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Aliases for CD3D Gene

Aliases for CD3D Gene

  • CD3d Molecule 2 3
  • CD3d Molecule, Delta (CD3-TCR Complex) 2 3 5
  • CD3d Antigen, Delta Polypeptide (TiT3 Complex) 2 3
  • T-Cell Receptor T3 Delta Chain 3 4
  • T3D 3 4
  • CD3 Antigen, Delta Subunit 3
  • OKT3, Delta Chain 3
  • CD3d Antigen 4
  • CD3 Delta 3
  • CD3-DELTA 3
  • IMD19 3

External Ids for CD3D Gene

Previous HGNC Symbols for CD3D Gene

  • T3D

Previous GeneCards Identifiers for CD3D Gene

  • GC11M120566
  • GC11M119721
  • GC11M118239
  • GC11M117747
  • GC11M117714
  • GC11M118212
  • GC11M114143

Summaries for CD3D Gene

Entrez Gene Summary for CD3D Gene

  • The protein encoded by this gene is part of the T-cell receptor/CD3 complex (TCR/CD3 complex) and is involved in T-cell development and signal transduction. The encoded membrane protein represents the delta subunit of the CD3 complex, and along with four other CD3 subunits, binds either TCR alpha/beta or TCR gamma/delta to form the TCR/CD3 complex on the surface of T-cells. Defects in this gene are a cause of severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (SCIDBNK). Two transcript variants encoding different isoforms have been found for this gene. Other variants may also exist, but the full-length natures of their transcripts has yet to be defined. [provided by RefSeq, Feb 2009]

GeneCards Summary for CD3D Gene

CD3D (CD3d Molecule) is a Protein Coding gene. Diseases associated with CD3D include Immunodeficiency 19 and T-B+ Severe Combined Immunodeficiency Due To Cd3delta/Cd3epsilon/Cd3zeta. Among its related pathways are CTLA4 Signaling and HTLV-I infection. GO annotations related to this gene include protein heterodimerization activity and transmembrane signaling receptor activity. An important paralog of this gene is CD3G.

UniProtKB/Swiss-Prot for CD3D Gene

  • The CD3 complex mediates signal transduction.

Gene Wiki entry for CD3D Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CD3D Gene

Genomics for CD3D Gene

Regulatory Elements for CD3D Gene

Enhancers for CD3D Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around CD3D on UCSC Golden Path with GeneCards custom track

Promoters for CD3D Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around CD3D on UCSC Golden Path with GeneCards custom track

Genomic Location for CD3D Gene

118,338,954 bp from pter
118,342,744 bp from pter
3,791 bases
Minus strand

Genomic View for CD3D Gene

Genes around CD3D on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CD3D Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CD3D Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CD3D Gene

Proteins for CD3D Gene

  • Protein details for CD3D Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    T-cell surface glycoprotein CD3 delta chain
    Protein Accession:
    Secondary Accessions:
    • A8MVP6

    Protein attributes for CD3D Gene

    171 amino acids
    Molecular mass:
    18930 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.

    Three dimensional structures from OCA and Proteopedia for CD3D Gene

    Alternative splice isoforms for CD3D Gene


neXtProt entry for CD3D Gene

Proteomics data for CD3D Gene at MOPED

Post-translational modifications for CD3D Gene

  • Ubiquitination at Lys 80
  • Glycosylation at Asn 38 and Asn 74
  • Modification sites at PhosphoSitePlus

Other Protein References for CD3D Gene

Antibody Products

  • R&D Systems Antibodies for CD3D (TCR gamma/delta)

No data available for DME Specific Peptides for CD3D Gene

Domains & Families for CD3D Gene

Gene Families for CD3D Gene

Suggested Antigen Peptide Sequences for CD3D Gene

Graphical View of Domain Structure for InterPro Entry



  • Contains 1 ITAM domain.
  • Contains 1 ITAM domain.
genes like me logo Genes that share domains with CD3D: view

Function for CD3D Gene

Molecular function for CD3D Gene

GENATLAS Biochemistry:
cell differentiation antigen CD3D (gp20),20kDa,delta polypeptide (see CD3@)
UniProtKB/Swiss-Prot Function:
The CD3 complex mediates signal transduction.
genes like me logo Genes that share phenotypes with CD3D: view

Human Phenotype Ontology for CD3D Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for CD3D Gene

MGI Knock Outs for CD3D:

Animal Model Products

miRNA for CD3D Gene

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for CD3D Gene

Localization for CD3D Gene

Subcellular locations from UniProtKB/Swiss-Prot for CD3D Gene

Membrane; Single-pass type I membrane protein.

Subcellular locations from

Jensen Localization Image for CD3D Gene COMPARTMENTS Subcellular localization image for CD3D gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
cytosol 1
extracellular 1
golgi apparatus 1

Gene Ontology (GO) - Cellular Components for CD3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm NAS 1831653
GO:0016021 integral component of membrane IEA --
GO:0042105 alpha-beta T cell receptor complex IEA --
genes like me logo Genes that share ontologies with CD3D: view

Pathways & Interactions for CD3D Gene

genes like me logo Genes that share pathways with CD3D: view

Gene Ontology (GO) - Biological Process for CD3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0031295 T cell costimulation TAS --
GO:0045944 positive regulation of transcription from RNA polymerase II promoter IDA 2017177
genes like me logo Genes that share ontologies with CD3D: view

No data available for SIGNOR curated interactions for CD3D Gene

Drugs & Compounds for CD3D Gene

(10) Drugs for CD3D Gene - From: DrugBank, DGIdb, and FDA Approved Drugs

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Muromonab Approved, Investigational Pharma binder, Target 0
Blinatumomab Approved Pharma Target, activator 21
Blincyto Approved December 2014 Pharma 0
Catumaxomab Pharma Antibody Others 0
genes like me logo Genes that share compounds with CD3D: view

Transcripts for CD3D Gene

Unigene Clusters for CD3D Gene

CD3d molecule, delta (CD3-TCR complex):
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for CD3D Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5a · 5b
SP2: -
SP3: -
SP4: - -

Relevant External Links for CD3D Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CD3D Gene

mRNA expression in normal human tissues for CD3D Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CD3D Gene

This gene is overexpressed in Whole Blood (x21.3), Spleen (x8.4), and Small Intestine - Terminal Ileum (x6.6).

Protein differential expression in normal tissues from HIPED for CD3D Gene

This gene is overexpressed in Tlymphocyte (43.3) and CD8 Tcells (7.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for CD3D Gene

SOURCE GeneReport for Unigene cluster for CD3D Gene Hs.504048

genes like me logo Genes that share expression patterns with CD3D: view

Protein tissue co-expression partners for CD3D Gene

- Elite partner

Primer Products

No data available for mRNA Expression by UniProt/SwissProt for CD3D Gene

Orthologs for CD3D Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD3D Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia CD3D 35
  • 77.31 (n)
  • 66.27 (a)
CD3D 36
  • 64 (a)
(Canis familiaris)
Mammalia CD3D 35
  • 80.51 (n)
  • 69.59 (a)
CD3D 36
  • 70 (a)
(Mus musculus)
Mammalia Cd3d 35
  • 75.24 (n)
  • 64.33 (a)
Cd3d 16
Cd3d 36
  • 64 (a)
(Pan troglodytes)
Mammalia CD3D 35
  • 99.03 (n)
  • 97.66 (a)
CD3D 36
  • 98 (a)
(Rattus norvegicus)
Mammalia Cd3d 35
  • 76.22 (n)
  • 69.01 (a)
(Monodelphis domestica)
Mammalia CD3D 36
  • 43 (a)
(Ornithorhynchus anatinus)
Mammalia CD3D 36
  • 38 (a)
(Gallus gallus)
Aves CD3D 35
  • 55.94 (n)
  • 45.89 (a)
CD3D 36
  • 38 (a)
(Anolis carolinensis)
Reptilia -- 36
  • 28 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cd3g 35
  • 53.17 (n)
  • 42.06 (a)
Species with no ortholog for CD3D:
  • 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)
  • 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)
  • zebrafish (Danio rerio)

Evolution for CD3D Gene

Gene Tree for CD3D (if available)
Gene Tree for CD3D (if available)

Paralogs for CD3D Gene

Paralogs for CD3D Gene

(1) SIMAP similar genes for CD3D Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with CD3D: view

Variants for CD3D Gene

Sequence variations from dbSNP and Humsavar for CD3D Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs45510201 - 118,339,461(+) AGACC(C/T)GGTCA reference, missense
rs551134 -- 118,339,464(+) CCTGG(G/T)CATTC reference, missense
rs1183409 -- 118,339,801(+) CATGT(C/G)CAGCA intron-variant, reference, missense
rs1185771 -- 118,339,630(+) CTTTA(G/T)GAGAT intron-variant
rs1186453 -- 118,339,528(+) GCCTA(G/T)CAGAT intron-variant

Variation tolerance for CD3D Gene

Residual Variation Intolerance Score: 45.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.59; 12.70% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for CD3D Gene

Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot and Structural Variations from Database of Genomic Variants (DGV) for CD3D Gene

Disorders for CD3D Gene

MalaCards: The human disease database

(7) MalaCards diseases for CD3D Gene - From: OMIM, ClinVar, GeneTests, Orphanet, DISEASES, Novoseek, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CD3D in MalaCards View complete list of genes associated with diseases


  • Immunodeficiency 19 (IMD19) [MIM:615617]: An autosomal recessive form of severe combined immunodeficiency characterized by onset in early infancy of recurrent bacterial, viral, and fungal infections. Patients usually have chronic diarrhea, recurrent respiratory infections, and failure to thrive. Immunologic work-up shows a T-cell negative, B-cell positive, NK-cell positive phenotype. {ECO:0000269 PubMed:15546002, ECO:0000269 PubMed:21883749}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Severe combined immunodeficiency autosomal recessive T-cell-negative/B-cell-positive/NK-cell-positive (T(-)B(+)NK(+) SCID) [MIM:608971]: A form of severe combined immunodeficiency (SCID), a genetically and clinically heterogeneous group of rare congenital disorders characterized by impairment of both humoral and cell-mediated immunity, leukopenia, and low or absent antibody levels. Patients present in infancy recurrent, persistent infections by opportunistic organisms. The common characteristic of all types of SCID is absence of T-cell-mediated cellular immunity due to a defect in T-cell development. {ECO:0000269 PubMed:14602880}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for CD3D

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 CD3D: view

No data available for Genatlas for CD3D Gene

Publications for CD3D Gene

  1. Severe combined immunodeficiency caused by deficiency in either the delta or the epsilon subunit of CD3. (PMID: 15546002) de Saint Basile G. … Le Deist F. (J. Clin. Invest. 2004) 3 4 23 67
  2. Composition of TCR-CD3 complex in human intestinal intraepithelial lymphocytes: lack of Fc epsilon RI gamma chain. (PMID: 7495730) Balk S.P. … Blumberg R.S. (Int. Immunol. 1995) 3 23
  3. Ontogeny of human natural killer (NK) cells: fetal NK cells mediate cytolytic function and express cytoplasmic CD3 epsilon,delta proteins. (PMID: 1372642) Phillips J.H. … Lanier L.L. (J. Exp. Med. 1992) 3 23
  4. Lentiviral Nef proteins manipulate T cells in a subset-specific manner. (PMID: 25505066) Yu H. … Kirchhoff F. (J. Virol. 2015) 3
  5. Identification of the Docking Site for CD3 on the T Cell Receptor I^ Chain by Solution NMR. (PMID: 26109064) He Y. … Orban J. (J. Biol. Chem. 2015) 3

Products for CD3D Gene

Sources for CD3D Gene