CD247 CD247 molecule [Homo sapiens (human)] - Gene

Summary

Official Symbol: CD247provided by HGNC
Official Full Name: CD247 moleculeprovided by HGNC
Primary source: HGNC:HGNC:1677
See related: Ensembl:ENSG00000198821 MIM:186780; AllianceGenome:HGNC:1677
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; CD3ZETA; 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: mouse all
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Genomic context

Location:: 1q24.2

Exon count:: 10

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (167430640..167518529, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (166781991..166869980, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (167399877..167487766, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CD3zeta as a novel predictive biomarker of PD-1 inhibitor resistance in melanoma.
Title: CD3ζ as a novel predictive biomarker of PD-1 inhibitor resistance in melanoma.
CD24 is a surrogate for 'immune-cold' phenotype in aggressive large B-cell lymphoma.
Title: CD24 is a surrogate for 'immune-cold' phenotype in aggressive large B-cell lymphoma.
CD3Z polymorphisms and promoter hypermethylation in dermatomyositis - the role of cytosine-phosphate-guanine-related single nucleotide polymorphisms.
Title: CD3Z polymorphisms and promoter hypermethylation in dermatomyositis - the role of cytosine-phosphate-guanine-related single nucleotide polymorphisms.
Phenotypic and molecular states of IDH1 mutation-induced CD24-positive glioma stem-like cells.
Title: Phenotypic and molecular states of IDH1 mutation-induced CD24-positive glioma stem-like cells.
The CD3zeta adaptor structure determines functional differences between human and mouse CD16 Fc receptor signaling.
Title: The CD3ζ adaptor structure determines functional differences between human and mouse CD16 Fc receptor signaling.
CD247, a Potential T Cell-Derived Disease Severity and Prognostic Biomarker in Patients With Idiopathic Pulmonary Fibrosis.
Title: CD247, a Potential T Cell-Derived Disease Severity and Prognostic Biomarker in Patients With Idiopathic Pulmonary Fibrosis.
A Bispecific DLL3/CD3 IgG-Like T-Cell Engaging Antibody Induces Antitumor Responses in Small Cell Lung Cancer.
Title: A Bispecific DLL3/CD3 IgG-Like T-Cell Engaging Antibody Induces Antitumor Responses in Small Cell Lung Cancer.
TREM-2 promotes Th1 responses by interacting with the CD3zeta-ZAP70 complex following Mycobacterium tuberculosis infection.
Title: TREM-2 promotes Th1 responses by interacting with the CD3ζ-ZAP70 complex following Mycobacterium tuberculosis infection.
Defects at the Posttranscriptional Level Account for the Low TCRzeta Chain Expression Detected in Gastric Cancer Independently of Caspase-3 Activity.
Title: Defects at the Posttranscriptional Level Account for the Low TCRζ Chain Expression Detected in Gastric Cancer Independently of Caspase-3 Activity.
In Vitro Characterization of Human CD24(hi)CD38(hi) Regulatory B Cells Shows CD9 Is Not a Stable Breg Cell Marker.
Title: In Vitro Characterization of Human CD24(hi)CD38(hi) Regulatory B Cells Shows CD9 Is Not a Stable Breg Cell Marker.

Submit: New GeneRIF Correction See all GeneRIFs (118)

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

Associated conditions

Description	Tests
Immunodeficiency 25 MedGen: C1857798 OMIM: 610163 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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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

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

CD3Z_527 (e-PCR)
- UniSTS:277074

D1S61 (e-PCR)
- UniSTS:472930

RH93108 (e-PCR)
- UniSTS:83576

RH17588 (e-PCR)
- UniSTS:43462

STS-M78967 (e-PCR)
- UniSTS:78282

PMC197251P5 (e-PCR)
- UniSTS:271854

CD3Z (e-PCR)
- UniSTS:479734

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein heterodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein homodimerization activity	IDA Inferred from Direct Assay more info	PubMed
enables protein tyrosine kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane signaling receptor activity	IC Inferred by Curator more info	PubMed

Process	Evidence Code	Pubs
involved_in Fc-gamma receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in T cell receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in T cell receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in T cell receptor signaling pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in adaptive immune response	NAS Non-traceable Author Statement more info	PubMed
involved_in alpha-beta T cell activation	NAS Non-traceable Author Statement more info	PubMed
involved_in cell surface receptor signaling pathway	IC Inferred by Curator more info	PubMed
involved_in gamma-delta T cell activation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of protein localization to cell surface	IEA Inferred from Electronic Annotation more info
involved_in protein complex oligomerization	EXP Inferred from Experiment more info	PubMed
involved_in protein complex oligomerization	IPI Inferred from Physical Interaction more info	PubMed
involved_in protein-containing complex assembly	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
part_of Fc-gamma receptor III complex	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi apparatus	IEA Inferred from Electronic Annotation more info
part_of T cell receptor complex	IDA Inferred from Direct Assay more info	PubMed
part_of alpha-beta T cell receptor complex	IBA Inferred from Biological aspect of Ancestor more info
part_of alpha-beta T cell receptor complex	IDA Inferred from Direct Assay more info	PubMed
part_of alpha-beta T cell receptor complex	IPI Inferred from Physical Interaction more info	PubMed
part_of alpha-beta T cell receptor complex	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of gamma-delta T cell receptor complex	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info

General protein information

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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; tissue factor-targeting CAR1 dimer; tissue factor-targeting CAR1 monomer

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.

Genomic

NG_007384.1 RefSeqGene

Range

5000..92970

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_36

mRNA and Protein(s)

NM_000734.4 → NP_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/TrEMBL

A0A8V8TPD5

Related

ENSP00000375969.3, ENST00000392122.4

Conserved Domains (2) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
NM_001378515.1 → NP_001365444.1 T-cell surface glycoprotein CD3 zeta chain isoform 3 precursor

Status: REVIEWED

Source sequence(s)

AL031733, AL359962

Conserved Domains (3) summary

smart00077
Location:100 → 120

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:170 → 189

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:59 → 89

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
NM_001378516.1 → NP_001365445.1 T-cell surface glycoprotein CD3 zeta chain isoform 4 precursor

Status: REVIEWED

Source sequence(s)

AL031733, AL359962

Conserved Domains (3) summary

smart00077
Location:100 → 120

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:169 → 188

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:59 → 89

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
NM_198053.3 → NP_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

B1AK49, P20963, Q5VX13, Q8TAX4

UniProtKB/TrEMBL

A0A8V8TPD5

Related

ENSP00000354782.5, ENST00000362089.10

Conserved Domains (3) summary

smart00077
Location:69 → 89

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:139 → 158

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:28 → 58

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

167430640..167518529 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011510145.2 → XP_011508447.1 T-cell surface glycoprotein CD3 zeta chain isoform X2

UniProtKB/TrEMBL

A0A8V8TQM0

Related

ENSP00000514803.1, ENST00000700107.1

Conserved Domains (3) summary

smart00077
Location:77 → 97

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:146 → 165

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:36 → 66

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain
XM_011510144.3 → XP_011508446.1 T-cell surface glycoprotein CD3 zeta chain isoform X1

UniProtKB/TrEMBL

A0A8V8TPP4

Related

ENSP00000514802.1, ENST00000700106.1

Conserved Domains (3) summary

smart00077
Location:77 → 97

ITAM; Immunoreceptor tyrosine-based activation motif

pfam02189
Location:147 → 166

ITAM; Immunoreceptor tyrosine-based activation motif

pfam11628
Location:36 → 66

TCR_zetazeta; T-cell surface glycoprotein CD3 zeta chain

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

166781991..166869980 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054339599.1 → XP_054195574.1 T-cell surface glycoprotein CD3 zeta chain isoform X2

UniProtKB/TrEMBL

A0A8V8TQM0
XM_054339598.1 → XP_054195573.1 T-cell surface glycoprotein CD3 zeta chain isoform X1

UniProtKB/TrEMBL

A0A8V8TPP4
XM_054339597.1 → XP_054195572.1 T-cell surface glycoprotein CD3 zeta chain isoform X3

UniProtKB/TrEMBL

Q6KAV0