CD3E (CD3 epsilon subunit of T-cell receptor complex)

Gene

• Entrez ID: 916
• Gene name: CD3 epsilon subunit of T-cell receptor complex
• Gene symbol: CD3E
• Synonyms (NCBI Gene): CD3epsilon, IMD18, T3E, TCRE
• Chromosome: 11
• Chromosome location: 11q23.3
• Summary: The protein encoded by this gene is the CD3-epsilon polypeptide, which together with CD3-gamma, -delta and -zeta, and the T-cell receptor alpha/beta and gamma/delta heterodimers, forms the T-cell receptor-CD3 complex. This complex plays an important role

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs121918659	G>A	Pathogenic	Coding sequence variant, stop gained
rs140639753	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs201543770	G>A,T	Likely-pathogenic	Splice donor variant
rs483352928	T>C,G	Pathogenic	Splice donor variant
rs483352929	CC>-	Pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT488524	hsa-miR-4781-5p	PAR-CLIP	23592263
MIRT488525	hsa-miR-4779	PAR-CLIP	23592263
MIRT488523	hsa-miR-3155a	PAR-CLIP	23592263
MIRT488522	hsa-miR-3155b	PAR-CLIP	23592263
MIRT488521	hsa-miR-484	PAR-CLIP	23592263
MIRT488520	hsa-miR-4419a	PAR-CLIP	23592263
MIRT488519	hsa-miR-4510	PAR-CLIP	23592263
MIRT488518	hsa-miR-6127	PAR-CLIP	23592263
MIRT488517	hsa-miR-6129	PAR-CLIP	23592263
MIRT488516	hsa-miR-6130	PAR-CLIP	23592263
MIRT488515	hsa-miR-6133	PAR-CLIP	23592263
MIRT488514	hsa-miR-4772-5p	PAR-CLIP	23592263
MIRT488513	hsa-miR-3135b	PAR-CLIP	23592263
MIRT488512	hsa-miR-1249-5p	PAR-CLIP	23592263
MIRT488510	hsa-miR-6797-5p	PAR-CLIP	23592263
MIRT488511	hsa-miR-3652	PAR-CLIP	23592263
MIRT488509	hsa-miR-4430	PAR-CLIP	23592263
MIRT488508	hsa-miR-6090	PAR-CLIP	23592263
MIRT488507	hsa-miR-4525	PAR-CLIP	23592263
MIRT488505	hsa-miR-5010-5p	PAR-CLIP	23592263
MIRT488524	hsa-miR-4781-5p	PAR-CLIP	23592263
MIRT488525	hsa-miR-4779	PAR-CLIP	23592263
MIRT488523	hsa-miR-3155a	PAR-CLIP	23592263
MIRT488522	hsa-miR-3155b	PAR-CLIP	23592263
MIRT488521	hsa-miR-484	PAR-CLIP	23592263
MIRT488520	hsa-miR-4419a	PAR-CLIP	23592263
MIRT488519	hsa-miR-4510	PAR-CLIP	23592263
MIRT488518	hsa-miR-6127	PAR-CLIP	23592263
MIRT488517	hsa-miR-6129	PAR-CLIP	23592263
MIRT488516	hsa-miR-6130	PAR-CLIP	23592263
MIRT488515	hsa-miR-6133	PAR-CLIP	23592263
MIRT488514	hsa-miR-4772-5p	PAR-CLIP	23592263
MIRT488513	hsa-miR-3135b	PAR-CLIP	23592263
MIRT488512	hsa-miR-1249-5p	PAR-CLIP	23592263
MIRT488510	hsa-miR-6797-5p	PAR-CLIP	23592263
MIRT488511	hsa-miR-3652	PAR-CLIP	23592263
MIRT488509	hsa-miR-4430	PAR-CLIP	23592263
MIRT488508	hsa-miR-6090	PAR-CLIP	23592263
MIRT488507	hsa-miR-4525	PAR-CLIP	23592263
MIRT488505	hsa-miR-5010-5p	PAR-CLIP	23592263
MIRT875237	hsa-miR-3191	CLIP-seq
MIRT875238	hsa-miR-4446-3p	CLIP-seq
MIRT875239	hsa-miR-4721	CLIP-seq
MIRT1959503	hsa-miR-185	CLIP-seq
MIRT1959504	hsa-miR-3150b-3p	CLIP-seq
MIRT1959505	hsa-miR-3199	CLIP-seq
MIRT1959506	hsa-miR-4306	CLIP-seq
MIRT1959507	hsa-miR-4515	CLIP-seq
MIRT1959508	hsa-miR-4644	CLIP-seq
MIRT1959509	hsa-miR-4652-5p	CLIP-seq
MIRT1959510	hsa-miR-4716-3p	CLIP-seq
MIRT1959511	hsa-miR-4784	CLIP-seq
MIRT1959512	hsa-miR-769-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0001772	Component	Immunological synapse	IEA
GO:0001954	Process	Positive regulation of cell-matrix adhesion	IEA
GO:0001954	Process	Positive regulation of cell-matrix adhesion	ISS	12652296
GO:0002250	Process	Adaptive immune response	IEA
GO:0002250	Process	Adaptive immune response	NAS	29789755, 30976362
GO:0002376	Process	Immune system process	IEA
GO:0002669	Process	Positive regulation of T cell anergy	IEA
GO:0002870	Process	T cell anergy	IEA
GO:0004888	Function	Transmembrane signaling receptor activity	IBA
GO:0004888	Function	Transmembrane signaling receptor activity	IC	9485181
GO:0004888	Function	Transmembrane signaling receptor activity	IDA	38614099
GO:0004888	Function	Transmembrane signaling receptor activity	IEA
GO:0005515	Function	Protein binding	IPI	7761456, 9485181, 9698567, 11855827, 17617578, 18424730, 18644376, 18955169, 32296183
GO:0005783	Component	Endoplasmic reticulum	IDA
GO:0005794	Component	Golgi apparatus	IDA
GO:0005886	Component	Plasma membrane	IDA	38614099
GO:0005886	Component	Plasma membrane	IDA	11390434, 31461748
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	ISS
GO:0005886	Component	Plasma membrane	NAS	9485181, 30976362
GO:0005886	Component	Plasma membrane	TAS
GO:0005911	Component	Cell-cell junction	IEA
GO:0007166	Process	Cell surface receptor signaling pathway	IBA
GO:0007166	Process	Cell surface receptor signaling pathway	IC	9485181
GO:0007166	Process	Cell surface receptor signaling pathway	IEA
GO:0007166	Process	Cell surface receptor signaling pathway	IEA
GO:0007166	Process	Cell surface receptor signaling pathway	NAS	12110186
GO:0007169	Process	Cell surface receptor protein tyrosine kinase signaling pathway	TAS	8530500
GO:0007172	Process	Signal complex assembly	TAS	8490660
GO:0007186	Process	G protein-coupled receptor signaling pathway	TAS	8530500
GO:0007224	Process	Smoothened signaling pathway	IEA
GO:0009897	Component	External side of plasma membrane	IBA
GO:0009897	Component	External side of plasma membrane	IDA	11390434, 17213291
GO:0009897	Component	External side of plasma membrane	IEA
GO:0009966	Process	Regulation of signal transduction	IEA
GO:0010628	Process	Positive regulation of gene expression	IEA
GO:0010628	Process	Positive regulation of gene expression	IMP	23817958
GO:0010629	Process	Negative regulation of gene expression	IMP	23817958
GO:0016020	Component	Membrane	IEA
GO:0016358	Process	Dendrite development	IEA
GO:0017124	Function	SH3 domain binding	IPI	12110186
GO:0019722	Process	Calcium-mediated signaling	IEA
GO:0019901	Function	Protein kinase binding	NAS	12110186
GO:0021549	Process	Cerebellum development	IEA
GO:0030159	Function	Signaling receptor complex adaptor activity	NAS	9886373
GO:0031295	Process	T cell costimulation	IEA
GO:0032729	Process	Positive regulation of type II interferon production	IEA
GO:0032743	Process	Positive regulation of interleukin-2 production	IEA
GO:0032753	Process	Positive regulation of interleukin-4 production	IEA
GO:0033634	Process	Positive regulation of cell-cell adhesion mediated by integrin	IEA
GO:0033634	Process	Positive regulation of cell-cell adhesion mediated by integrin	ISS	12652296
GO:0035739	Process	CD4-positive, alpha-beta T cell proliferation	IEA
GO:0042098	Process	T cell proliferation	IEA
GO:0042101	Component	T cell receptor complex	IDA	8176201
GO:0042102	Process	Positive regulation of T cell proliferation	IEA
GO:0042102	Process	Positive regulation of T cell proliferation	IEA
GO:0042102	Process	Positive regulation of T cell proliferation	IMP	12110186
GO:0042105	Component	Alpha-beta T cell receptor complex	IBA
GO:0042105	Component	Alpha-beta T cell receptor complex	IDA	9485181
GO:0042105	Component	Alpha-beta T cell receptor complex	IEA
GO:0042105	Component	Alpha-beta T cell receptor complex	IPI	31461748
GO:0042105	Component	Alpha-beta T cell receptor complex	ISS
GO:0042106	Component	Gamma-delta T cell receptor complex	NAS	16418397
GO:0042110	Process	T cell activation	IEA
GO:0042110	Process	T cell activation	NAS	12110186
GO:0042608	Function	T cell receptor binding	NAS	11186279
GO:0042802	Function	Identical protein binding	IDA	14967045
GO:0042981	Process	Regulation of apoptotic process	NAS	12567487
GO:0043197	Component	Dendritic spine	IEA
GO:0043410	Process	Positive regulation of MAPK cascade	IDA	11368773
GO:0044297	Component	Cell body	IEA
GO:0045059	Process	Positive thymic T cell selection	IBA
GO:0045060	Process	Negative thymic T cell selection	IEA
GO:0045879	Process	Negative regulation of smoothened signaling pathway	IEA
GO:0046629	Process	Gamma-delta T cell activation	NAS	30976362
GO:0046631	Process	Alpha-beta T cell activation	NAS	29789755
GO:0046649	Process	Lymphocyte activation	IEA
GO:0050850	Process	Positive regulation of calcium-mediated signaling	IEA
GO:0050852	Process	T cell receptor signaling pathway	IDA	11368773, 38614099
GO:0050852	Process	T cell receptor signaling pathway	IDA	38614099
GO:0050852	Process	T cell receptor signaling pathway	IEA
GO:0050852	Process	T cell receptor signaling pathway	IEA
GO:0050852	Process	T cell receptor signaling pathway	NAS	29789755, 30976362
GO:0050870	Process	Positive regulation of T cell activation	IEA
GO:0065003	Process	Protein-containing complex assembly	NAS	9886373
GO:0097190	Process	Apoptotic signaling pathway	IEA
GO:2000563	Process	Positive regulation of CD4-positive, alpha-beta T cell proliferation	IEA

Other IDs

• MIM: 186830
• HGNC: 1674
• e!Ensembl: ENSG00000198851

Protein

• UniProt ID: P07766
• Protein name: T-cell surface glycoprotein CD3 epsilon chain (T-cell surface antigen T3/Leu-4 epsilon chain) (CD antigen CD3e)
• Protein 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
• PDB: 1A81, 1SY6, 1XIW, 2ROL, 5QU2, 6JXR, 7FJD, 7FJE, 7FJF, 7PHR, 8ES7, 8ES8, 8ES9, 8F0L, 8JC0, 8JCB, 8TW4, 8TW6, 8VY4, 8WXE, 8WY0, 8WYI, 8YC0, 9BBC, 9C3E, 9CI8, 9CIA, 9CQ4
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF16681	Ig_5	36 → 127		Domain
  PF02189	ITAM	185 → 204	Immunoreceptor tyrosine-based activation motif	Motif

• Sequence:

  MQSGTHWRVLGLCLLSVGVWGQDGNEEMGGITQTPYKVSISGTTVILTCPQYPGSEILWQ
  HNDKNIGGDEDDKNIGSDEDHLSLKEFSELEQSGYYVCYPRGSKPEDANFYLYLRARVCE
  NCMEMDVMSVATIVIVDICITGGLLLLVYYWSKNRKAKAKPVTRGAGAGGRQRGQNKERP
  PPVPNPDYEPIRKGQRDLYSGLNQRRI

• Sequence length: 207

Pathways

KEGG:

Hematopoietic cell lineage
Th1 and Th2 cell differentiation
Th17 cell differentiation
T cell receptor signaling pathway
Chagas disease
Measles
Human T-cell leukemia virus 1 infection
Epstein-Barr virus infection
Human immunodeficiency virus 1 infection
PD-L1 expression and PD-1 checkpoint pathway in cancer
Primary immunodeficiency

Reactome:

Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
Downstream TCR signaling
Phosphorylation of CD3 and TCR zeta chains
Translocation of ZAP-70 to Immunological synapse
Generation of second messenger molecules
PD-1 signaling

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Immunodeficiency 18	Likely pathogenic; Pathogenic	rs908640922, rs1419311230, rs483352928, rs121918659, rs2496834883, rs2496836773, rs1948142385, rs2496837183, rs147435007, rs1213870519, rs2496837031, rs201543770, rs1249197356, rs201840561	RCV001976053 RCV003778929 RCV000087024 RCV000087025 RCV003583244 RCV003583278 RCV003583322 RCV003583363 RCV003583628 RCV003583629 RCV003745739 RCV003743222 RCV000690815 RCV001051527 RCV001051528 RCV001036329
Immunodeficiency 18, severe combined immunodeficiency variant	Pathogenic	rs483352929	RCV000087026
Severe combined immunodeficiency disease	Likely pathogenic; Pathogenic	rs1419311230	RCV003155755

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
CD3E-related disorder	Benign; Likely benign	rs78373007, rs35299792	RCV004757952 RCV003915624
Lung cancer	Benign; Likely benign; Conflicting classifications of pathogenicity	rs78373007, rs140639753	RCV005888701 RCV005898610
Malignant tumor of esophagus	Likely benign	rs139878287	RCV005931677
Thymoma	Likely benign	rs1194389924	RCV005928677
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs78373007	RCV005888702

Associations from Text Mining
Disease Name	Relationship Type	References
Adenocarcinoma	Associate	32509861
Adenocarcinoma of Lung	Inhibit	17668204
Anemia Aplastic	Stimulate	22401598
Bone Neoplasms	Inhibit	33095470
Brain Injuries	Associate	24610929
Breast Neoplasms	Associate	33968066, 34867821
Bronchiolitis Obliterans Syndrome	Associate	27232948
Bruton type agammaglobulinemia	Associate	30564228
Carcinoma Basal Cell	Associate	21980389, 22664550
Carcinoma Hepatocellular	Associate	34218795
Carcinoma Non Small Cell Lung	Inhibit	17668204
Colorectal Neoplasms	Associate	34975867
Diabetes Mellitus Type 1	Associate	1671006
Disorder of Sex Development 46 XY	Associate	11877434
Encephalitis	Stimulate	24330827
Endometrial Neoplasms	Associate	34124265
GATA2 Deficiency	Associate	11971211
Head and Neck Neoplasms	Associate	35090306
HIV Infections	Associate	18036256, 29770136, 35710869
Lung Neoplasms	Inhibit	17668204
Lymphoma	Stimulate	12890821
Lymphoma	Associate	18815285, 21274672
Lymphoma Extranodal NK T Cell	Associate	9858215
Lymphoma T Cell Peripheral	Associate	35905535
Lymphopenia	Associate	34539671
Multiple Myeloma	Associate	10848781
Mycobacterium Infections Nontuberculous	Associate	11722641
Nasopharyngeal Carcinoma	Associate	37274867
Neoplasms	Associate	10098746, 11971211, 12456216, 1353752, 1372642, 18612427, 21980389, 25674293, 31753017, 31817155, 31842801, 34124265, 36291540, 36403209, 37841886, 38017109, 9616229
Neoplasms	Inhibit	34218795
Osteoarthritis	Stimulate	14715568
Ovarian Neoplasms	Associate	34633990, 37841886, 9616229
Papillomavirus Infections	Associate	35090306
Paraparesis Tropical Spastic	Stimulate	26358743
Paroxysmal nonkinesigenic dyskinesia	Associate	21264308
Pleural Effusion	Associate	17668204
Primary Immunodeficiency Diseases	Associate	30564228, 32265901
Pulmonary Disease Chronic Obstructive	Associate	36655999
Rhabdomyosarcoma	Stimulate	33095470
Severe Combined Immunodeficiency	Associate	15546002, 30564228, 32265901, 33040328, 35303369
Squamous Cell Carcinoma of Head and Neck	Stimulate	21264308
Squamous Cell Carcinoma of Head and Neck	Associate	33134377, 34091115
Thyroiditis Autoimmune	Associate	37501789
Tuberculosis Meningeal	Inhibit	35710869
Urinary Bladder Neoplasms	Associate	33204728
Uterine Cervical Neoplasms	Associate	33901225, 35090306
Uveal melanoma	Associate	19369244
X Linked Combined Immunodeficiency Diseases	Associate	15545990, 31921117