525
    2. CD48: A co-stimulatory receptor of immunity. Elishmereni M, et al. Int J Biochem Cell Biol, 2011 Jan. PMID 20833258
    3. No association of polymorphisms in human endogenous retrovirus K18 and CD48 with schizophrenia. Nyegaard M, et al. Psychiatr Genet, 2012 Jun. PMID 22495247
    4. Polymorphisms in human endogenous retrovirus K-18 and risk of type 2 diabetes in individuals with schizophrenia. Dickerson F, et al. Schizophr Res, 2008 Sep. PMID 18617371
    5. Engagement of SLAMF2/CD48 prolongs the time frame of effective T cell activation by supporting mature dendritic cell survival. Kis-Toth K, et al. J Immunol, 2014 May 1. PMID 24670806, Free PMC Article

    See all (76) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. CD48 suppresses proliferation and migration as an immune-related prognostic signature in the cervical cancer immune microenvironment.
      Title: CD48 suppresses proliferation and migration as an immune-related prognostic signature in the cervical cancer immune microenvironment.
    2. Programmed Cell Death-1 (PD-1) anchoring to the GPI-linked co-receptor CD48 reveals a novel mechanism to modulate PD-1-dependent inhibition of human T cells.
      Title: Programmed Cell Death-1 (PD-1) anchoring to the GPI-linked co-receptor CD48 reveals a novel mechanism to modulate PD-1-dependent inhibition of human T cells.
    3. Patients with coronavirus disease 2019 characterized by dysregulated levels of membrane and soluble cluster of differentiation 48.
      Title: Patients with coronavirus disease 2019 characterized by dysregulated levels of membrane and soluble cluster of differentiation 48.
    4. Elevated levels of sCD48 are inversely correlated with markers of disease activity in bullous pemphigoid.
      Title: Elevated levels of sCD48 are inversely correlated with markers of disease activity in bullous pemphigoid.
    5. Boosting of tau protein aggregation by CD40 and CD48 gene expression in Alzheimer's disease.
      Title: Boosting of tau protein aggregation by CD40 and CD48 gene expression in Alzheimer's disease.
    6. sCD48 is elevated in non-allergic but not in allergic persistent rhinitis.
      Title: sCD48 is elevated in non-allergic but not in allergic persistent rhinitis.
    7. GDF15 induces immunosuppression via CD48 on regulatory T cells in hepatocellular carcinoma.
      Title: GDF15 induces immunosuppression via CD48 on regulatory T cells in hepatocellular carcinoma.
    8. Human innate lymphoid cell precursors express CD48 that modulates ILC differentiation through 2B4 signaling.
      Title: Human innate lymphoid cell precursors express CD48 that modulates ILC differentiation through 2B4 signaling.
    9. this study demonstrates recurrent inflammatory disease caused by a heterozygous mutation in CD48
      Title: Recurrent inflammatory disease caused by a heterozygous mutation in CD48.
    10. CD48 mRNA expression was significantly lower in patients than in normal healthy individuals.
      Title: Acute myeloid leukemia immune escape by epigenetic CD48 silencing.
    Submit: New GeneRIF Correction See all GeneRIFs (38)

    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
    Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
    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
    Nef nef Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD48 (SLAMF2) PubMed
    Vpu vpu Both HIV-1 Nef and Vpu downregulate the cell surface expression of CD48 (SLAMF2) 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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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables receptor ligand activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in defense response TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in immune response IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in natural killer cell activation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in signal transduction IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in membrane HDA PubMed 
    is_active_in membrane raft IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane raft IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in plasma membrane TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in side of membrane IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    CD48 antigen
    Names
    B-lymphocyte activation marker BLAST-1
    BCM1 surface antigen
    CD48 antigen (B-cell membrane protein)
    SLAM family member 2
    TCT.1
    leukocyte antigen MEM-102
    signaling lymphocytic activation molecule 2

    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.

    mRNA and Protein(s)

    1. NM_001256030.2 → NP_001242959.1  CD48 antigen isoform 2 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 3' UTR and coding region compared to variant 1. The resulting protein (isoform 2) is longer and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AK225636, AL121985
      Consensus CDS
      CCDS72955.1
      UniProtKB/TrEMBL
      A0A087X1S7, Q6IAZ2
      Related
      ENSP00000484431.1, ENST00000613788.1
      Conserved Domains (3) summary
      cd05741
      Location:38 → 127
      Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins
      smart00410
      Location:32 → 127
      IG_like; Immunoglobulin like
      pfam13895
      Location:148 → 217
      Ig_2; Immunoglobulin domain

    2. NM_001778.4 → NP_001769.2  CD48 antigen isoform 1 precursor

      See identical proteins and their annotated locations for NP_001769.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter protein (isoform 1).
      Source sequence(s)
      AL121985, BC016182, BG505217
      Consensus CDS
      CCDS1208.1
      UniProtKB/Swiss-Prot
      P09326, Q5U055, Q8MGR0
      UniProtKB/TrEMBL
      Q6IAZ2
      Related
      ENSP00000357025.3, ENST00000368046.8
      Conserved Domains (2) summary
      pfam13895
      Location:133 → 217
      Ig_2; Immunoglobulin domain
      cd05775
      Location:35 → 128
      Ig_CD2_like_N; N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2 and similar domains

    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_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      160678746..160711822 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002867.3 → XP_016858356.1  CD48 antigen isoform X3

    2. XM_005245625.1 → XP_005245682.1  CD48 antigen isoform X2

      Conserved Domains (2) summary
      cd05741
      Location:38 → 127
      Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins
      smart00410
      Location:32 → 127
      IG_like; Immunoglobulin like

    3. XM_047435011.1 → XP_047290967.1  CD48 antigen isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      159815851..159848940 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054339721.1 → XP_054195696.1  CD48 antigen isoform X3

    2. XM_054339720.1 → XP_054195695.1  CD48 antigen isoform X2

    3. XM_054339719.1 → XP_054195694.1  CD48 antigen isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P09326.2 GenPept UniProtKB/Swiss-Prot:P09326

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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