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Aliases for PDCD10 Gene

Aliases for PDCD10 Gene

  • Programmed Cell Death 10 2 3 5
  • Cerebral Cavernous Malformations 3 Protein 3 4
  • TF-1 Cell Apoptosis-Related Protein 15 3 4
  • TFAR15 3 4
  • CCM3 3 4
  • Cerebral Cavernous Malformations 3 2
  • Programmed Cell Death Protein 10 3
  • Apoptosis-Related Protein 15 3

External Ids for PDCD10 Gene

Previous HGNC Symbols for PDCD10 Gene

  • CCM3

Previous GeneCards Identifiers for PDCD10 Gene

  • GC03M164691
  • GC03M168454
  • GC03M168803
  • GC03M168722
  • GC03M168884
  • GC03M167381

Summaries for PDCD10 Gene

Entrez Gene Summary for PDCD10 Gene

  • 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]

GeneCards Summary for PDCD10 Gene

PDCD10 (Programmed Cell Death 10) is a Protein Coding gene. Diseases associated with PDCD10 include Cerebral Cavernous Malformations 3 and Cerebral Cavernous Malformations. Among its related pathways are Validated targets of C-MYC transcriptional activation. Gene Ontology (GO) annotations related to this gene include protein homodimerization activity and protein N-terminus binding.

UniProtKB/Swiss-Prot for PDCD10 Gene

  • 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).

Gene Wiki entry for PDCD10 Gene

Additional gene information for PDCD10 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDCD10 Gene

Genomics for PDCD10 Gene

GeneHancer (GH) Regulatory Elements for PDCD10 Gene

Promoters and enhancers for PDCD10 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH03I167732 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 556.7 +0.9 916 4.7 HDGF PKNOX1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B IRF4 SERPINI1 PDCD10 HMGN1P8
GH03I167691 Enhancer 0.8 ENCODE 11.4 +43.9 43864 0.2 PKNOX1 BACH1 EBF1 BMI1 BATF IRF4 RELA POLR2A NFATC1 ZNF143 SERPINI1 PDCD10 ZBBX HMGN1P8 GC03P167665
GH03I167683 Enhancer 0.6 UCNEbase 11.1 +51.3 51333 0.2 CTCF ATF4 WDR49 PDCD10 SERPINI1 ZBBX HMGN1P8 GC03P167665
GH03I167684 Enhancer 0.6 ENCODE 11.1 +50.8 50834 0.2 CTCF ZNF654 CEBPB CEBPG ATF2 RAD21 ATF4 ATF3 CEBPA ZNF143 SERPINI1 WDR49 PDCD10 ZBBX HMGN1P8 GC03P167665
GH03I167882 Enhancer 0.6 Ensembl 10.5 -146.7 -146679 0.2 CTCF ZNF654 ZNF362 TRIM22 RAD21 ZNF592 PRDM6 ZNF366 SMC3 ZNF143 LRRC77P SERPINI1 PDCD10 MEMO1P3 ENSG00000244706
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PDCD10 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDCD10 gene promoter:

Genomic Locations for PDCD10 Gene

Genomic Locations for PDCD10 Gene
chr3:167,683,298-167,735,422
(GRCh38/hg38)
Size:
52,125 bases
Orientation:
Minus strand
chr3:167,401,086-167,452,727
(GRCh37/hg19)

Genomic View for PDCD10 Gene

Genes around PDCD10 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDCD10 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDCD10 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDCD10 Gene

Proteins for PDCD10 Gene

  • Protein details for PDCD10 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BUL8-PDC10_HUMAN
    Recommended name:
    Programmed cell death protein 10
    Protein Accession:
    Q9BUL8
    Secondary Accessions:
    • A8K515
    • D3DNN5
    • O14811

    Protein attributes for PDCD10 Gene

    Size:
    212 amino acids
    Molecular mass:
    24702 Da
    Quaternary structure:
    • Homodimer (PubMed:20489202). Interacts (via C-terminus) with CCM2 (PubMed:17360971, PubMed:20489202). Interacts (via C-terminus) with PXN (PubMed:20489202). Interacts (via N-terminus) with STK25 (PubMed:17360971, PubMed:20332113). Interacts (via N-terminus) with STK26 (PubMed:17360971, PubMed:20332113, PubMed:27807006). Interacts (via N-terminus) with STK24 (PubMed:20332113, PubMed:27807006). Interacts with GOLGA2 (PubMed:20332113). Identified in a complex with KRIT1 and CCM2. Interacts with KDR/VEGFR2. Interaction with KDR/VEGFR2 is enhanced by stimulation with VEGFA (By similarity). Interacts with RIPOR1 (via C-terminus); this interaction is required for the association of RIPOR1 with either STK24 and STK26 kinases and occurs in a Rho-independent manner (PubMed:27807006).

    Three dimensional structures from OCA and Proteopedia for PDCD10 Gene

neXtProt entry for PDCD10 Gene

Post-translational modifications for PDCD10 Gene

  • Ubiquitination at isoforms=132 and Lys179
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PDCD10 Gene

Domains & Families for PDCD10 Gene

Gene Families for PDCD10 Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for PDCD10 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for PDCD10 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9BUL8

UniProtKB/Swiss-Prot:

PDC10_HUMAN :
  • Belongs to the PDCD10 family.
Family:
  • Belongs to the PDCD10 family.
genes like me logo Genes that share domains with PDCD10: view

Function for PDCD10 Gene

Molecular function for PDCD10 Gene

UniProtKB/Swiss-Prot 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).

Phenotypes From GWAS Catalog for PDCD10 Gene

Gene Ontology (GO) - Molecular Function for PDCD10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16189514
GO:0019901 protein kinase binding IPI 20332113
GO:0042803 protein homodimerization activity IPI 20489202
GO:0047485 protein N-terminus binding IPI 20489202
genes like me logo Genes that share ontologies with PDCD10: view
genes like me logo Genes that share phenotypes with PDCD10: view

Human Phenotype Ontology for PDCD10 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PDCD10 Gene

MGI Knock Outs for PDCD10:

Animal Model Products

miRNA for PDCD10 Gene

miRTarBase miRNAs that target PDCD10

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PDCD10 Gene

Localization for PDCD10 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDCD10 Gene

Cytoplasm. Golgi apparatus membrane; Peripheral membrane protein; Cytoplasmic side. Cell membrane; Peripheral membrane protein; Cytoplasmic side. Note=Partially co-localizes with endogenous PXN at the leading edges of migrating cells.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PDCD10 gene
Compartment Confidence
plasma membrane 5
extracellular 5
cytosol 5
golgi apparatus 5
nucleus 2
cytoskeleton 1
mitochondrion 1

Gene Ontology (GO) - Cellular Components for PDCD10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IEA --
GO:0005737 cytoplasm IDA,IEA 22652780
GO:0005794 colocalizes_with Golgi apparatus IEA,IDA 22652780
GO:0005829 cytosol IDA 17360971
GO:0005886 plasma membrane IEA --
genes like me logo Genes that share ontologies with PDCD10: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PDCD10 Gene

Pathways & Interactions for PDCD10 Gene

genes like me logo Genes that share pathways with PDCD10: view

Pathways by source for PDCD10 Gene

1 BioSystems pathway for PDCD10 Gene

SIGNOR curated interactions for PDCD10 Gene

Is inactivated by:
Other effect:

Gene Ontology (GO) - Biological Process for PDCD10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0001525 angiogenesis IEA --
GO:0006915 apoptotic process IEA --
GO:0008284 positive regulation of cell proliferation IDA 17360971
GO:0010628 positive regulation of gene expression IMP 23388056
GO:0010629 negative regulation of gene expression IMP 23388056
genes like me logo Genes that share ontologies with PDCD10: view

Drugs & Compounds for PDCD10 Gene

No Compound Related Data Available

Transcripts for PDCD10 Gene

Unigene Clusters for PDCD10 Gene

Programmed cell death 10:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDCD10 Gene

ExUns: 1a · 1b · 1c · 1d ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b · 9c ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c
SP1: - - - - - - -
SP2: - - - - - -
SP3: - - - - - - - -
SP4: - - - - - - -
SP5: - - - - -
SP6: - - - - - - -
SP7: - - - - -
SP8: - - - -
SP9: - - - - - - -
SP10: - - - -
SP11: - - - - -

Relevant External Links for PDCD10 Gene

GeneLoc Exon Structure for
PDCD10
ECgene alternative splicing isoforms for
PDCD10

Expression for PDCD10 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDCD10 Gene

Protein differential expression in normal tissues from HIPED for PDCD10 Gene

This gene is overexpressed in Platelet (8.3), Peripheral blood mononuclear cells (6.5), and Brain (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PDCD10 Gene



Protein tissue co-expression partners for PDCD10 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDCD10 Gene:

PDCD10

SOURCE GeneReport for Unigene cluster for PDCD10 Gene:

Hs.478150

mRNA Expression by UniProt/SwissProt for PDCD10 Gene:

Q9BUL8-PDC10_HUMAN
Tissue specificity: Ubiquitous.

Evidence on tissue expression from TISSUES for PDCD10 Gene

  • Blood(4.4)
  • Skin(4.2)
  • Nervous system(3.1)
  • Heart(2.8)
  • Spleen(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDCD10 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • skeletal muscle
Regions:
Head and neck:
  • brain
  • eye
  • head
  • meninges
  • neck
Abdomen:
  • liver
General:
  • blood
  • blood vessel
  • coagulation system
  • skin
  • spinal cord
genes like me logo Genes that share expression patterns with PDCD10: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA differential expression in normal tissues for PDCD10 Gene

Orthologs for PDCD10 Gene

This gene was present in the common ancestor of animals.

Orthologs for PDCD10 Gene

Organism Taxonomy Gene Similarity Type Details
oppossum
(Monodelphis domestica)
Mammalia PDCD10 34
  • 100 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDCD10 34
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDCD10 33 34
  • 99.69 (n)
dog
(Canis familiaris)
Mammalia PDCD10 33 34
  • 96.23 (n)
cow
(Bos Taurus)
Mammalia PDCD10 33 34
  • 95.6 (n)
mouse
(Mus musculus)
Mammalia Pdcd10 33 16 34
  • 94.81 (n)
rat
(Rattus norvegicus)
Mammalia Pdcd10 33
  • 94.13 (n)
chicken
(Gallus gallus)
Aves PDCD10 33 34
  • 90.72 (n)
lizard
(Anolis carolinensis)
Reptilia PDCD10 34
  • 100 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdcd10 33
  • 85.53 (n)
Str.2496 33
African clawed frog
(Xenopus laevis)
Amphibia pdcd10-prov 33
zebrafish
(Danio rerio)
Actinopterygii pdcd10b 34
  • 93 (a)
OneToMany
pdcd10a 33 34
  • 80.32 (n)
-- 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9691 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008287 33
  • 55.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5073 33 34 35
  • 54.65 (n)
worm
(Caenorhabditis elegans)
Secernentea C14A4.11 33
  • 51.87 (n)
ccm-3 34
  • 33 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10448 34
  • 50 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5553 33
Species where no ortholog for PDCD10 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PDCD10 Gene

ENSEMBL:
Gene Tree for PDCD10 (if available)
TreeFam:
Gene Tree for PDCD10 (if available)

Paralogs for PDCD10 Gene

Pseudogenes.org Pseudogenes for PDCD10 Gene

genes like me logo Genes that share paralogs with PDCD10: view

No data available for Paralogs for PDCD10 Gene

Variants for PDCD10 Gene

Sequence variations from dbSNP and Humsavar for PDCD10 Gene

SNP ID Clin Chr 03 pos Variation AA Info Type
rs1038529380 uncertain-significance, Encephalopathy, familial, with neuroserpin inclusion bodies 167,735,819(-) G/A upstream_transcript_variant
rs1042012552 uncertain-significance, Cerebral cavernous malformation 167,684,221(-) T/A 3_prime_UTR_variant
rs145045884 likely-benign, Encephalopathy, familial, with neuroserpin inclusion bodies, Cerebral cavernous malformation 167,735,940(-) A/G upstream_transcript_variant
rs146858915 likely-benign, benign, Cerebral cavernous malformation, not specified 167,720,282(-) A/G intron_variant
rs151267430 uncertain-significance, Cerebral cavernous malformation 167,684,373(-) C/A/G/T coding_sequence_variant, missense_variant

Structural Variations from Database of Genomic Variants (DGV) for PDCD10 Gene

Variant ID Type Subtype PubMed ID
nsv4105 CNV insertion 18451855
nsv965231 CNV duplication 23825009

Variation tolerance for PDCD10 Gene

Residual Variation Intolerance Score: 43.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.01; 20.66% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDCD10 Gene

Human Gene Mutation Database (HGMD)
PDCD10
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDCD10

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDCD10 Gene

Disorders for PDCD10 Gene

MalaCards: The human disease database

(10) MalaCards diseases for PDCD10 Gene - From: HGMD, OMIM, ClinVar, GTR, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cerebral cavernous malformations 3
  • cavernous angiomatous malformations
cerebral cavernous malformations
  • ccm
cerebral cavernous malformations 2
  • cavernous angiomatous malformations
central nervous system hemangioma
  • hemangioma of cns
klippel-trenaunay-weber syndrome
  • ktw syndrome
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

PDC10_HUMAN
  • Cerebral cavernous malformations 3 (CCM3) [MIM:603285]: A congenital vascular anomaly of the central nervous system that can result in hemorrhagic stroke, seizures, recurrent headaches, and focal neurologic deficits. The lesions are characterized by grossly enlarged blood vessels consisting of a single layer of endothelium and without any intervening neural tissue, ranging in diameter from a few millimeters to several centimeters. {ECO:0000269 PubMed:15543491}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PDCD10

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PDCD10: view

No data available for Genatlas for PDCD10 Gene

Publications for PDCD10 Gene

  1. Mutations within the programmed cell death 10 gene cause cerebral cavernous malformations. (PMID: 15543491) Bergametti F … Société Française de Neurochirurgie (American journal of human genetics 2005) 2 3 4 22 58
  2. Functional analyses of human and zebrafish 18-amino acid in-frame deletion pave the way for domain mapping of the cerebral cavernous malformation 3 protein. (PMID: 19370760) Voss K … Felbor U (Human mutation 2009) 3 4 22 58
  3. RHO binding to FAM65A regulates Golgi reorientation during cell migration. (PMID: 27807006) Mardakheh FK … Marshall CJ (Journal of cell science 2016) 3 4 58
  4. Risk of meningioma and common variation in genes related to innate immunity. (PMID: 20406964) Rajaraman P … Inskip PD (Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 2010) 3 44 58
  5. Polymorphisms in innate immunity genes and risk of childhood leukemia. (PMID: 20438785) Han S … Kang D (Human immunology 2010) 3 44 58

Products for PDCD10 Gene

Sources for PDCD10 Gene

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