PDCD2 (programmed cell death 2)

Gene

• Entrez ID: 5134
• Gene name: Programmed cell death 2
• Gene symbol: PDCD2
• Synonyms (NCBI Gene): RP8, ZMYND7
• Chromosome: 6
• Chromosome location: 6q27
• Summary: This gene encodes a nuclear protein expressed in a variety of tissues. Expression of this gene has been shown to be repressed by B-cell CLL/lymphoma 6 (BCL6), a transcriptional repressor required for lymph node germinal center development, suggesting that

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT054135	hsa-miR-129-1-3p	Luciferase reporter assay, qRT-PCR, Western blot	25111461
MIRT054135	hsa-miR-129-1-3p	Luciferase reporter assay, qRT-PCR, Western blot	25111461
MIRT054135	hsa-miR-129-1-3p	Luciferase reporter assay, qRT-PCR, Western blot	25111461
MIRT054135	hsa-miR-129-1-3p	Luciferase reporter assay, qRT-PCR, Western blot	25111461
MIRT1219276	hsa-miR-1197	CLIP-seq
MIRT1219277	hsa-miR-1305	CLIP-seq
MIRT1219278	hsa-miR-3143	CLIP-seq
MIRT1219279	hsa-miR-3658	CLIP-seq
MIRT1219280	hsa-miR-3922-5p	CLIP-seq
MIRT1219281	hsa-miR-4426	CLIP-seq
MIRT1219282	hsa-miR-4477a	CLIP-seq
MIRT1219283	hsa-miR-4647	CLIP-seq
MIRT1219284	hsa-miR-4662b	CLIP-seq
MIRT1219285	hsa-miR-498	CLIP-seq
MIRT1219286	hsa-miR-543	CLIP-seq
MIRT1219287	hsa-miR-3065-3p	CLIP-seq
MIRT1219288	hsa-miR-4662a-3p	CLIP-seq
MIRT1219289	hsa-miR-890	CLIP-seq
MIRT1219290	hsa-miR-369-3p	CLIP-seq
MIRT1219291	hsa-miR-374c	CLIP-seq
MIRT1219292	hsa-miR-411	CLIP-seq
MIRT1219293	hsa-miR-4727-5p	CLIP-seq
MIRT1219294	hsa-miR-4760-5p	CLIP-seq
MIRT1219295	hsa-miR-4775	CLIP-seq
MIRT1219296	hsa-miR-562	CLIP-seq
MIRT1219297	hsa-miR-590-3p	CLIP-seq
MIRT1219298	hsa-miR-655	CLIP-seq
MIRT1219299	hsa-miR-892a	CLIP-seq
MIRT2063412	hsa-miR-3614-3p	CLIP-seq
MIRT2063413	hsa-miR-4432	CLIP-seq
MIRT2063414	hsa-miR-499-5p	CLIP-seq
MIRT1219299	hsa-miR-892a	CLIP-seq
MIRT2456047	hsa-miR-3163	CLIP-seq
MIRT1219292	hsa-miR-411	CLIP-seq
MIRT2456048	hsa-miR-4275	CLIP-seq
MIRT2456049	hsa-miR-4480	CLIP-seq
MIRT2456050	hsa-miR-4662a-5p	CLIP-seq
MIRT2589543	hsa-miR-3616-5p	CLIP-seq
MIRT2589544	hsa-miR-362-5p	CLIP-seq
MIRT2589545	hsa-miR-3647-5p	CLIP-seq
MIRT2589546	hsa-miR-370	CLIP-seq
MIRT2589547	hsa-miR-3910	CLIP-seq
MIRT2589548	hsa-miR-4267	CLIP-seq
MIRT2589549	hsa-miR-4793-5p	CLIP-seq
MIRT2589550	hsa-miR-500b	CLIP-seq
MIRT2589551	hsa-miR-573	CLIP-seq
MIRT2589552	hsa-miR-640	CLIP-seq
MIRT2687293	hsa-miR-3619-3p	CLIP-seq
MIRT2687294	hsa-miR-4287	CLIP-seq
MIRT2687295	hsa-miR-4469	CLIP-seq
MIRT2687296	hsa-miR-4520b-3p	CLIP-seq
MIRT2687297	hsa-miR-4529-3p	CLIP-seq
MIRT2687298	hsa-miR-4535	CLIP-seq
MIRT2687299	hsa-miR-4685-3p	CLIP-seq
MIRT2687300	hsa-miR-4776-5p	CLIP-seq
MIRT2687301	hsa-miR-642a	CLIP-seq

Transcription factors

Transcription factor	Regulation	Reference
BCL6	Repression	20605493
BCL6	Unknown	11854457;17468402

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0003677	Function	DNA binding	IEA
GO:0005515	Function	Protein binding	IPI	19146857, 28514442, 32296183, 32814053, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IEA
GO:0006915	Process	Apoptotic process	IEA
GO:0006915	Process	Apoptotic process	TAS	7606924
GO:0008270	Function	Zinc ion binding	IEA
GO:0012501	Process	Programmed cell death	IEA
GO:0019899	Function	Enzyme binding	IPI	23382074
GO:0043065	Process	Positive regulation of apoptotic process	IDA	20605493
GO:0046872	Function	Metal ion binding	IEA
GO:0070062	Component	Extracellular exosome	HDA	19056867
GO:1901532	Process	Regulation of hematopoietic progenitor cell differentiation	IMP	22922207
GO:1902035	Process	Positive regulation of hematopoietic stem cell proliferation	IMP	22922207

Other IDs

• MIM: 600866
• HGNC: 8762
• e!Ensembl: ENSG00000071994

Protein

• UniProt ID: Q16342
• Protein name: Programmed cell death protein 2 (Zinc finger MYND domain-containing protein 7) (Zinc finger protein Rp-8)
• Protein function: May be a DNA-binding protein with a regulatory function. May play an important role in cell death and/or in regulation of cell proliferation.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF01753	zf-MYND	135 → 172	MYND finger	Domain
  PF04194	PDCD2_C	189 → 339	Programmed cell death protein 2, C-terminal putative domain	Domain

• Tissue specificity: TISSUE SPECIFICITY: Ubiquitous.
• Sequence:

  MAAAGARPVELGFAESAPAWRLRSEQFPSKVGGRPAWLGAAGLPGPQALACELCGRPLSF
  LLQVYAPLPGRPDAFHRCIFLFCCREQPCCAGLRVFRNQLPRKNDFYSYEPPSENPPPET
  GESVCLQLKSGAHLCRVCGCLGPKTCSRCHKAYYCSKEHQTLDWRLGHKQACAQPDHLDH
  IIPDHNFLFPEFEIVIETEDEIMPEVVEKEDYSEIIGSMGEALEEELDSMAKHESREDKI
  FQKFKTQIALEPEQILRYGRGIAPIWISGENIPQEKDIPDCPCGAKRILEFQVMPQLLNY
  LKADRLGKSIDWGILAVFTCAESCSLGTGYTEEFVWKQDVTDTP

• Sequence length: 344

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
ENDOGENOUS DEPRESSION	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	BEFREE	16609906		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma of lung (disorder)	Lung adenocarcinoma	BEFREE	16609906		★☆☆☆☆ Found in Text Mining only
B-Cell Lymphomas	B-Cell Lymphoma	BEFREE	12800155		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	21320484		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	37338518	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma	Carcinoma	BEFREE	12536316		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	30664177	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma of lung	Lung carcinoma	BEFREE	12536316, 16609906		★☆☆☆☆ Found in Text Mining only
Depressive Disorder	Major depressive disorder	Pubtator	19955554	Stimulate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus, Insulin-Dependent	Diabetes Mellitus	BEFREE	15848047		★☆☆☆☆ Found in Text Mining only
Endogenous depression	Mental Depression	PSYGENET_DG	19955554		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Fatigue Syndrome Chronic	Fatigue syndrome	Pubtator	16049284	Associate	★☆☆☆☆ Found in Text Mining only
Gastrointestinal Stromal Tumors	Gastrointestinal stromal tumor	BEFREE	26589942		★☆☆☆☆ Found in Text Mining only
Leukemia	Leukemia	Pubtator	22922207, 23760497	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	23760497	Associate	★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	BEFREE	12800155, 17468402, 20605493		★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	LHGDN	17468402		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	21320484		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	30664177		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of lung	Lung Cancer	BEFREE	12536316, 16609906		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of stomach	Stomach Neoplasms	BEFREE	26589942		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	16609906, 23760497, 30664177		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	12800155		★☆☆☆☆ Found in Text Mining only
Non-Small Cell Lung Carcinoma	Lung carcinoma	BEFREE	12536316		★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	19146857		★☆☆☆☆ Found in Text Mining only
Stomach Carcinoma	Stomach Carcinoma	BEFREE	26589942		★☆☆☆☆ Found in Text Mining only
T-Cell Lymphoma	T-Cell Lymphoma	BEFREE	17468402		★☆☆☆☆ Found in Text Mining only