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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 Malformation, Familial. Among its related pathways are Validated targets of C-MYC transcriptional activation. 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. Important for cell migration, and for normal structure and assembly of the Golgi complex. 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

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

Genomics for PDCD10 Gene

Regulatory Elements for PDCD10 Gene

Enhancers for PDCD10 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03F167691 0.7 ENCODE 11.4 +43.9 43865 0.2 PKNOX1 BMI1 EBF1 RELA CBX5 EED ETV6 CREM MTA2 CBFB SERPINI1 PDCD10 ZBBX HMGN1P8 GC03P167665
GH03F167684 0.6 ENCODE 11.1 +50.8 50835 0.2 CTCF ZNF654 CEBPB CEBPG RAD21 ATF4 ATF3 CEBPA SMC3 SERPINI1 WDR49 PDCD10 ZBBX HMGN1P8 GC03P167665
GH03F167882 0.5 Ensembl 10.5 -146.7 -146679 0.2 CTCF ZNF362 ZNF654 ZNF366 SMC3 TRIM22 RAD21 LINC01330 PDCD10 SERPINI1 MEMO1P3 ENSG00000244706
GH03F167732 0.8 ENCODE 6.6 +0.9 917 4.7 HDGF PKNOX1 CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 HMGN1P8 SERPINI1 PDCD10
GH03F167749 0.9 Ensembl ENCODE 0.3 -15.1 -15142 1.5 ELF3 TBP PKNOX1 TBL1XR1 RARA CREM THAP11 MIXL1 NFYC USF2 SERPINI1 PDCD10 LINC01330
- Elite enhancer/Elite enhancer-gene association Download Table
Download GeneHancer data dump

Enhancers around PDCD10 on UCSC Golden Path with GeneCards custom track

Promoters for PDCD10 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00001378685 422 3601 HDGF PKNOX1 CREB3L1 WRNIP1 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2

Genomic Location for PDCD10 Gene

Chromosome:
3
Start:
167,683,298 bp from pter
End:
167,735,422 bp from pter
Size:
52,125 bases
Orientation:
Minus strand

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. Interacts (via C-terminus) with CCM2 and PXN. Interacts (via N-terminus) with STK24, STK25 and STK26. Interacts with GOLGA2. Identified in a complex with CCM1 and CCM2. Interacts with KDR/VEGFR2. Interaction with KDR/VEGFR2 is enhanced by stimulation with VEGFA (By similarity).

    Three dimensional structures from OCA and Proteopedia for PDCD10 Gene

neXtProt entry for PDCD10 Gene

Post-translational modifications for PDCD10 Gene

  • Ubiquitination at Lys 132 and Lys 179
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Abcam antibodies for PDCD10

No data available for DME Specific Peptides for PDCD10 Gene

Domains & Families for PDCD10 Gene

Gene Families for PDCD10 Gene

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. Important for cell migration, and for normal structure and assembly of the Golgi complex. 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 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

Inhibitory RNA Products

Flow Cytometry 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
Jensen Localization Image for PDCD10 Gene COMPARTMENTS Subcellular localization image for PDCD10 gene
Compartment Confidence
cytosol 5
extracellular 5
golgi apparatus 5
plasma membrane 5
nucleus 3
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 IEA,IDA 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

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

Transcripts for PDCD10 Gene

Unigene Clusters for PDCD10 Gene

Programmed cell death 10:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry 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 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.
genes like me logo Genes that share expression patterns with PDCD10: view

Primer Products

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 35
  • 100 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PDCD10 35
  • 100 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia PDCD10 34 35
  • 99.69 (n)
dog
(Canis familiaris)
Mammalia PDCD10 34 35
  • 96.23 (n)
cow
(Bos Taurus)
Mammalia PDCD10 34 35
  • 95.6 (n)
mouse
(Mus musculus)
Mammalia Pdcd10 34 16 35
  • 94.81 (n)
rat
(Rattus norvegicus)
Mammalia Pdcd10 34
  • 94.13 (n)
chicken
(Gallus gallus)
Aves PDCD10 34 35
  • 90.72 (n)
lizard
(Anolis carolinensis)
Reptilia PDCD10 35
  • 100 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pdcd10 34
  • 85.53 (n)
Str.2496 34
African clawed frog
(Xenopus laevis)
Amphibia pdcd10-prov 34
zebrafish
(Danio rerio)
Actinopterygii pdcd10b 35
  • 93 (a)
OneToMany
pdcd10a 34 35
  • 80.32 (n)
-- 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.9691 34
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008287 34
  • 55.33 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG5073 36 34 35
  • 54.65 (n)
worm
(Caenorhabditis elegans)
Secernentea C14A4.11 34
  • 51.87 (n)
ccm-3 35
  • 33 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea CSA.10448 35
  • 50 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5553 34
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 Sequence Context AA Info Type
rs10513636 -- 167,690,615(-) AGTAC(A/G)TTTGA intron-variant
rs10635950 -- 167,717,549(+) AACTA(-/TAGT)TAAAC intron-variant
rs10663308 -- 167,719,081(+) AATAA(-/AC)AACTG intron-variant
rs10936543 -- 167,709,421(+) ATGTG(C/T)ACTTG intron-variant
rs111282008 -- 167,725,542(+) TGATG(C/T)CTTAA intron-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)

Relevant External Links 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

(11) MalaCards diseases for PDCD10 Gene - From: OMIM, ClinVar, GeneTests, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cerebral cavernous malformations 3
  • cavernous angiomatous malformations
cerebral cavernous malformation, familial
  • familial cavernous hemangioma
familial cerebral cavernous malformation 3
  • cerebral cavernous malformations 3
cerebral cavernous malformations-1
  • hyperkeratotic cutaneous capillary-venous malformations associated with cerebral capillary malformations
vascular hemostatic disease
  • hemostatic disorders
- 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.

Relevant External Links for PDCD10

Genetic Association Database (GAD)
PDCD10
Human Genome Epidemiology (HuGE) Navigator
PDCD10
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDCD10
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PDCD10
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. … Tournier-Lasserve E. (Am. J. Hum. Genet. 2005) 2 3 4 22 64
  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. (Hum. Mutat. 2009) 3 4 22 64
  3. CCM3/PDCD10 stabilizes GCKIII proteins to promote Golgi assembly and cell orientation. (PMID: 20332113) Fidalgo M. … Zalvide J. (J. Cell Sci. 2010) 3 4 64
  4. Risk of meningioma and common variation in genes related to innate immunity. (PMID: 20406964) Rajaraman P. … Inskip P.D. (Cancer Epidemiol. Biomarkers Prev. 2010) 3 46 64
  5. An approach based on a genome-wide association study reveals candidate loci for narcolepsy. (PMID: 20677014) Shimada M. … Tokunaga K. (Hum. Genet. 2010) 3 46 64

Products for PDCD10 Gene

Sources for PDCD10 Gene

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