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PDCD10 programmed cell death 10 [ Homo sapiens (human) ]

Gene ID: 11235, updated on 3-Nov-2024

Summary

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Official Symbol
PDCD10provided by HGNC
Official Full Name
programmed cell death 10provided by HGNC
Primary source
HGNC:HGNC:8761
See related
Ensembl:ENSG00000114209 MIM:609118; AllianceGenome:HGNC:8761
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CCM3; TFAR15
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]
Expression
Ubiquitous expression in colon (RPKM 13.1), lymph node (RPKM 11.6) and 25 other tissues See more
Orthologs
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Genomic context

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See PDCD10 in Genome Data Viewer
Location:
3q26.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (167683298..167734892, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (170467195..170518819, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (167401086..167452680, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene serpin family I member 2 Neighboring gene uncharacterized LOC105374197 Neighboring gene WD repeat domain 49 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_66573 Neighboring gene NANOG hESC enhancer GRCh37_chr3:167370944-167371467 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:167371468-167371990 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14866 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 8 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14867 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20771 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20772 Neighboring gene serpin family I member 1 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:167533895-167534094 Neighboring gene MEMO1 pseudogene 3

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Programmed cell death-10 enhances proliferation and protects malignant T cells from apoptosis. Lauenborg B, et al. APMIS, 2010 Oct. PMID 20854465, Free PMC Article
  2. Loss of programmed cell death 10 activates tumor cells and leads to temozolomide-resistance in glioblastoma. Nickel AC, et al. J Neurooncol, 2019 Jan. PMID 30392087
  3. Phenotypic variability in xeroderma pigmentosum group G: An uncommon case with severe prenatal-onset Cockayne syndrome features. Ricotti R, et al. Clin Genet, 2018 Oct. PMID 29749609
  4. Dual function of programmed cell death 10 (PDCD10) in drug resistance. Urfali-Mamatoglu C, et al. Biomed Pharmacother, 2018 May. PMID 29482058
  5. Downregulation of programmed cell death 10 is associated with tumor cell proliferation, hyperangiogenesis and peritumoral edema in human glioblastoma. Lambertz N, et al. BMC Cancer, 2015 Oct 21. PMID 26490252, Free PMC Article

See all (137) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Study on the role of CCM3 gene and lead exposure induced neurotoxicity through neurovascular units.
    Title: Study on the role of CCM3 gene and lead exposure induced neurotoxicity through neurovascular units.
  2. Programmed cell death 10 can be used as a potential biomarker for ankylosing spondylitis diagnosis and treatment.
    Title: Programmed cell death 10 can be used as a potential biomarker for ankylosing spondylitis diagnosis and treatment.
  3. Comprehensive CCM3 Mutational Analysis in Two Patients with Syndromic Cerebral Cavernous Malformation.
    Title: Comprehensive CCM3 Mutational Analysis in Two Patients with Syndromic Cerebral Cavernous Malformation.
  4. Knockdown of CCM3 promotes angiogenesis through activation and nuclear translocation of YAP/TAZ.
    Title: Knockdown of CCM3 promotes angiogenesis through activation and nuclear translocation of YAP/TAZ.
  5. PDCD10 promotes proliferation, migration, and invasion of osteosarcoma by inhibiting apoptosis and activating EMT pathway.
    Title: PDCD10 promotes proliferation, migration, and invasion of osteosarcoma by inhibiting apoptosis and activating EMT pathway.
  6. PDCD10 promotes the aggressive behaviors of pituitary adenomas by up-regulating CXCR2 and activating downstream AKT/ERK signaling.
    Title: PDCD10 promotes the aggressive behaviors of pituitary adenomas by up-regulating CXCR2 and activating downstream AKT/ERK signaling.
  7. Improving clinical interpretation of five KRIT1 and PDCD10 intronic variants.
    Title: Improving clinical interpretation of five KRIT1 and PDCD10 intronic variants.
  8. Programmed cell death 10 promotes metastasis and epithelial-mesenchymal transition of hepatocellular carcinoma via PP2Ac-mediated YAP activation.
    Title: Programmed cell death 10 promotes metastasis and epithelial-mesenchymal transition of hepatocellular carcinoma via PP2Ac-mediated YAP activation.
  9. CircSMARCA5 Facilitates the Progression of Prostate Cancer Through miR-432/PDCD10 Axis.
    Title: CircSMARCA5 Facilitates the Progression of Prostate Cancer Through miR-432/PDCD10 Axis.
  10. Programmed Cell Death 10 Mediated CXCL2-CXCR2 Signaling in Regulating Tumor-Associated Microglia/Macrophages Recruitment in Glioblastoma.
    Title: Programmed Cell Death 10 Mediated CXCL2-CXCR2 Signaling in Regulating Tumor-Associated Microglia/Macrophages Recruitment in Glioblastoma.
Submit: New GeneRIF Correction See all GeneRIFs (80)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Cerebral cavernous malformation 3
MedGen: C1864040 OMIM: 603285 GeneReviews: Familial Cerebral Cavernous Malformation
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC1212, MGC24477

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein homodimerization activity IPI
Inferred from Physical Interaction
more info
 PubMed 
enables protein kinase binding IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in Golgi reassembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in Golgi reassembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in angiogenesis IEA
Inferred from Electronic Annotation
more info
  
involved_in cellular response to leukemia inhibitory factor IEA
Inferred from Electronic Annotation
more info
  
involved_in endothelium development NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in establishment of Golgi localization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intracellular signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in intrinsic apoptotic signaling pathway in response to hydrogen peroxide IGI
Inferred from Genetic Interaction
more info
 PubMed 
involved_in negative regulation of apoptotic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of blood vessel endothelial cell proliferation involved in sprouting angiogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of cell migration involved in sprouting angiogenesis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of MAP kinase activity IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of Notch signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell migration IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of cell migration IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell population proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of gene expression IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of intracellular protein transport IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of peptidyl-serine phosphorylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of protein serine/threonine kinase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of stress-activated MAPK cascade IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein stabilization IMP
Inferred from Mutant Phenotype
more info
 PubMed 
NOT involved_in regulation of Rho protein signal transduction IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in regulation of angiogenesis NAS
Non-traceable Author Statement
more info
 PubMed 
NOT involved_in stress fiber assembly IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in wound healing, spreading of cells IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
part_of FAR/SIN/STRIPAK complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of FAR/SIN/STRIPAK complex IDA
Inferred from Direct Assay
more info
 PubMed 
colocalizes_with Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi apparatus IDA
Inferred from Direct Assay
more info
 PubMed 
located_in Golgi membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular exosome HDA PubMed 
located_in plasma membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
programmed cell death protein 10
Names
TF-1 cell apoptosis-related protein 15
apoptosis-related protein 15
cerebral cavernous malformations 3 protein

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_008158.1 RefSeqGene

    Range
    4972..56566
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_651

mRNA and Protein(s)

  1. NM_007217.4 → NP_009148.2  programmed cell death protein 10

    See identical proteins and their annotated locations for NP_009148.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same isoform.
    Source sequence(s)
    AC079822
    Consensus CDS
    CCDS3202.1
    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Related
    ENSP00000376506.2, ENST00000392750.7
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  2. NM_145859.2 → NP_665858.1  programmed cell death protein 10

    See identical proteins and their annotated locations for NP_665858.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform.
    Source sequence(s)
    AC079822
    Consensus CDS
    CCDS3202.1
    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Related
    ENSP00000418317.2, ENST00000473645.6
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  3. NM_145860.2 → NP_665859.1  programmed cell death protein 10

    See identical proteins and their annotated locations for NP_665859.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same isoform.
    Source sequence(s)
    AC079822
    Consensus CDS
    CCDS3202.1
    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Related
    ENSP00000420553.2, ENST00000497056.6
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    167683298..167734892 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005247086.6 → XP_005247143.1  programmed cell death protein 10 isoform X1

    See identical proteins and their annotated locations for XP_005247143.1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Related
    ENSP00000417202.1, ENST00000470131.5
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  2. XM_011512368.4 → XP_011510670.1  programmed cell death protein 10 isoform X1

    See identical proteins and their annotated locations for XP_011510670.1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  3. XM_005247087.6 → XP_005247144.1  programmed cell death protein 10 isoform X1

    See identical proteins and their annotated locations for XP_005247144.1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  4. XM_011512369.4 → XP_011510671.1  programmed cell death protein 10 isoform X1

    See identical proteins and their annotated locations for XP_011510671.1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  5. XM_006713485.5 → XP_006713548.1  programmed cell death protein 10 isoform X1

    See identical proteins and their annotated locations for XP_006713548.1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Related
    ENSP00000417118.2, ENST00000475915.6
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  6. XM_005247088.5 → XP_005247145.1  programmed cell death protein 10 isoform X1

    See identical proteins and their annotated locations for XP_005247145.1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Related
    ENSP00000420021.1, ENST00000461494.5
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  7. XM_017005644.3 → XP_016861133.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
    UniProtKB/TrEMBL
    C9J5C3
    Conserved Domains (1) summary
    pfam06840
    Location:14 → 161
    DUF1241; Protein of unknown function (DUF1241)

  8. XM_047447375.1 → XP_047303331.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  9. XM_047447374.1 → XP_047303330.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    170467195..170518819 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054345101.1 → XP_054201076.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  2. XM_054345100.1 → XP_054201075.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  3. XM_054345098.1 → XP_054201073.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  4. XM_054345099.1 → XP_054201074.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  5. XM_054345094.1 → XP_054201069.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  6. XM_054345095.1 → XP_054201070.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  7. XM_054345093.1 → XP_054201068.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  8. XM_054345096.1 → XP_054201071.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8

  9. XM_054345097.1 → XP_054201072.1  programmed cell death protein 10 isoform X1

    UniProtKB/Swiss-Prot
    A8K515, D3DNN5, O14811, Q9BUL8
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BUL8.1 GenPept UniProtKB/Swiss-Prot:Q9BUL8

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