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CD48 CD48 molecule [ Homo sapiens (human) ]

Gene ID: 962, updated on 16-Feb-2020

Summary

Official Symbol
CD48provided by HGNC
Official Full Name
CD48 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1683
See related
Ensembl:ENSG00000117091 MIM:109530
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

Genomic context

See CD48 in Genome Data Viewer
Location:
1q23.3
Exon count:
5
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (160678746..160711851, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (160648536..160681641, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene signaling lymphocytic activation molecule family member 1 Neighboring gene uncharacterized LOC107985220 Neighboring gene SET pseudogene 9 Neighboring gene SLAM family member 7 Neighboring gene uncharacterized LOC105371470

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 Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
NHGRI GWA Catalog

HIV-1 interactions

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
antigen binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
defense response TAS
Traceable Author Statement
more info
PubMed 
leukocyte migration TAS
Traceable Author Statement
more info
 
regulation of adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
anchored component of membrane IEA
Inferred from Electronic Annotation
more info
 
extracellular exosome HDA PubMed 
intrinsic component of plasma membrane TAS
Traceable Author Statement
more info
PubMed 
membrane HDA PubMed 
membrane raft IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

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)

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_001256030.1NP_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
    Related
    ENSP00000484431.1, ENST00000613788.1
    Conserved Domains (3) summary
    cd05741
    Location:38127
    Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins
    smart00410
    Location:32127
    IG_like; Immunoglobulin like
    pfam13895
    Location:148217
    Ig_2; Immunoglobulin domain
  2. NM_001778.4NP_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
    Related
    ENSP00000357025.3, ENST00000368046.8
    Conserved Domains (2) summary
    pfam13895
    Location:133217
    Ig_2; Immunoglobulin domain
    cd05775
    Location:35128
    Ig_CD2_like_N; N-terminal immunoglobulin (Ig)-like domain of T-cell surface antigen CD2 and similar domains

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    160678746..160711851 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017002867.2XP_016858356.1  CD48 antigen isoform X3

  2. XM_011510171.2XP_011508473.1  CD48 antigen isoform X1

    Conserved Domains (3) summary
    cd05741
    Location:695
    Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins
    smart00410
    Location:195
    IG_like; Immunoglobulin like
    pfam13895
    Location:116185
    Ig_2; Immunoglobulin domain
  3. XM_005245625.1XP_005245682.1  CD48 antigen isoform X2

    Conserved Domains (2) summary
    cd05741
    Location:38127
    Ig_CEACAM_D1_like; First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins
    smart00410
    Location:32127
    IG_like; Immunoglobulin like
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