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Aliases for CD3D Gene

Aliases for CD3D Gene

  • CD3d Molecule 2 3 5
  • CD3d Antigen, Delta Polypeptide (TiT3 Complex) 2 3
  • CD3d Molecule, Delta (CD3-TCR Complex) 2 3
  • T-Cell Receptor T3 Delta Chain 3 4
  • T3D 3 4
  • T-Cell Surface Glycoprotein CD3 Delta Chain 3
  • 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 Hematopoietic cell lineage and G-protein signaling N-RAS regulation pathway. 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

Additional gene information for CD3D Gene

No data available for CIViC summary , 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 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
GH11H118309 1.9 FANTOM5 Ensembl ENCODE dbSUPER 17 +27.6 27644 11 HDGF PKNOX1 FOXA2 ATF1 ARNT FEZF1 ZNF766 CBX5 GATA2 ZNF143 CD3G CD3D MPZL3 UBE4A KMT2A CD3E ENSG00000255384 HMBS ARCN1 ENSG00000271751
GH11H118210 1.5 Ensembl ENCODE dbSUPER 12 +128.4 128361 8 HDGF FOXA2 ATF1 MLX ARID4B DMAP1 YY1 ZNF143 ATF7 RUNX3 MPZL3 JAML CD3D CD3G CD3E MPZL2 GC11M118201 HSPE1P18
GH11H118321 1.3 Ensembl ENCODE dbSUPER 13.3 +21.0 21036 1.4 HDAC1 FOXA2 ZBTB40 RAD21 RFX5 YY1 TCF12 RCOR1 ELF1 REST CD3G CD3D ENSG00000255384 KMT2A IFT46 ENSG00000254992 CD3E
GH11H118204 1.1 Ensembl ENCODE dbSUPER 12 +136.5 136475 2.7 FOXK2 ZMYM3 HNF4A ELF1 ATF7 KDM1A SPI1 MPZL3 JAML CD3G CD3D CD3E IFT46 HSPE1P18 SCN2B
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around CD3D on UCSC Golden Path with GeneCards custom track

Genomic Locations for CD3D Gene

Genomic Locations for CD3D Gene
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

Post-translational modifications for CD3D Gene

  • Ubiquitination at Lys80
  • Glycosylation at Asn38 and Asn74
  • Modification sites at PhosphoSitePlus

Other Protein References for CD3D Gene

No data available for DME Specific Peptides for CD3D Gene

Domains & Families for CD3D Gene

Gene Families for CD3D Gene

Human Protein Atlas (HPA):
  • CD markers
  • Disease related genes
  • FDA approved drug targets
  • Predicted intracellular proteins
  • Predicted membrane proteins
  • Predicted secreted proteins

Suggested Antigen Peptide Sequences for CD3D Gene

Graphical View of Domain Structure for InterPro Entry

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

No data available for UniProtKB/Swiss-Prot for CD3D Gene

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.

Phenotypes From GWAS Catalog for CD3D Gene

Gene Ontology (GO) - Molecular Function for CD3D Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003713 transcription coactivator activity IDA 2017177
GO:0004888 transmembrane signaling receptor activity IC 9485181
GO:0042803 protein homodimerization activity IMP 14967045
GO:0046982 protein heterodimerization activity IPI 9485181
genes like me logo Genes that share ontologies with CD3D: view
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

Clone Products

No data available for Enzyme Numbers (IUBMB) , 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

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 CD3D gene
Compartment Confidence
plasma membrane 5
endoplasmic reticulum 2
extracellular 1
nucleus 1
cytosol 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:0005886 plasma membrane TAS --
GO:0016020 membrane IEA --
GO:0016021 integral component of membrane IEA --
GO:0030665 clathrin-coated vesicle membrane TAS --
genes like me logo Genes that share ontologies with CD3D: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for CD3D Gene

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:0007166 cell surface receptor signaling pathway IC 9485181
GO:0030217 T cell differentiation IDA 2017177
GO:0031295 T cell costimulation TAS --
GO:0045059 positive thymic T cell selection ISS --
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 38
Blincyto Approved December 2014 Pharma 0
Otelixizumab Investigational Pharma antibody 0
Visilizumab Investigational Pharma 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:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for CD3D Gene

Protein tissue co-expression partners for CD3D Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CD3D Gene:


SOURCE GeneReport for Unigene cluster for CD3D Gene:


Evidence on tissue expression from TISSUES for CD3D Gene

  • Blood(4.6)
  • Intestine(2.5)
  • Spleen(2.1)
  • Lymph node(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CD3D Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • immune
  • integumentary
  • lymphatic
  • nervous
  • reproductive
  • respiratory
Head and neck:
  • brain
  • ear
  • head
  • middle ear
  • intestine
  • large intestine
  • liver
  • small intestine
  • spleen
  • blood
  • bone marrow
  • lymph node
  • skin
  • white blood cell
genes like me logo Genes that share expression patterns with CD3D: view

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
(Pan troglodytes)
Mammalia CD3D 33 34
  • 99.03 (n)
(Canis familiaris)
Mammalia CD3D 33 34
  • 80.51 (n)
(Bos Taurus)
Mammalia CD3D 33 34
  • 77.31 (n)
(Rattus norvegicus)
Mammalia Cd3d 33
  • 76.22 (n)
(Mus musculus)
Mammalia Cd3d 33 16 34
  • 75.24 (n)
(Monodelphis domestica)
Mammalia CD3D 34
  • 43 (a)
(Ornithorhynchus anatinus)
Mammalia CD3D 34
  • 38 (a)
(Gallus gallus)
Aves CD3D 33 34
  • 55.94 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 28 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia cd3g 33
  • 53.17 (n)
Species where no ortholog for CD3D 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)
  • 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
rs104894199 Pathogenic 118,344,424(+) CTGAC(A/G)TGGAA upstream-variant-2KB, reference, missense
rs111033580 Pathogenic 118,340,447(-) ACCCA(A/C/T)GAGGA reference, synonymous-codon, stop-gained
rs111033581 Pathogenic 118,339,902(-) GTGTG(A/C)CAGAG intron-variant, reference, stop-gained
rs730880296 Pathogenic 118,340,370(-) AGTAC(A/G)TGCTT intron-variant
rs150376137 Likely benign 118,344,361(+) GCTGG(-/GGCT)CTGCT upstream-variant-2KB, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for CD3D Gene

Variant ID Type Subtype PubMed ID
esv3341931 CNV duplication 20981092

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CD3D Gene

Disorders for CD3D Gene

MalaCards: The human disease database

(9) MalaCards diseases for CD3D Gene - From: HGMD, 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:14602880, ECO:0000269 PubMed:15546002, ECO:0000269 PubMed:21883749}. 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 (The Journal of clinical investigation 2004) 3 4 22 60
  2. Evaluation of 6 candidate genes on chromosome 11q23 for coeliac disease susceptibility: a case control study. (PMID: 20478055) Brophy K … McManus R (BMC medical genetics 2010) 3 45 60
  3. A haplotype in the inducible T-cell tyrosine kinase is a risk factor for seasonal allergic rhinitis. (PMID: 19222422) Benson M … Cardell LO (Allergy 2009) 3 45 60
  4. Homooligomerization of the cytoplasmic domain of the T cell receptor zeta chain and of other proteins containing the immunoreceptor tyrosine-based activation motif. (PMID: 14967045) Sigalov A … Stern L (Biochemistry 2004) 3 22 60
  5. PCR isolation and cloning of novel splice variant mRNAs from known drug target genes. (PMID: 15028279) Jin P … Stuve LL (Genomics 2004) 3 4 60

Products for CD3D Gene

Sources for CD3D Gene

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