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Aliases for CD247 Gene

Aliases for CD247 Gene

  • CD247 Molecule 2 3 5
  • CD3z Antigen, Zeta Polypeptide (TiT3 Complex) 2 3
  • T-Cell Receptor T3 Zeta Chain 3 4
  • CD247 Antigen 2 4
  • CD3Z 3 4
  • TCRZ 3 4
  • T3Z 3 4
  • T-Cell Antigen Receptor Complex, Zeta Subunit Of CD3 3
  • T-Cell Surface Glycoprotein CD3 Zeta Chain 3
  • CD247 Antigen, Zeta Subunit 3
  • TCR Zeta Chain 3
  • CD3zeta Chain 3
  • CD3-ZETA 3
  • IMD25 3
  • CD3H 3
  • CD3Q 3

External Ids for CD247 Gene

Previous HGNC Symbols for CD247 Gene

  • CD3Z

Previous GeneCards Identifiers for CD247 Gene

  • GC01M165666
  • GC01M138645

Summaries for CD247 Gene

Entrez Gene Summary for CD247 Gene

  • 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]

GeneCards Summary for CD247 Gene

CD247 (CD247 Molecule) is a Protein Coding gene. Diseases associated with CD247 include Immunodeficiency 25 and T-B+ Severe Combined Immunodeficiency Due To Cd3delta/Cd3epsilon/Cd3zeta. Among its related pathways are ICos-ICosL Pathway in T-Helper Cell and CTLA4 Signaling. GO annotations related to this gene include protein homodimerization activity and transmembrane signaling receptor activity.

UniProtKB/Swiss-Prot for CD247 Gene

  • Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.

Gene Wiki entry for CD247 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD247 Gene

Genomics for CD247 Gene

Regulatory Elements for CD247 Gene

Enhancers for CD247 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH01G167471 1.9 FANTOM5 Ensembl ENCODE dbSUPER 33.8 +29.7 29685 35.7 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 ZNF2 YY1 ZNF766 ZNF143 CD247 MPZL1 DUTP6 AKR1D1P1 RCSD1 POU2F1 ENSG00000273160
GH01G167445 1.9 FANTOM5 Ensembl ENCODE dbSUPER 30.2 +66.4 66385 13.8 PKNOX1 SIN3A FEZF1 ZNF2 YY1 ZNF766 ZNF263 SP3 JUNB CBX8 CD247 AKR1D1P1 CREG1 GPA33 ENSG00000273160 RCSD1 POU2F1 LOC101928512 ENSG00000272033
GH01G167507 1.8 FANTOM5 Ensembl ENCODE dbSUPER 30.7 +5.3 5334 12.2 HDGF PKNOX1 ATF1 CBX3 PTBP1 ARNT NFRKB NFXL1 ZBTB40 ZNF121 CD247 MPZL1 DUTP6 GPA33 RCSD1 ENSG00000272033 CREG1 POU2F1 ENSG00000273160
GH01G167426 1.6 FANTOM5 Ensembl ENCODE dbSUPER 8.4 +87.8 87782 8.3 HDAC1 HDGF ELF3 PKNOX1 RB1 RAD21 TCF12 ZNF766 CREM REST CD247 LOC101928512 ENSG00000272033
GH01G167464 0.7 FANTOM5 dbSUPER 18.9 +53.5 53464 0.4 REST CD247 CREG1 RCSD1 POU2F1 ENSG00000273160
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CD247 on UCSC Golden Path with GeneCards custom track

Genomic Location for CD247 Gene

167,430,640 bp from pter
167,518,616 bp from pter
87,977 bases
Minus strand

Genomic View for CD247 Gene

Genes around CD247 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD247 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CD247 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CD247 Gene

Proteins for CD247 Gene

  • Protein details for CD247 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    T-cell surface glycoprotein CD3 zeta chain
    Protein Accession:
    Secondary Accessions:
    • B1AK49
    • Q5VX13
    • Q8TAX4

    Protein attributes for CD247 Gene

    164 amino acids
    Molecular mass:
    18696 Da
    Quaternary structure:
    • The TCR/CD3 complex of T-lymphocytes consists of either a TCR alpha/beta or TCR gamma/delta heterodimer coexpressed at the cell surface with the invariant subunits of CD3 labeled gamma, delta, epsilon, zeta, and eta (PubMed:17055436). CD3-zeta forms either homodimers or heterodimers with CD3-eta (PubMed:17055436). Interacts with SLA (PubMed:10449770). Interacts with TRAT1 (PubMed:11390434). Interacts with DOCK2 (PubMed:12176041). Interacts with SLA2. Interacts with SHB (PubMed:9484780). Interacts with ZAP70 (PubMed:26783323, PubMed:7659156). Interacts (tyrosine phosphorylated) with SHC1 (via SH2 domain) (PubMed:7544002). Interacts with PTPRC (PubMed:15684325).
    • (Microbial infection) Interacts with HIV-1; this interaction up-regulates the expression of the Fas ligand (FASLG) at the cell surface (PubMed:10224289). Interacts with HIV-2 Nef protein; this interaction induces down-regulation of cell surface TCR/CD3 complexes (PubMed:9811718, PubMed:16051847).

    Three dimensional structures from OCA and Proteopedia for CD247 Gene

    Alternative splice isoforms for CD247 Gene


neXtProt entry for CD247 Gene

Post-translational modifications for CD247 Gene

  • Phosphorylated on Tyr residues after T-cell receptor triggering.
  • Ubiquitination at Lys88, posLast=9999, Lys104, posLast=118118, posLast=129129, Lys136, and posLast=150150
  • Modification sites at PhosphoSitePlus

Other Protein References for CD247 Gene

No data available for DME Specific Peptides for CD247 Gene

Domains & Families for CD247 Gene

Gene Families for CD247 Gene

Suggested Antigen Peptide Sequences for CD247 Gene

Graphical View of Domain Structure for InterPro Entry



  • The ITAM domains mediate interaction with SHB.
  • Belongs to the CD3Z/FCER1G family.
  • The ITAM domains mediate interaction with SHB.
  • Belongs to the CD3Z/FCER1G family.
genes like me logo Genes that share domains with CD247: view

Function for CD247 Gene

Molecular function for CD247 Gene

UniProtKB/Swiss-Prot Function:
Probable role in assembly and expression of the TCR complex as well as signal transduction upon antigen triggering.

Gene Ontology (GO) - Molecular Function for CD247 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004888 transmembrane signaling receptor activity IEA --
GO:0005515 protein binding IPI 7509083
GO:0042802 identical protein binding IPI 17055436
GO:0042803 protein homodimerization activity NAS 12110186
GO:1990782 protein tyrosine kinase binding IPI 8681956
genes like me logo Genes that share ontologies with CD247: view
genes like me logo Genes that share phenotypes with CD247: view

Human Phenotype Ontology for CD247 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CD247 Gene

MGI Knock Outs for CD247:

Animal Model Products

CRISPR Products

miRNA for CD247 Gene

miRTarBase miRNAs that target CD247

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CD247

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for CD247 Gene

Localization for CD247 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD247 Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CD247 gene
Compartment Confidence
plasma membrane 5
extracellular 2
endoplasmic reticulum 2
cytoskeleton 1
mitochondrion 1
peroxisome 1
cytosol 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CD247 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA 11390434
GO:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0042101 T cell receptor complex IDA 8176201
genes like me logo Genes that share ontologies with CD247: view

Pathways & Interactions for CD247 Gene

genes like me logo Genes that share pathways with CD247: view

SIGNOR curated interactions for CD247 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for CD247 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007166 cell surface receptor signaling pathway IEA --
GO:0016032 viral process IEA --
GO:0031295 T cell costimulation TAS --
GO:0038096 Fc-gamma receptor signaling pathway involved in phagocytosis TAS --
GO:0050690 regulation of defense response to virus by virus TAS --
genes like me logo Genes that share ontologies with CD247: view

Drugs & Compounds for CD247 Gene

(8) Drugs for CD247 Gene - From: DrugBank, DGIdb, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Muromonab Approved, Investigational Pharma binder, Target 0
MT-103 Pharma 0

(4) Additional Compounds for CD247 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CD247: view

Transcripts for CD247 Gene

Unigene Clusters for CD247 Gene

CD247 molecule:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Addgene plasmids for CD247

Alternative Splicing Database (ASD) splice patterns (SP) for CD247 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b · 4c ^ 5a · 5b · 5c · 5d ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9
SP1: - - - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - -
SP4: - - -
SP5: -
SP6: - - - - - -
SP7: - -
SP8: - -
SP9: - - -

Relevant External Links for CD247 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CD247 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CD247 Gene

mRNA differential expression in normal tissues according to GTEx for CD247 Gene

This gene is overexpressed in Whole Blood (x30.8) and Spleen (x5.7).

Protein differential expression in normal tissues from HIPED for CD247 Gene

This gene is overexpressed in NK cells (27.9), Peripheral blood mononuclear cells (22.0), and CD8 Tcells (7.6).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for CD247 Gene

Protein tissue co-expression partners for CD247 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CD247 Gene:


SOURCE GeneReport for Unigene cluster for CD247 Gene:


Evidence on tissue expression from TISSUES for CD247 Gene

  • Liver(4.1)
  • Muscle(4)
  • Pancreas(4)
  • Lymph node(3.2)
  • Spleen(3.2)
  • Blood(2.9)
  • Intestine(2.9)
  • Bone marrow(2.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CD247 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
  • skeleton
Head and neck:
  • brain
  • ear
  • eye
  • head
  • jaw
  • mandible
  • maxilla
  • middle ear
  • mouth
  • skull
  • tooth
  • intestine
  • large intestine
  • liver
  • small intestine
  • spleen
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
  • blood
  • bone marrow
  • lymph node
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with CD247: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for CD247 Gene

Orthologs for CD247 Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD247 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CD247 34 35
  • 99.59 (n)
(Canis familiaris)
Mammalia CD247 34 35
  • 85.96 (n)
(Rattus norvegicus)
Mammalia Cd247 34
  • 83.94 (n)
(Bos Taurus)
Mammalia CD247 34 35
  • 83.33 (n)
(Mus musculus)
Mammalia Cd247 34 16 35
  • 81.71 (n)
(Monodelphis domestica)
Mammalia CD247 35
  • 78 (a)
(Gallus gallus)
Aves CD247 34 35
  • 69.12 (n)
(Anolis carolinensis)
Reptilia CD247 35
  • 52 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cd247 34
  • 56.28 (n)
(Danio rerio)
Actinopterygii cd247l 35
  • 28 (a)
Species where no ortholog for CD247 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CD247 Gene

Gene Tree for CD247 (if available)
Gene Tree for CD247 (if available)

Paralogs for CD247 Gene

(2) SIMAP similar genes for CD247 Gene using alignment to 4 proteins:

genes like me logo Genes that share paralogs with CD247: view

No data available for Paralogs for CD247 Gene

Variants for CD247 Gene

Sequence variations from dbSNP and Humsavar for CD247 Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs193922740 Pathogenic 167,439,354(-) GAACC(A/C/T)GCTCT reference, missense
rs672601318 Pathogenic 167,518,464(-) CAAGA(C/T)GAAGT reference, missense, utr-variant-5-prime
rs74315290 Pathogenic 167,439,355(-) AGAAC(C/T)AGCTC reference, stop-gained
rs201494226 Uncertain significance 167,518,400(+) ACGTC(A/G)GCCCT intron-variant
rs374209381 Uncertain significance 167,440,658(+) GTGGT(A/G)CCCAC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for CD247 Gene

Variant ID Type Subtype PubMed ID
esv1365494 CNV deletion 17803354
esv2665370 CNV deletion 23128226
esv2719206 CNV deletion 23290073
esv3587846 CNV loss 21293372
esv3890749 CNV gain 25118596
esv998064 CNV deletion 20482838
nsv1078878 OTHER inversion 25765185
nsv3432 CNV insertion 18451855
nsv528248 CNV loss 19592680
nsv528380 CNV loss 19592680
nsv528710 CNV gain 19592680
nsv831814 CNV loss 17160897

Variation tolerance for CD247 Gene

Residual Variation Intolerance Score: 46.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.60; 12.96% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CD247 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD247 Gene

Disorders for CD247 Gene

MalaCards: The human disease database

(10) MalaCards diseases for CD247 Gene - From: OMIM, ClinVar, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
immunodeficiency 25
  • immunodeficiency due to defect in cd3-zeta
t-b+ severe combined immunodeficiency due to cd3delta/cd3epsilon/cd3zeta
  • t-b+ scid due to cd3delta/cd3epsilon/cd3zeta
t cell deficiency
  • t-lymphocyte deficiency
skin conditions
  • dermatologic disorders
cd3zeta deficiency
- elite association - COSMIC cancer census association via MalaCards
Search CD247 in MalaCards View complete list of genes associated with diseases


  • Immunodeficiency 25 (IMD25) [MIM:610163]: An immunological deficiency characterized by T-cells impaired immune response to alloantigens, tetanus toxoid and mitogens. {ECO:0000269 PubMed:16672702}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CD247

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with CD247: view

No data available for Genatlas for CD247 Gene

Publications for CD247 Gene

  1. Inherited and somatic CD3zeta mutations in a patient with T-cell deficiency. (PMID: 16672702) Rieux-Laucat F. … Le Deist F. (N. Engl. J. Med. 2006) 3 4 22 64
  2. Molecular cloning and chromosomal localization of the human T-cell receptor zeta chain: distinction from the molecular CD3 complex. (PMID: 2974162) Weissman A.M. … Klausner R.D. (Proc. Natl. Acad. Sci. U.S.A. 1988) 2 3 4 64
  3. A novel human autoimmune syndrome caused by combined hypomorphic and activating mutations in ZAP-70. (PMID: 26783323) Chan A.Y. … Puck J.M. (J. Exp. Med. 2016) 3 4 64
  4. Meta-analysis of genome-wide association studies in celiac disease and rheumatoid arthritis identifies fourteen non-HLA shared loci. (PMID: 21383967) Zhernakova A. … Plenge R.M. (PLoS Genet. 2011) 3 46 64
  5. Genome-wide scan identifies TNIP1, PSORS1C1, and RHOB as novel risk loci for systemic sclerosis. (PMID: 21750679) Allanore Y. … Martinez M. (PLoS Genet. 2011) 3 46 64

Products for CD247 Gene

  • Addgene plasmids for CD247

Sources for CD247 Gene

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