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Aliases for PDP2 Gene

Aliases for PDP2 Gene

  • Pyruvate Dehyrogenase Phosphatase Catalytic Subunit 2 2 3 5
  • Protein Phosphatase 2C, Magnesium-Dependent, Catalytic Subunit 2 2 3
  • Protein Phosphatase, Mg2+/Mn2+ Dependent 2B 2 3
  • PDPC 2 3 4
  • [Pyruvate Dehydrogenase [Acetyl-Transferring]]-Phosphatase 2, Mitochondrial 3
  • [Pyruvate Dehydrogenase (Acetyl-Transferring)]-Phosphatase 2
  • Pyruvate Dehydrogenase Phosphatase Catalytic Subunit 2 4
  • Pyruvate Dehydrogenase Phosphatase Isoenzyme 2 3
  • EC 4
  • KIAA1348 4
  • PPM2C2 3
  • PPM2B 3
  • PDP 2 4

External Ids for PDP2 Gene

Previous GeneCards Identifiers for PDP2 Gene

  • GC16P066690
  • GC16P065471
  • GC16P066914
  • GC16P052788

Summaries for PDP2 Gene

Entrez Gene Summary for PDP2 Gene

  • This gene is a mitochondrial protein that functions as a phosphatase and is involved in the enzymatic resetting of the pyruvate dehydrogenase complex. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2016]

GeneCards Summary for PDP2 Gene

PDP2 (Pyruvate Dehyrogenase Phosphatase Catalytic Subunit 2) is a Protein Coding gene. Among its related pathways are Metabolism and Pyruvate metabolism and Citric Acid (TCA) cycle. Gene Ontology (GO) annotations related to this gene include protein serine/threonine phosphatase activity and magnesium-dependent protein serine/threonine phosphatase activity. An important paralog of this gene is PDP1.

UniProtKB/Swiss-Prot for PDP2 Gene

  • Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.

Additional gene information for PDP2 Gene

No data available for CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDP2 Gene

Genomics for PDP2 Gene

GeneHancer (GH) Regulatory Elements for PDP2 Gene

Promoters and enhancers for PDP2 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH16J066879 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 650.7 +2.2 2183 2 PKNOX1 CLOCK SMAD1 MLX ARNT ZFP64 ARID4B SIN3A DMAP1 YY1 PDP2 EDC4 CTCF CES2 CENPT E2F4 ENSG00000260465 CDH16 RRAD NAE1
GH16J066877 Enhancer 0.9 Ensembl ENCODE 650.7 -0.5 -488 0.6 LEF1 ZNF223 CEBPG THRB ZNF335 ZFHX2 POLR2A PATZ1 EED ATF7 PDP2 CA7 CES2 CIAO2B NAE1
GH16J066878 Promoter 0.9 EPDnew 650.7 0.0 -20 0.1 LEF1 RXRA NR2F1 ETV5 ZNF592 EED HNF4A ATF7 PRDM4 PDP2 CA7 CES2 CIAO2B NAE1
GH16J066616 Enhancer 1.2 Ensembl ENCODE 9.8 -260.1 -260054 4.4 PKNOX1 ATF1 FOXA2 ARNT FEZF1 YY1 TCF12 ZNF766 GLIS2 ZNF213 PIR38551 PIR36038 GC16M066618 BEAN1 NAE1 TK2 PDP2 CMTM4 GC16M066615
GH16J066871 Promoter/Enhancer 1.9 FANTOM5 Ensembl ENCODE 3.2 -4.7 -4749 5.1 HDGF PKNOX1 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 ZNF213 NAE1 E2F4 CTCF CES2 CA7 EDC4 CENPT PLEKHG4 ZDHHC1 ACD
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDP2 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PDP2 gene promoter:
  • USF1
  • USF-1
  • ZIC2
  • AML1a
  • Tal-1beta
  • ITF-2
  • STAT3
  • C/EBPbeta

Genomic Locations for PDP2 Gene

Genomic Locations for PDP2 Gene
17,166 bases
Plus strand
17,166 bases
Plus strand

Genomic View for PDP2 Gene

Genes around PDP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDP2 Gene

Proteins for PDP2 Gene

  • Protein details for PDP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • A8K924

    Protein attributes for PDP2 Gene

    529 amino acids
    Molecular mass:
    59978 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Heterodimer of a catalytic subunit and a FAD protein of unknown function.
    • Sequence=BAA92586.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for PDP2 Gene

Post-translational modifications for PDP2 Gene

  • Ubiquitination at Lys459 and isoforms=438
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PDP2 Gene

Domains & Families for PDP2 Gene

Gene Families for PDP2 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for PDP2 Gene

Suggested Antigen Peptide Sequences for PDP2 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the PP2C family.
  • Belongs to the PP2C family.
genes like me logo Genes that share domains with PDP2: view

Function for PDP2 Gene

Molecular function for PDP2 Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the dephosphorylation and concomitant reactivation of the alpha subunit of the E1 component of the pyruvate dehydrogenase complex.
UniProtKB/Swiss-Prot CatalyticActivity:
[Pyruvate dehydrogenase (acetyl-transferring)] phosphate + H(2)O = [pyruvate dehydrogenase (acetyl-transferring)] + phosphate.

Enzyme Numbers (IUBMB) for PDP2 Gene

Gene Ontology (GO) - Molecular Function for PDP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004722 protein serine/threonine phosphatase activity IEA --
GO:0004741 [pyruvate dehydrogenase (lipoamide)] phosphatase activity EXP,IEA 9651365
GO:0016787 hydrolase activity IEA --
GO:0043169 cation binding IEA --
genes like me logo Genes that share ontologies with PDP2: view
genes like me logo Genes that share phenotypes with PDP2: view

Animal Model Products

  • Taconic Biosciences Mouse Models for PDP2

miRNA for PDP2 Gene

miRTarBase miRNAs that target PDP2

Clone Products

No data available for Phenotypes From GWAS Catalog , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PDP2 Gene

Localization for PDP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDP2 Gene

Mitochondrion matrix.

Subcellular locations from

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 PDP2 gene
Compartment Confidence
mitochondrion 5
cytosol 2
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PDP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005739 mitochondrion IEA --
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with PDP2: view

Pathways & Interactions for PDP2 Gene

genes like me logo Genes that share pathways with PDP2: view

SIGNOR curated interactions for PDP2 Gene


Gene Ontology (GO) - Biological Process for PDP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006470 protein dephosphorylation IEA --
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate TAS --
genes like me logo Genes that share ontologies with PDP2: view

Drugs & Compounds for PDP2 Gene

(4) Drugs for PDP2 Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
FAD Approved Pharma 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Magnesium Approved Nutra 0

(2) Additional Compounds for PDP2 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Hydrogen phosphate
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
  • [po(OH)3]
  • Acide phosphorique
  • Acidum phosphoricum
  • H3PO4
  • Orthophosphoric acid
genes like me logo Genes that share compounds with PDP2: view

Transcripts for PDP2 Gene

Unigene Clusters for PDP2 Gene

Pyruvate dehyrogenase phosphatase catalytic subunit 2:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDP2 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f · 1g · 1h · 1i ^ 2 ^ 3a · 3b · 3c · 3d · 3e · 3f · 3g
SP2: - - - -
SP3: - - -
SP4: - - - - -
SP5: -
SP6: - -

Relevant External Links for PDP2 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDP2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDP2 Gene

This gene is overexpressed in Lung (43.7) and Breast (24.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PDP2 Gene

Protein tissue co-expression partners for PDP2 Gene

NURSA nuclear receptor signaling pathways regulating expression of PDP2 Gene:


SOURCE GeneReport for Unigene cluster for PDP2 Gene:


Evidence on tissue expression from TISSUES for PDP2 Gene

  • Nervous system(4.7)
genes like me logo Genes that share expression patterns with PDP2: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PDP2 Gene

Orthologs for PDP2 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PDP2 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDP2 34 33
  • 99.43 (n)
(Canis familiaris)
Mammalia PDP2 34 33
  • 88.34 (n)
(Bos Taurus)
Mammalia PDP2 34 33
  • 87.12 (n)
(Rattus norvegicus)
Mammalia Pdp2 33
  • 83.49 (n)
(Mus musculus)
Mammalia Pdp2 16 34 33
  • 83.27 (n)
(Monodelphis domestica)
Mammalia PDP2 34
  • 76 (a)
(Ornithorhynchus anatinus)
Mammalia PDP2 34
  • 67 (a)
(Gallus gallus)
Aves PDP2 34 33
  • 65.4 (n)
(Anolis carolinensis)
Reptilia PDP2 34
  • 61 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pdp2 33
  • 63.46 (n)
African clawed frog
(Xenopus laevis)
Amphibia Xl.17333 33
(Danio rerio)
Actinopterygii pdp2 34 33 33
  • 62.07 (n)
fruit fly
(Drosophila melanogaster)
Insecta Pdp 34
  • 38 (a)
(Caenorhabditis elegans)
Secernentea pdp-1 34
  • 35 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACL083C 33
  • 46.63 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PTC5 34 33
  • 46.34 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C13706g 33
  • 45.27 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU01767 33
  • 46.12 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC10F6.17c 33
  • 45.7 (n)
Species where no ortholog for PDP2 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 PDP2 Gene

Gene Tree for PDP2 (if available)
Gene Tree for PDP2 (if available)
Evolutionary constrained regions (ECRs) for PDP2: view image

Paralogs for PDP2 Gene

Paralogs for PDP2 Gene

(2) SIMAP similar genes for PDP2 Gene using alignment to 7 proteins:

  • H3BV50_HUMAN
genes like me logo Genes that share paralogs with PDP2: view

Variants for PDP2 Gene

Sequence variations from dbSNP and Humsavar for PDP2 Gene

SNP ID Clin Chr 16 pos Variation AA Info Type
rs193921129 uncertain-significance, Malignant tumor of prostate 66,885,174(+) A/G coding_sequence_variant, missense_variant
rs1000429102 -- 66,882,296(+) C/A intron_variant
rs1000481657 -- 66,882,589(+) T/C intron_variant
rs1000765762 -- 66,883,713(+) G/T intron_variant
rs1000831915 -- 66,891,573(+) T/A downstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for PDP2 Gene

Variant ID Type Subtype PubMed ID
nsv572904 CNV loss 21841781

Variation tolerance for PDP2 Gene

Residual Variation Intolerance Score: 12.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.08; 22.05% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDP2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PDP2 Gene

Disorders for PDP2 Gene

Additional Disease Information for PDP2

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for PDP2 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for PDP2 Gene

Publications for PDP2 Gene

  1. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  2. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  3. Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 3 4 58
  4. Isoenzymes of pyruvate dehydrogenase phosphatase. DNA-derived amino acid sequences, expression, and regulation. (PMID: 9651365) Huang B … Popov KM (The Journal of biological chemistry 1998) 2 3 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for PDP2 Gene

Sources for PDP2 Gene

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