Free for academic non-profit institutions. Other users need a Commercial license

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 T cell receptor signaling pathway and Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell. Gene Ontology (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

  • Part of the TCR-CD3 complex present on T-lymphocyte cell surface that plays an essential role in adaptive immune response. When antigen presenting cells (APCs) activate T-cell receptor (TCR), TCR-mediated signals are transmitted across the cell membrane by the CD3 chains CD3D, CD3E, CD3G and CD3Z. All CD3 chains contain immunoreceptor tyrosine-based activation motifs (ITAMs) in their cytoplasmic domain. Upon TCR engagement, these motifs become phosphorylated by Src family protein tyrosine kinases LCK and FYN, resulting in the activation of downstream signaling pathways (PubMed:2470098). In addition of this role of signal transduction in T-cell activation, CD3D plays an essential role in thymocyte differentiation. Indeed, participates in correct intracellular TCR-CD3 complex assembly and surface expression. In absence of a functional TCR-CD3 complex, thymocytes are unable to differentiate properly. Interacts with CD4 and CD8 and thus serves to establish a functional link between the TCR and coreceptors CD4 and CD8, which is needed for activation and positive selection of CD4 or CD8 T-cells(PubMed:12215456).

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

GeneHancer (GH) Regulatory Elements for CD3D Gene

Promoters and enhancers for CD3D Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH11J118336 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.9 891 9.9 HDGF PKNOX1 ATF1 ARNT TCF12 ATF7 NCOA1 ZNF592 MEF2D NFIL3 CD3D CD3G LOC105369519 UBE4A MPZL3 CD3E TREHP1 IFT46 ENSG00000254992
GH11J118309 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 17 +27.6 27643 11 HDGF PKNOX1 FOXA2 ARNT FEZF1 IRF4 ZNF766 CBX5 ZNF143 SP5 UBE4A ARCN1 ENSG00000254909 RPL23AP64 ENSG00000254428 BCL9L CD3G CD3D MPZL3 KMT2A
GH11J118210 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE dbSUPER 12 +128.4 128360 8 HDGF FOXA2 MLX ARID4B DMAP1 IRF4 YY1 ZNF143 REST KAT8 JAML MPZL3 CD3G CD3D CD3E MPZL2 GC11M118201 HSPE1P18
GH11J118145 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 11.4 +197.0 196960 0.8 PKNOX1 ATF1 ARID4B SIN3A DMAP1 GLIS2 ZNF207 ZNF143 KLF7 ATF7 SCN4B SCN2B CD3G CD3D CD3E TMPRSS4 TMPRSS13 PIR33394
GH11J118273 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 11.9 +67.0 67015 5.3 PKNOX1 NEUROD1 BATF BRCA1 RFX5 RCOR1 FOS IKZF2 SMARCC1 CEBPB CD3E MPZL3 SCN4B CD3D CD3G UBE4A ENSG00000271751 JAML MPZL2 FXYD6
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around CD3D on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CD3D gene promoter:
  • TBP
  • TFIID
  • POU3F2
  • GATA-1
  • NF-1
  • NF-1/L
  • RP58
  • En-1

Genomic Locations for CD3D Gene

Genomic Locations for CD3D Gene
chr11:118,338,954-118,342,744
(GRCh38/hg38)
Size:
3,791 bases
Orientation:
Minus strand
chr11:118,209,669-118,213,459
(GRCh37/hg19)
Size:
3,791 bases
Orientation:
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:
    P04234-CD3D_HUMAN
    Recommended name:
    T-cell surface glycoprotein CD3 delta chain
    Protein Accession:
    P04234
    Secondary Accessions:
    • A8MVP6

    Protein attributes for CD3D Gene

    Size:
    171 amino acids
    Molecular mass:
    18930 Da
    Quaternary structure:
    • The TCR-CD3 complex is composed of a CD3D/CD3E and a CD3G/CD3E heterodimers that preferentially associate with TCRalpha and TCRbeta, respectively, to form TCRalpha/CD3E/CD3G and TCRbeta/CD3G/CD3E trimers. In turn, the hexamer interacts with CD3Z homodimer to form the TCR-CD3 complex. Alternatively, TCRalpha and TCRbeta can be replaced by TCRgamma and TCRdelta. Interacts with coreceptors CD4 and CD8 (PubMed:1396954, PubMed:12215456).

    Three dimensional structures from OCA and Proteopedia for CD3D Gene

    Alternative splice isoforms for CD3D Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for CD3D Gene

Post-translational modifications for CD3D Gene

  • Phosphorylated on Tyr residues after T-cell receptor triggering by LCK in association with CD4/CD8.
  • Glycosylation at Asn74 and Asn38
  • Ubiquitination at Lys80
  • 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

HGNC:
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

UniProtKB/Swiss-Prot Function:
Part of the TCR-CD3 complex present on T-lymphocyte cell surface that plays an essential role in adaptive immune response. When antigen presenting cells (APCs) activate T-cell receptor (TCR), TCR-mediated signals are transmitted across the cell membrane by the CD3 chains CD3D, CD3E, CD3G and CD3Z. All CD3 chains contain immunoreceptor tyrosine-based activation motifs (ITAMs) in their cytoplasmic domain. Upon TCR engagement, these motifs become phosphorylated by Src family protein tyrosine kinases LCK and FYN, resulting in the activation of downstream signaling pathways (PubMed:2470098). In addition of this role of signal transduction in T-cell activation, CD3D plays an essential role in thymocyte differentiation. Indeed, participates in correct intracellular TCR-CD3 complex assembly and surface expression. In absence of a functional TCR-CD3 complex, thymocytes are unable to differentiate properly. Interacts with CD4 and CD8 and thus serves to establish a functional link between the TCR and coreceptors CD4 and CD8, which is needed for activation and positive selection of CD4 or CD8 T-cells(PubMed:12215456).
GENATLAS Biochemistry:
cell differentiation antigen CD3D (gp20),20kDa,delta polypeptide (see CD3@)

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

miRTarBase miRNAs that target CD3D

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

Cell membrane; Single-pass type I membrane protein.

Subcellular locations from

COMPARTMENTS
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:0002250 adaptive immune response IEA --
GO:0002376 immune system process IEA --
GO:0007166 cell surface receptor signaling pathway IC 9485181
GO:0030217 T cell differentiation IDA 2017177
GO:0031295 T cell costimulation TAS --
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, Investigational Pharma Target, activator 42
Catumaxomab Approved, Investigational, Withdrawn Pharma Antibody Others 0
Blincyto Approved December 2014 Pharma 0
Otelixizumab Investigational Pharma antibody 0
genes like me logo Genes that share compounds with CD3D: view

Transcripts for CD3D Gene

mRNA/cDNA 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
SP1:
SP2: -
SP3: -
SP4: - -

Relevant External Links for CD3D Gene

GeneLoc Exon Structure for
CD3D
ECgene alternative splicing isoforms for
CD3D

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, 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:

CD3D

SOURCE GeneReport for Unigene cluster for CD3D Gene:

Hs.504048

mRNA Expression by UniProt/SwissProt for CD3D Gene:

P04234-CD3D_HUMAN
Tissue specificity: CD3D is mostly present on T-lymphocytes with its TCR-CD3 partners. Present also in fetal NK-cells.

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

Orthologs for CD3D Gene

This gene was present in the common ancestor of chordates.

Orthologs for CD3D Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia CD3D 34 33
  • 99.03 (n)
OneToOne
dog
(Canis familiaris)
Mammalia CD3D 34 33
  • 80.51 (n)
OneToOne
cow
(Bos Taurus)
Mammalia CD3D 34 33
  • 77.31 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Cd3d 33
  • 76.22 (n)
mouse
(Mus musculus)
Mammalia Cd3d 16 34 33
  • 75.24 (n)
oppossum
(Monodelphis domestica)
Mammalia CD3D 34
  • 43 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia CD3D 34
  • 38 (a)
OneToOne
chicken
(Gallus gallus)
Aves CD3D 34 33
  • 55.94 (n)
OneToMany
lizard
(Anolis carolinensis)
Reptilia -- 34
  • 28 (a)
OneToMany
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

ENSEMBL:
Gene Tree for CD3D (if available)
TreeFam:
Gene Tree for CD3D (if available)
Aminode:
Evolutionary constrained regions (ECRs) for CD3D: view image

Paralogs for CD3D Gene

Paralogs for CD3D Gene

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

  • CD3D_HUMAN
  • B0YIY4_HUMAN
  • E9PMT5_HUMAN
  • G8H453_HUMAN
  • H0YE18_HUMAN
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 Variation AA Info Type
rs104894199 pathogenic, Immunodeficiency 17 118,344,424(-) A/G upstream_transcript_variant
rs111033580 pathogenic, Immunodeficiency 19 118,340,447(-) G/A/T coding_sequence_variant, stop_gained, synonymous_variant
rs111033581 pathogenic, Immunodeficiency 19 118,339,902(-) G/T coding_sequence_variant, intron_variant, stop_gained
rs113271462 uncertain-significance, Severe Combined Immune Deficiency 118,339,103(-) G/A 3_prime_UTR_variant
rs145293635 uncertain-significance, Immunodeficiency due to defect in CD3-gamma 118,344,407(-) G/A/T upstream_transcript_variant

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)

Additional Variant Information for CD3D Gene

Human Gene Mutation Database (HGMD)
CD3D
SNPedia medical, phenotypic, and genealogical associations of SNPs for
CD3D

SNP Genotyping and Copy Number Assay Products

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

Disorders for CD3D Gene

MalaCards: The human disease database

(8) MalaCards diseases for CD3D Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
immunodeficiency 19
  • imd19
t-b+ severe combined immunodeficiency due to cd3delta/cd3epsilon/cd3zeta
  • t-b+ scid due to cd3delta/cd3epsilon/cd3zeta
severe combined immunodeficiency
  • combined t and b cell inborn immunodeficiency
immunodeficiency 17
  • imd17
immunodeficiency 18
  • imd18
- elite association - COSMIC cancer census association via MalaCards
Search CD3D in MalaCards View complete list of genes associated with diseases

UniProtKB/Swiss-Prot

CD3D_HUMAN
  • 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.

Additional Disease Information for CD3D

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
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 58
  2. Ontogeny of human natural killer (NK) cells: fetal NK cells mediate cytolytic function and express cytoplasmic CD3 epsilon,delta proteins. (PMID: 1372642) Phillips JH … Lanier LL (The Journal of experimental medicine 1992) 3 4 22 58
  3. 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 44 58
  4. 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 44 58
  5. 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 58

Products for CD3D Gene

Sources for CD3D Gene

Content
Loading form....