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PDCD10 Gene

protein-coding   GIFtS: 60
GCID: GC03M167381

Programmed Cell Death 10

(Previous name: cerebral cavernous malformations 3)
(Previous symbol: CCM3)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Programmed Cell Death 101 2     TF-1 Cell Apoptosis-Related Protein 152 3
CCM31 2 3 5     Cerebral Cavernous Malformations 31
TFAR152 3 5     Apoptosis-Related Protein 152
Cerebral Cavernous Malformations 3 Protein2 3     Programmed Cell Death Protein 102

External Ids:    HGNC: 87611   Entrez Gene: 112352   Ensembl: ENSG000001142097   OMIM: 6091185   UniProtKB: Q9BUL83   
ORGUL members:         

Export aliases for PDCD10 gene to outside databases

Previous GC identifers: GC03M164691 GC03M168454 GC03M168803 GC03M168722 GC03M168884


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 familial cerebral cavernous malformation 3, and cerebral cavernous malformation, familial. GO annotations related to this gene include protein homodimerization activity and protein N-terminus binding.

UniProtKB/Swiss-Prot: PDC10_HUMAN, Q9BUL8
Function: Promotes cell proliferation. Modulates apoptotic pathways. Increases mitogen-activated protein kinase
activity and MST4 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


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000003.12  NT_005612.17  NC_018914.2  
Regulatory elements:
   Regulatory transcription factor binding sites in the PDCD10 gene promoter:
         p300   NF-E2 p45   NF-E2   GATA-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidPDCD10 promoter sequence
   Search Chromatin IP Primers for PDCD10

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat PDCD10


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 3q26.1   Ensembl cytogenetic band:  3q26.1   HGNC cytogenetic band: 3q26.1

PDCD10 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
PDCD10 gene location

GeneLoc information about chromosome 3         GeneLoc Exon Structure

GeneLoc location for GC03M167381:  view genomic region     (about GC identifiers)

Start:
167,401,086 bp from pter      End:
167,452,727 bp from pter
Size:
51,642 bases      Orientation:
minus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, Cloud-Clone Corp, and/or others.)
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UniProtKB/Swiss-Prot: PDC10_HUMAN, Q9BUL8 (See protein sequence)
Recommended Name: Programmed cell death protein 10  
Size: 212 amino acids; 24702 Da
Subunit: Homodimer. Interacts (via C-terminus) with CCM2 and PXN. Interacts (via N-terminus) with MST4, STK24 and
STK25. 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)
Selected PDB 3D structures from and Proteopedia for PDCD10 (see all 9):
3AJM (3D)        3L8I (3D)        3L8J (3D)        3RQE (3D)        3RQF (3D)        3RQG (3D)    
Secondary accessions: A8K515 D3DNN5 O14811

Explore the universe of human proteins at neXtProt for PDCD10: NX_Q9BUL8

Explore proteomics data for PDCD10 at MOPED

Post-translational modifications: 

  • Ubiquitination2 at Lys132, Lys179
  • Modification sites at PhosphoSitePlus

  • See PDCD10 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (3 alternative transcripts): 
    NP_009148.2  NP_665858.1  NP_665859.1  

    ENSEMBL proteins: 
     ENSP00000376506   ENSP00000418317   ENSP00000420553   ENSP00000417309   ENSP00000420021  
     ENSP00000417202   ENSP00000417118   ENSP00000420266   ENSP00000417876   ENSP00000420308  
     ENSP00000420424   ENSP00000420014   ENSP00000420450   ENSP00000418160  

    PDCD10 Human Recombinant Protein Products:

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    1 InterPro protein domain:
     IPR009652 DUF1241

    Graphical View of Domain Structure for InterPro Entry Q9BUL8

    ProtoNet protein and cluster: Q9BUL8

    UniProtKB/Swiss-Prot: PDC10_HUMAN, Q9BUL8
    Similarity: Belongs to the PDCD10 family


    PDCD10 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: PDC10_HUMAN, Q9BUL8
    Function: Promotes cell proliferation. Modulates apoptotic pathways. Increases mitogen-activated protein kinase
    activity and MST4 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): 3 molecular function terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005515protein binding IPI16189514
    GO:0042803protein homodimerization activity IPI--
    GO:0047485protein N-terminus binding IPI--
         
    PDCD10 for ontologies           About GeneDecksing


    Phenotypes:
         1 GenomeRNAi human phenotype for PDCD10:
     Increased cell death HMECs cel 

         15 MGI mutant phenotypes (inferred from 5 alleles(MGI details for Pdcd10):
     behavior/neurological  cardiovascular system  cellular  craniofacial  embryogenesis 
     growth/size/body  hematopoietic system  immune system  integument  mortality/aging 
     muscle  nervous system  normal  tumorigenesis  vision/eye 

    PDCD10 for phenotypes           About GeneDecksing

    Animal Models:
         MGI mouse knock-out Pdcd10tm1.1Wami for PDCD10

       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for PDCD10
       inGenious Targeting Laboratory: Contact us about creating complex and humanized mouse models for PDCD10

       genOway customized KO model: permanent, tissue-specific or time-controlled inactivation for PDCD10
       genOway customized Knockin model: humanization, point mutation, expression monitoring, etc. for PDCD10

    miRNA
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    miRTarBase miRNAs that target PDCD10:
    hsa-let-7b-5p (MIRT032330), hsa-mir-30a-5p (MIRT028601), hsa-mir-1 (MIRT023815), hsa-mir-155-5p (MIRT020819), hsa-mir-30b-5p (MIRT023428)

    Block miRNA regulation of human, mouse, rat PDCD10 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PDCD10 (see all 39):
    hsa-miR-21* hsa-miR-4272 hsa-miR-30d hsa-miR-4315 hsa-miR-374a hsa-miR-30a hsa-miR-186 hsa-miR-642b
    SwitchGear 3'UTR luciferase reporter plasmidPDCD10 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for PDCD10
    Predesigned siRNA for gene silencing in human, mouse, rat PDCD10

    Gene Editing
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    Clone
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    OriGene clones in human, mouse for PDCD10 (see all 16)
    OriGene ORF clones in mouse, rat for PDCD10
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 3): PDCD10 (NM_145859)
    Sino Biological Human cDNA Clone for PDCD10
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PDCD10
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PDCD10

    Cell Line
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    Browse ESI BIO Cell Lines and PureStem Progenitors for PDCD10 
    In Situ Assay
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    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDCD10


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    PDC10_HUMAN, Q9BUL8: 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: 

    CompartmentConfidence
    cytosol5
    golgi apparatus5
    plasma membrane5
    nucleus2
    mitochondrion1

    Gene Ontology (GO): 4 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0000139Golgi membrane IEA--
    GO:0005829cytosol IDA17360971
    GO:0005886plasma membrane IEA--
    GO:0070062extracellular vesicular exosome IDA19056867

    PDCD10 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for PDCD10 About    
    See pathways by source

    SuperPathContained pathways About
    1Validated targets of C-MYC transcriptional activation
    Validated targets of C-MYC transcriptional activation


    1 BioSystems Pathway for PDCD10
        Validated targets of C-MYC transcriptional activation



        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for PDCD10
    Interactions:

        GeneGlobe Interaction Network for PDCD10

    Selected Interacting proteins for PDCD10 (Q9BUL81, 2, 3) via UniProtKB, MINT, STRING, and/or I2D (see all 28)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    CCM2Q9BSQ51, 2, 3EBI-740195,EBI-1573056 MINT-8404432 I2D: score=1 
    STK24Q9Y6E01, 3EBI-740195,EBI-740175 I2D: score=5 
    STK25O005061, 3EBI-740195,EBI-618295 I2D: score=5 
    STRNO438151, 3EBI-740195,EBI-1046642 I2D: score=2 
    PTPN13Q129231, 3EBI-740195,EBI-355227 I2D: score=1 
    About this table

    Gene Ontology (GO): 5 biological process terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0001525angiogenesis IEA--
    GO:0006915apoptotic process IEA--
    GO:0008284positive regulation of cell proliferation IDA17360971
    GO:0043066negative regulation of apoptotic process IDA17360971
    GO:0043406positive regulation of MAP kinase activity IDA17360971

    PDCD10 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for PDCD10 (PDC10)



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for PDCD10 gene (3 alternative transcripts): 
    NM_007217.3  NM_145859.1  NM_145860.1  

    Unigene Cluster for PDCD10:

    Programmed cell death 10
    Hs.478150  [show with all ESTs]
    Unigene Representative Sequence: BC002506
    18 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000392750(uc003fex.3) ENST00000473645(uc003fey.3 uc003fez.3)
    ENST00000497056 ENST00000492396 ENST00000461494 ENST00000470131 ENST00000475915
    ENST00000487947 ENST00000471885 ENST00000479121 ENST00000462725 ENST00000492139
    ENST00000483451 ENST00000494502 ENST00000462830 ENST00000464360 ENST00000481136
    ENST00000487678
    miRNA
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    Block miRNA regulation of human, mouse, rat PDCD10 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate PDCD10 (see all 39):
    hsa-miR-21* hsa-miR-4272 hsa-miR-30d hsa-miR-4315 hsa-miR-374a hsa-miR-30a hsa-miR-186 hsa-miR-642b
    SwitchGear 3'UTR luciferase reporter plasmidPDCD10 3' UTR sequence
    Inhib. RNA
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    OriGene RNAi products in human, mouse, rat for PDCD10
    Predesigned siRNA for gene silencing in human, mouse, rat PDCD10
    Clone
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    OriGene clones in human, mouse for PDCD10 (see all 16)
    OriGene ORF clones in mouse, rat for PDCD10
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 3): PDCD10 (NM_145859)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for PDCD10
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat PDCD10
    Primer
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    OriGene qPCR primer pairs and template standards for PDCD10
    OriGene qSTAR qPCR primer pairs in human, mouse for PDCD10
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat PDCD10
      QuantiTect SYBR Green Assays in human, mouse, rat PDCD10
      QuantiFast Probe-based Assays in human, mouse, rat PDCD10

    Additional mRNA sequence: 

    AF022385.1 AK291130.1 BC002506.1 BC016353.1 CR457107.1 

    17 DOTS entries:

    DT.92446702  DT.311371  DT.100886934  DT.91729418  DT.40110826  DT.100886933  DT.92446708  DT.91640498 
    DT.91651122  DT.97814093  DT.100886931  DT.120869271  DT.120869312  DT.92338755  DT.92446710  DT.92446712 
    DT.97777196 

    Selected AceView cDNA sequences (see all 332):

    AI352636 BQ018007 BM843544 BX459901 BM843724 BU948431 BQ004569 BQ643761 
    BQ278545 BM804624 AW383024 AA195035 AI253079 BI260338 AA599041 CD512747 
    BQ650198 CR616910 BE504502 CB528710 NM_145859 CR603036 CB241583 BG677399 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for PDCD10 (see all 11)    About this scheme

    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:                                            -     -                       -     -     -                                                   


    ECgene alternative splicing isoforms for PDCD10

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    PDCD10 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TATCCTGTGT
    PDCD10 Expression
    About this image


    PDCD10 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     selected tissues (see all 8) fully expand
     
     Brain (Nervous System)    fully expand to see all 4 entries
             Cerebral Cortex
     
     Neural Tube (Nervous System)
             Telencephalon
     
     Trophoblast (Extraembryonic Tissues)
             Trophoblast Cells Trophoblast
     
     Testis (Reproductive System)
             Leydig Cells Testis Interstitium
     
     Pancreas (Endocrine System)
             Islets of Langerhans
    PDCD10 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    PDCD10 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.478150

    UniProtKB/Swiss-Prot: PDC10_HUMAN, Q9BUL8
    Tissue specificity: Ubiquitous

        Custom PCR Arrays for PDCD10
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    QuantiFast Probe-based Assays in human, mouse, rat PDCD10
    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for PDCD10

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of animals.

    Orthologs for PDCD10 gene from Selected species (see all 18)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Pdcd101 , 5 programmed cell death 101, 5 94.81(n)1
    99.53(a)1
      3 (33.76 cM)5
    564261  NM_019745.41  NP_062719.21 
     755164905 
    chicken
    (Gallus gallus)
    Aves PDCD101 programmed cell death 10 90.72(n)
    99.06(a)
      425003  NM_001006554.1  NP_001006554.1 
    lizard
    (Anolis carolinensis)
    Reptilia PDCD106
    programmed cell death 10
    100(a)
    1 ↔ 1
    3(9311759-9336131)
    African clawed frog
    (Xenopus laevis)
    Amphibia pdcd10-prov2 programmed cell death 10 87.1(n)    BC041501.1 
    zebrafish
    (Danio rerio)
    Actinopterygii BC056552.12   -- 80.84(n)   393527  BC056552.1 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG50731 , 3 CG50731 48(a)3
    54.65(n)1
    50.25(a)1
      418761  NM_142202.31  NP_650459.11 
    worm
    (Caenorhabditis elegans)
    Secernentea C14A4.111 C14A4.11 51.87(n)
    40.24(a)
      174638  NM_063889.5  NP_496290.2 


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

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for PDCD10 gene

    PDCD10 for paralogs           About GeneDecksing


    1 Pseudogenes.org Pseudogene for PDCD10
    PGOHUM00000249655


    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for PDCD10 (see all 909)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 3 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs771443491,2
    C,F--164781248(+) TACAAC/TTGAGG 3 -- int11Minor allele frequency- T:0.15WA 118
    rs749005521,2
    C,F--167264336(+) ATATAA/GTATTA 3 -- ds50011Minor allele frequency- G:0.05NA 120
    rs1883206551,2
    --167264366(+) TCCAAC/TCGTTG 3 -- ds50010--------
    rs2019230931,2
    C--167264410(-) TTTCCA/CAAAAA 3 -- ds50010--------
    rs1808424631,2
    --167264440(+) AGGGCA/CCAGTA 3 -- ds50010--------
    rs778988391,2
    C,F--167264449(+) TATACG/AAAAGG 3 -- ds50011Minor allele frequency- A:0.02EA 120
    rs1861383511,2
    --167264681(+) ATTATC/TTGATA 3 -- ds50010--------
    rs1909414161,2
    --167264935(+) CAATTA/CTTTTA 3 -- ut310--------
    rs1835892841,2
    --167265021(+) AGTGAG/TGCAAA 3 -- ut310--------
    rs1868831111,2
    --167265057(+) GCTACA/GTTTTA 3 -- ut310--------

    HapMap Linkage Disequilibrium report for PDCD10 (167401086 - 167452727 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 1 variation for PDCD10:    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv4105CNV Insertion18451855

    Human Gene Mutation Database (HGMD): PDCD10
    Site Specific Mutation Identification with PCR Assays
    1 Copy Number PCR Panel containing PDCD10:
    Ovarian Cancer
    SeqTarget long-range PCR primers for resequencing PDCD10
    DNA2.0 Custom Variant and Variant Library Synthesis for PDCD10

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 609118   
    OMIM disorders: 603285  
    UniProtKB/Swiss-Prot: PDC10_HUMAN, Q9BUL8
  • 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. Note=The disease is caused by mutations affecting the gene represented in this entry

  • Selected diseases for PDCD10 (see all 24):    
    About MalaCards
    familial cerebral cavernous malformation 3    cerebral cavernous malformation, familial    cerebral cavernous malformations 3    cerebritis
    cavernous malformation    cerebral cavernous malformation    cerebral cavernous malformations-1    proteus syndrome
    klippel-trenaunay syndrome    headache    narcolepsy    brain disease
    childhood leukemia    meningioma    tonsillitis    retinitis
    endotheliitis    multiple myeloma    myeloma    malaria

    2 diseases from the University of Copenhagen DISEASES database for PDCD10:
    Klippel-Trenaunay syndrome     Coats disease

    PDCD10 for disorders           About GeneDecksing

    4 Novoseek inferred disease relationships for PDCD10 gene    About this table

    Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    cerebral cavernous malformations 98.4 19 16284570 (2), 18496199 (2), 17657516 (2), 19151727 (1) (see all 11)
    vascular anomaly 72 1 15905966 (1)
    malformation venous 70.2 1 16379592 (1)
    klippel-trenaunay syndrome 65.4 1 16379592 (1)

    GeneTests: PDCD10
    GeneReviews: PDCD10
    Genetic Association Database (GAD): PDCD10
    Human Genome Epidemiology (HuGE) Navigator: PDCD10 (5 documents)

    Export disorders for PDCD10 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for PDCD10 gene, integrated from 10 sources (see all 85):
    (articles sorted by number of sources associating them with PDCD10)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Mutations within the programmed cell death 10 gene cause cerebral cavernous malformations. (PubMed id 15543491)1, 2, 3, 9 Bergametti F....Tournier-Lasserve E. (Am. J. Hum. Genet. 2005)
    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. (PubMed id 19370760)1, 2, 9 Voss K.... Felbor U. (Hum. Mutat. 2009)
    3. CCM3/PDCD10 stabilizes GCKIII proteins to promote Golgi assembly and cell orientation. (PubMed id 20332113)1, 2 Fidalgo M.... Zalvide J. (J. Cell Sci. 2010)
    4. Risk of meningioma and common variation in genes related to innate immunity. (PubMed id 20406964)1, 4 Rajaraman P....Inskip P.D. (amp 2010)
    5. Crystal structure of CCM3, a cerebral cavernous malformation protein critical for vascular integrity. (PubMed id 20489202)1, 2 Li X.... Boggon T.J. (J. Biol. Chem. 2010)
    6. Polymorphisms in innate immunity genes and risk of childhood leukemia. (PubMed id 20438785)1, 4 Han S....Kang D. (Hum. Immunol. 2010)
    7. An approach based on a genome-wide association study reveals candidate loci for narcolepsy. (PubMed id 20677014)1, 4 Shimada M....Tokunaga K. (Hum. Genet. 2010)
    8. PDCD10 interacts with Ste20-related kinase MST4 to promote cell growth and transformation via modulation of the ERK pathway. (PubMed id 17360971)1, 2 Ma X....Ma D. (Mol. Biol. Cell 2007)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    10. Mutations in apoptosis-related gene, PDCD10, cause cerebral cavernous malformation 3. (PubMed id 16284570)1, 9 Guclu B....Gunel M. (Neurosurgery 2005)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Disorders
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 11235 HGNC: 8761 AceView: PDCD10 Ensembl:ENSG00000114209 euGenes: HUgn11235
    ECgene: PDCD10 H-InvDB: PDCD10

    (According to HUGE)
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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for PDCD10 Pharmacogenomics, SNPs, Pathways
    GeneReviewshttp://www.ncbi.nlm.nih.gov/books/NBK1116/?term=PDCD10[genesymbol]

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for PDCD10 gene:
    Search GeneIP for patents involving PDCD10

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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