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CD247 CD247 molecule [ Homo sapiens (human) ]

Gene ID: 919, updated on 1-Aug-2020

Summary

Official Symbol
CD247provided by HGNC
Official Full Name
CD247 moleculeprovided by HGNC
Primary source
HGNC:HGNC:1677
See related
Ensembl:ENSG00000198821 MIM:186780
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
T3Z; CD3H; CD3Q; CD3Z; TCRZ; IMD25; CD3-ZETA
Summary
The protein encoded by this gene is T-cell receptor zeta, which together with T-cell receptor alpha/beta and gamma/delta heterodimers, and with CD3-gamma, -delta and -epsilon, forms the T-cell receptor-CD3 complex. The zeta chain plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. Low expression of the antigen results in impaired immune response. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in lymph node (RPKM 25.8), spleen (RPKM 18.4) and 11 other tissues See more
Orthologs

Genomic context

See CD247 in Genome Data Viewer
Location:
1q24.2
Exon count:
10
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (167430640..167518542, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (167399877..167487847, complement)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene long intergenic non-protein coding RNA 1363 Neighboring gene POU class 2 homeobox 1 Neighboring gene VISTA enhancer hs1331 Neighboring gene uncharacterized LOC101928512 Neighboring gene uncharacterized LOC107985224 Neighboring gene aldo-keto reductase family 1 member D1 pseudogene 1 Neighboring gene GATA motif-containing MPRA enhancer 235 Neighboring gene cellular repressor of E1A stimulated genes 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 Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Immunodeficiency due to defect in cd3-zeta
MedGen: C1857798 OMIM: 610163 GeneReviews: Not available
Compare labs

NHGRI GWAS Catalog

Description
Genome-wide association study meta-analysis identifies seven new rheumatoid arthritis risk loci.
NHGRI GWA Catalog
Genome-wide association study of systemic sclerosis identifies CD247 as a new susceptibility locus.
NHGRI GWA Catalog
Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis.
NHGRI GWA Catalog
Identification of novel genetic markers associated with clinical phenotypes of systemic sclerosis through a genome-wide association strategy.
NHGRI GWA Catalog
Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci.
NHGRI GWA Catalog
Multiple common variants for celiac disease influencing immune gene expression.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Lck phosphorylates CD3zeta and the TCR-CD3 complex is recruited to a virological synapse (VS) when cells interact with gp120+ICAM-1 bilayers, leading to the creation of an F-actin-depleted zone PubMed
Nef nef HIV-1 Nef increases the association of the src family tyrosine kinase, Lck, and TCRzeta with rafts in human T cells, suggesting Nef primes resting T cells for activation by increasing the levels of signaling molecules within rafts PubMed
nef An HIV-1 Nef isoform (R-Nef) efficiently interacts with signaling molecules of the T cell receptor (TCR) in primary T cells, including TCR-zeta, Lck, and Vav; the PxxP motif in Nef is involved in the interactions PubMed
nef HIV-1 Nef co-localizes with CD8-CD3 zeta on the HEK293 cell surface PubMed
nef HIV-1 Nef directly interacts with TCR-zeta; this interaction is mediated through amino acids 73-82 in Nef and is required for HIV-mediated upregulation of Fas ligand expression PubMed
Pr55(Gag) gag Monocyte-derived macrophages selectively capture and engulf HIV-1-infected CD4+ T cells as HIV-1 Gag interacts with CD3 and Caspase 3 markers, leading to efficient macrophage infection PubMed
gag CD3/28-treated resting CD4+ T cells produce more HIV-1 Gag protein than untreated cells PubMed
gag Interferon-gamma can counteract the inhibitory effect of peptides based on the Capsid protein of HIV-1 Gag on antibody response to SRC PubMed
gag Peptides corresponding to amino acids 218-238 of the Capsid protein of HIV-1 Gag inhibited anti-CD3-induced lymphoproliferation but did not directly affect anti-CD2 activation PubMed
gag Synthetic peptides corresponding to amino acids 218-238 of the Capsid protein of HIV-1 Gag have been shown to inhibit in a dose dependent manner the induction of a specific antibody response to the sheep red cell (SRC) antigen through the T3-Ti complex PubMed
Tat tat HIV-1 Tat upregulates CD247 in HEK 293T cells PubMed
tat HIV-1 Tat interacts with CD3 and CD28 to co-stimulate IL-2 and IL-8 expression PubMed
Vpu vpu HIV-1 Vpu interacts with CD3 in living cells PubMed
capsid gag Interferon-gamma can counteract the inhibitory effect of HIV-1 Capsid based peptides on antibody response to SRC PubMed
gag Peptides corresponding to amino acids 218-238 of HIV-1 Capsid inhibited anti-CD3-induced lymphoproliferation but did not directly affect anti-CD2 activation PubMed
gag Synthetic peptides corresponding to amino acids 218-238 of HIV-1 Capsid have been shown to inhibit in a dose dependent manner the induction of a specific antibody response to the sheep red cell (SRC) antigen through the T3-Ti complex PubMed
matrix gag HIV-1 MA co-localizes with CD3 marker protein in monocyte-derived macrophages cocultured with HIV-1-infected primary CD4+ T-cells 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
identical protein binding IDA
Inferred from Direct Assay
more info
PubMed 
identical protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein tyrosine kinase binding IPI
Inferred from Physical Interaction
more info
PubMed 
transmembrane signaling receptor activity IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
Fc-gamma receptor signaling pathway involved in phagocytosis TAS
Traceable Author Statement
more info
 
T cell receptor signaling pathway IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
T cell receptor signaling pathway TAS
Traceable Author Statement
more info
 
adaptive immune response IEA
Inferred from Electronic Annotation
more info
 
interleukin-2 production IEA
Inferred from Electronic Annotation
more info
 
positive regulation of protein localization to cell surface IEA
Inferred from Electronic Annotation
more info
 
regulation of defense response to virus by virus TAS
Traceable Author Statement
more info
 
regulation of immune response TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
T cell receptor complex IDA
Inferred from Direct Assay
more info
PubMed 
alpha-beta T cell receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
integral component of membrane IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
T-cell surface glycoprotein CD3 zeta chain
Names
CD247 antigen, zeta subunit
CD3Z antigen, zeta polypeptide (TiT3 complex)
CD3zeta chain
T-cell antigen receptor complex, zeta subunit of CD3
T-cell receptor T3 zeta chain
TCR zeta chain

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_007384.1 RefSeqGene

    Range
    5000..92970
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_36

mRNA and Protein(s)

  1. NM_000734.4NP_000725.1  T-cell surface glycoprotein CD3 zeta chain isoform 2 precursor

    See identical proteins and their annotated locations for NP_000725.1

    Status: REVIEWED

    Source sequence(s)
    AL031733, AL359962
    Consensus CDS
    CCDS1260.1
    UniProtKB/Swiss-Prot
    P20963
    Related
    ENSP00000375969.3, ENST00000392122.3
    Conserved Domains (3) summary
    smart00077
    Location:6989
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam02189
    Location:138157
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam11628
    Location:2858
    TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
  2. NM_001378515.1NP_001365444.1  T-cell surface glycoprotein CD3 zeta chain isoform 3 precursor

    Status: REVIEWED

    Source sequence(s)
    AL031733, AL359962
  3. NM_001378516.1NP_001365445.1  T-cell surface glycoprotein CD3 zeta chain isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AL031733, AL359962
  4. NM_198053.3NP_932170.1  T-cell surface glycoprotein CD3 zeta chain isoform 1 precursor

    See identical proteins and their annotated locations for NP_932170.1

    Status: REVIEWED

    Source sequence(s)
    AL031733, AL359962
    Consensus CDS
    CCDS1261.1
    UniProtKB/Swiss-Prot
    P20963
    Related
    ENSP00000354782.5, ENST00000362089.9
    Conserved Domains (3) summary
    smart00077
    Location:6989
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam02189
    Location:139158
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam11628
    Location:2858
    TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20200522

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
    167430640..167518542 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011510145.1XP_011508447.1  T-cell surface glycoprotein CD3 zeta chain isoform X4

    Conserved Domains (3) summary
    smart00077
    Location:7797
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam02189
    Location:146165
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam11628
    Location:3666
    TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
  2. XM_011510144.2XP_011508446.1  T-cell surface glycoprotein CD3 zeta chain isoform X3

    Conserved Domains (3) summary
    smart00077
    Location:7797
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam02189
    Location:147166
    ITAM; Immunoreceptor tyrosine-based activation motif
    pfam11628
    Location:3666
    TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
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