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CD48 CD48 molecule [ Homo sapiens (human) ]

Gene ID: 962, updated on 11-Apr-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_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (160678746..160711822, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (159815851..159848940, complement)
105.20220307 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
  • 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. Patients with coronavirus disease 2019 characterized by dysregulated levels of membrane and soluble cluster of differentiation 48. Pahima H, et al. Ann Allergy Asthma Immunol, 2023 Feb. PMID 36280100, Free PMC Article
  2. Elevated levels of sCD48 are inversely correlated with markers of disease activity in bullous pemphigoid. Treco E, et al. Exp Dermatol, 2023 Jan. PMID 36134505, Free PMC Article
  3. sCD48 is elevated in non-allergic but not in allergic persistent rhinitis. Branicka O, et al. Immunopharmacol Immunotoxicol, 2021 Dec. PMID 34477021
  4. Acute myeloid leukemia immune escape by epigenetic CD48 silencing. Wang Z, et al. Clin Sci (Lond), 2020 Jan 31. PMID 31922199
  5. Recurrent inflammatory disease caused by a heterozygous mutation in CD48. Volkmer B, et al. J Allergy Clin Immunol, 2019 Nov. PMID 31419545

See all (75) 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 
Process Evidence Code Pubs
involved_in defense response TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular exosome HDA PubMed 
located_in membrane HDA PubMed 
located_in membrane raft IDA
Inferred from Direct Assay
more info
 PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 PubMed 

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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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_2023_10

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

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