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

    Gene ID: 11235, updated on 28-Oct-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
    mouse all
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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. Dual function of programmed cell death 10 (PDCD10) in drug resistance. Urfali-Mamatoglu C, et al. Biomed Pharmacother, 2018 May. PMID 29482058
    2. Identification of an Arg35X mutation in the PDCD10 gene in a patient with cerebral and multiple spinal cavernous malformations. Lee ST, et al. J Neurol Sci, 2008 Apr 15. PMID 18035376
    3. Apoptotic functions of PDCD10/CCM3, the gene mutated in cerebral cavernous malformation 3. Chen L, et al. Stroke, 2009 Apr. PMID 19246713, Free PMC Article
    4. Multiple cerebral cavernous malformations and a novel CCM3 germline deletion in a German family. Choe CU, et al. J Neurol, 2010 Dec. PMID 20623299
    5. Defining the functional domain of programmed cell death 10 through its interactions with phosphatidylinositol-3,4,5-trisphosphate. Dibble CF, et al. PLoS One, 2010 Jul 23. PMID 20668527, Free PMC Article

    See all (136) 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
    		Compare labs

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    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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    NEW Try the new Transcript table

    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

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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