PDCD10 (programmed cell death 10)

Gene

• Entrez ID: 11235
• Gene name: Programmed cell death 10
• Gene symbol: PDCD10
• Synonyms: CCM3, TFAR15
• Chromosome: 3
• Chromosome location: 3q26.1
• Summary: This gene encodes an evolutionarily conserved protein associated with cell apoptosis. The protein interacts with the serine/threonine protein kinase MST4 to modulate the extracellular signal-regulated kinase (ERK) pathway. It also interacts with and is phosphoryated by serine/threonine kinase 25, and is thought to function in a signaling pathway essential for vascular developent. Mutations in this gene are one cause of cerebral cavernous malformations, which are vascular malformations that cause seizures and cerebral hemorrhages. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs886041888	->T	Pathogenic	Frameshift variant, coding sequence variant
rs1057517786	G>A	Pathogenic	Stop gained, 5 prime UTR variant, coding sequence variant
rs1303470125	G>A,C	Pathogenic	Missense variant, stop gained, coding sequence variant
rs1357917630	G>A	Pathogenic	Stop gained, coding sequence variant
rs1404676956	G>A	Pathogenic	Coding sequence variant, stop gained
rs1553758385	T>A,G	Uncertain-significance, likely-pathogenic	Splice acceptor variant
rs1553759042	ACTT>-	Pathogenic	Splice donor variant, intron variant, coding sequence variant
rs1553759059	G>C	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs1553759139	C>T	Pathogenic, likely-pathogenic	Intron variant
rs1553760888	->T	Pathogenic	Frameshift variant, coding sequence variant
rs1553760900	G>A	Pathogenic	Stop gained, coding sequence variant
rs1553761217	C>T	Pathogenic	Splice donor variant
rs1553761266	CTTT>-	Pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1553762839	C>A,T	Likely-pathogenic	Splice donor variant
rs1559941951	->A	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1559944592	A>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1559944602	C>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1559945126	T>A	Likely-pathogenic	Splice acceptor variant
rs1559945136	G>C	Pathogenic	Intron variant
rs1559952217	A>C	Likely-pathogenic	Splice donor variant
rs1559952220	C>T	Likely-pathogenic	Splice donor variant
rs1559952317	->T	Pathogenic	Frameshift variant, coding sequence variant
rs1559952461	CT>-	Likely-pathogenic	Splice acceptor variant, coding sequence variant
rs1559952467	C>G	Likely-pathogenic	Splice acceptor variant
rs1559953791	C>-	Likely-pathogenic	Splice donor variant, coding sequence variant
rs1559960758	A>-	Likely-pathogenic	Frameshift variant, 5 prime UTR variant, coding sequence variant
rs1577317859	C>T	Pathogenic	Splice acceptor variant
rs1577329627	T>A	Pathogenic	Stop gained, coding sequence variant
rs1577329665	G>A	Pathogenic	Stop gained, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT020819	hsa-miR-155-5p	Proteomics	18668040
MIRT023428	hsa-miR-30b-5p	Sequencing	20371350
MIRT023428	hsa-miR-30b-5p	PAR-CLIP	21572407
MIRT023815	hsa-miR-1-3p	Proteomics	18668040
MIRT023815	hsa-miR-1-3p	Proteomics;Microarray	18668037
MIRT028601	hsa-miR-30a-5p	Proteomics	18668040
MIRT028601	hsa-miR-30a-5p	PAR-CLIP	21572407
MIRT032330	hsa-let-7b-5p	Proteomics	18668040
MIRT208901	hsa-miR-4776-3p	PAR-CLIP	21572407
MIRT521993	hsa-miR-1277-5p	PAR-CLIP	23446348
MIRT521993	hsa-miR-1277-5p	PAR-CLIP, HITS-CLIP	21572407
MIRT521993	hsa-miR-1277-5p	HITS-CLIP	23824327
MIRT521994	hsa-miR-4652-3p	PAR-CLIP	23446348
MIRT521994	hsa-miR-4652-3p	HITS-CLIP	21572407
MIRT521995	hsa-miR-5007-3p	PAR-CLIP	23446348
MIRT521995	hsa-miR-5007-3p	HITS-CLIP	21572407
MIRT521996	hsa-miR-190a-3p	PAR-CLIP	23446348
MIRT521996	hsa-miR-190a-3p	PAR-CLIP, HITS-CLIP	21572407
MIRT521996	hsa-miR-190a-3p	HITS-CLIP	23824327
MIRT521997	hsa-miR-4789-5p	PAR-CLIP	23446348
MIRT521997	hsa-miR-4789-5p	PAR-CLIP, HITS-CLIP	21572407
MIRT521997	hsa-miR-4789-5p	HITS-CLIP	23824327
MIRT521998	hsa-miR-3941	PAR-CLIP	23446348
MIRT521998	hsa-miR-3941	PAR-CLIP, HITS-CLIP	21572407
MIRT521998	hsa-miR-3941	HITS-CLIP	23824327
MIRT521999	hsa-miR-6853-3p	PAR-CLIP	23446348
MIRT521999	hsa-miR-6853-3p	HITS-CLIP	21572407
MIRT522000	hsa-miR-1206	PAR-CLIP	23446348
MIRT522000	hsa-miR-1206	HITS-CLIP	21572407
MIRT522001	hsa-miR-26b-3p	PAR-CLIP	23446348
MIRT522001	hsa-miR-26b-3p	HITS-CLIP	21572407
MIRT522002	hsa-miR-5011-5p	PAR-CLIP	23446348
MIRT522002	hsa-miR-5011-5p	PAR-CLIP, HITS-CLIP	21572407
MIRT522002	hsa-miR-5011-5p	HITS-CLIP	23824327
MIRT522003	hsa-miR-4789-3p	PAR-CLIP	23446348
MIRT522003	hsa-miR-4789-3p	PAR-CLIP, HITS-CLIP	21572407
MIRT522003	hsa-miR-4789-3p	HITS-CLIP	23824327
MIRT522004	hsa-miR-603	PAR-CLIP	23446348
MIRT522004	hsa-miR-603	PAR-CLIP, HITS-CLIP	21572407
MIRT522004	hsa-miR-603	HITS-CLIP	23824327
MIRT522005	hsa-miR-362-3p	PAR-CLIP	23446348
MIRT522005	hsa-miR-362-3p	PAR-CLIP, HITS-CLIP	21572407
MIRT522005	hsa-miR-362-3p	HITS-CLIP	23824327
MIRT522006	hsa-miR-329-3p	PAR-CLIP	23446348
MIRT522006	hsa-miR-329-3p	PAR-CLIP, HITS-CLIP	21572407
MIRT522006	hsa-miR-329-3p	HITS-CLIP	23824327
MIRT522007	hsa-miR-8485	PAR-CLIP	23446348
MIRT522007	hsa-miR-8485	PAR-CLIP, HITS-CLIP	21572407
MIRT522007	hsa-miR-8485	HITS-CLIP	23824327
MIRT555731	hsa-miR-335-3p	PAR-CLIP	21572407
MIRT555732	hsa-miR-1305	PAR-CLIP	21572407
MIRT555733	hsa-miR-498	PAR-CLIP	21572407
MIRT555734	hsa-miR-302c-5p	PAR-CLIP	21572407
MIRT555735	hsa-miR-2053	PAR-CLIP	21572407
MIRT555736	hsa-miR-4715-3p	PAR-CLIP	21572407
MIRT555737	hsa-miR-3064-3p	PAR-CLIP	21572407
MIRT555738	hsa-miR-5585-3p	PAR-CLIP	21572407
MIRT555739	hsa-miR-4465	PAR-CLIP	21572407
MIRT555740	hsa-miR-26b-5p	PAR-CLIP	21572407
MIRT555741	hsa-miR-26a-5p	PAR-CLIP	21572407
MIRT555742	hsa-miR-1297	PAR-CLIP	21572407
MIRT555743	hsa-miR-203a-3p	PAR-CLIP	21572407
MIRT555744	hsa-miR-153-5p	PAR-CLIP	21572407
MIRT555745	hsa-miR-5697	PAR-CLIP	21572407
MIRT555746	hsa-miR-4495	PAR-CLIP	21572407
MIRT555747	hsa-miR-586	PAR-CLIP	21572407
MIRT555748	hsa-miR-5680	PAR-CLIP	21572407
MIRT555749	hsa-miR-5683	PAR-CLIP	21572407
MIRT555750	hsa-miR-33a-3p	PAR-CLIP	21572407
MIRT555751	hsa-miR-186-5p	PAR-CLIP	21572407
MIRT555752	hsa-miR-3133	PAR-CLIP	21572407
MIRT555753	hsa-miR-7844-5p	PAR-CLIP	21572407
MIRT555754	hsa-miR-30c-5p	PAR-CLIP	21572407
MIRT555755	hsa-miR-30d-5p	PAR-CLIP	21572407
MIRT555756	hsa-miR-30e-5p	PAR-CLIP	21572407
MIRT707974	hsa-miR-6740-3p	HITS-CLIP	21572407
MIRT707975	hsa-miR-3182	HITS-CLIP	21572407
MIRT731465	hsa-miR-425-5p	Luciferase reporter assay	27132035
MIRT731465	hsa-miR-425-5p	Luciferase reporter assay, Western blot	26647742
MIRT732792	hsa-miR-103a-2-5p	Luciferase reporter assay, qRT-PCR, Western blot	26707063
MIRT733050	hsa-miR-200c-3p	Luciferase reporter assay, Microarray, qRT-PCR, Western blot	26400441
MIRT734173	hsa-miR-181b-5p	Western blot	26046358

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	IEA
GO:0001525	Process	Angiogenesis	IEA
GO:0005515	Function	Protein binding	IPI	16189514, 17360971, 17657516, 18782753, 20332113, 20489202, 21516116, 21561863, 23266514, 23455922, 23541896, 23665169, 24366813, 25416956, 26496610, 27807006, 28514442, 31515488, 32296183
GO:0005737	Component	Cytoplasm	IDA	22652780
GO:0005794	Component	Golgi apparatus	IBA	21873635
GO:0005794	Component	Golgi apparatus	IDA	20332113
GO:0005794	Component	Golgi apparatus	IDA	22652780
GO:0005829	Component	Cytosol	IDA	17360971, 20489202
GO:0005886	Component	Plasma membrane	IEA
GO:0008284	Process	Positive regulation of cell population proliferation	IDA	17360971, 23541896
GO:0010628	Process	Positive regulation of gene expression	IMP	23388056
GO:0010629	Process	Negative regulation of gene expression	IMP	23388056
GO:0019901	Function	Protein kinase binding	IBA	21873635
GO:0019901	Function	Protein kinase binding	IPI	20332113, 22652780
GO:0030335	Process	Positive regulation of cell migration	IDA	23541896
GO:0030335	Process	Positive regulation of cell migration	IMP	20332113
GO:0032874	Process	Positive regulation of stress-activated MAPK cascade	IDA	22652780
GO:0033138	Process	Positive regulation of peptidyl-serine phosphorylation	IMP	20332113
GO:0035023	Process	Regulation of Rho protein signal transduction	IMP	20332113
GO:0036481	Process	Intrinsic apoptotic signaling pathway in response to hydrogen peroxide	IGI	22652780
GO:0042542	Process	Response to hydrogen peroxide	IDA	22291017
GO:0042803	Function	Protein homodimerization activity	IPI	20489202, 21561863
GO:0043066	Process	Negative regulation of apoptotic process	IDA	17360971
GO:0043149	Process	Stress fiber assembly	IMP	20332113
GO:0043406	Process	Positive regulation of MAP kinase activity	IBA	21873635
GO:0043406	Process	Positive regulation of MAP kinase activity	IDA	17360971
GO:0044319	Process	Wound healing, spreading of cells	IMP	20332113
GO:0045747	Process	Positive regulation of Notch signaling pathway	IMP	23388056
GO:0047485	Function	Protein N-terminus binding	IPI	20489202
GO:0050821	Process	Protein stabilization	IMP	20332113, 22652780
GO:0051683	Process	Establishment of Golgi localization	IMP	20332113
GO:0070062	Component	Extracellular exosome	HDA	19056867, 20458337, 23533145
GO:0071902	Process	Positive regulation of protein serine/threonine kinase activity	IMP	20332113
GO:0090051	Process	Negative regulation of cell migration involved in sprouting angiogenesis	IMP	23388056
GO:0090168	Process	Golgi reassembly	IMP	20332113
GO:0090316	Process	Positive regulation of intracellular protein transport	IMP	27807006
GO:0090443	Component	FAR/SIN/STRIPAK complex	IBA	21873635
GO:1903358	Process	Regulation of Golgi organization	IBA	21873635
GO:1903588	Process	Negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis	IMP	23388056
GO:1990830	Process	Cellular response to leukemia inhibitory factor	IEA

Other IDs

• MIM: 609118
• HGNC: 8761
• e!Ensembl: ENSG00000114209

Protein

• UniProt ID: Q9BUL8
• Protein name: Programmed cell death protein 10 (Cerebral cavernous malformations 3 protein) (TF-1 cell apoptosis-related protein 15)
• Protein function: Promotes cell proliferation. Modulates apoptotic pathways. Increases mitogen-activated protein kinase activity and STK26 activity (PubMed:27807006). Important for cell migration, and for normal structure and assembly of the Golgi complex (PubMed:27807006). Important for KDR/VEGFR2 signaling. Increases the stability of KDR/VEGFR2 and prevents its breakdown. Required for normal cardiovascular development. Required for normal angiogenesis, vasculogenesis and hematopoiesis during embryonic development (By similarity).
• PDB: 3AJM, 3L8I, 3L8J, 3RQE, 3RQF, 3RQG, 3W8H, 3W8I, 4GEH, 4TVQ
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF06840	DUF1241	14 → 161		Family

• Sequence:

  MRMTMEEMKNEAETTSMVSMPLYAVMYPVFNELERVNLSAAQTLRAAFIKAEKENPGLTQ
  DIIMKILEKKSVEVNFTESLLRMAADDVEEYMIERPEPEFQDLNEKARALKQILSKIPDE
  INDRVRFLQTIKDIASAIKELLDTVNNVFKKYQYQNRRALEHQKKEFVKYSKSFSDTLKT
  YFKDGKAINVFVSANRLIHQTNLILQTFKTVA

• Sequence length: 212