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Aliases for PDP1 Gene

Aliases for PDP1 Gene

  • Pyruvate Dehyrogenase Phosphatase Catalytic Subunit 1 2 3 3 5
  • Protein Phosphatase 2C, Magnesium-Dependent, Catalytic Subunit 2 3
  • Pyruvate Dehydrogenase Phosphatase Catalytic Subunit 1 3 4
  • Protein Phosphatase, Mg2+/Mn2+ Dependent 2A 2 3
  • PDPC 1 3 4
  • PPM2C 3 4
  • PDP 1 3 4
  • PDP 3 4
  • [Pyruvate Dehydrogenase [Acetyl-Transferring]]-Phosphatase 1, Mitochondrial 3
  • Pyruvate Dehydrogenase (Lipoamide) Phosphatase-Phosphatase 3
  • Protein Phosphatase 2C 4
  • EC 4
  • PPM2A 3
  • PDPC 3
  • PDH 3

External Ids for PDP1 Gene

Previous HGNC Symbols for PDP1 Gene

  • PPM2C

Previous GeneCards Identifiers for PDP1 Gene

  • GC08P094999
  • GC08P090137
  • GC08P094870

Summaries for PDP1 Gene

Entrez Gene Summary for PDP1 Gene

  • Pyruvate dehydrogenase (E1) is one of the three components (E1, E2, and E3) of the large pyruvate dehydrogenase complex. Pyruvate dehydrogenase kinases catalyze phosphorylation of serine residues of E1 to inactivate the E1 component and inhibit the complex. Pyruvate dehydrogenase phosphatases catalyze the dephosphorylation and activation of the E1 component to reverse the effects of pyruvate dehydrogenase kinases. Pyruvate dehydrogenase phosphatase is a heterodimer consisting of catalytic and regulatory subunits. Two catalytic subunits have been reported; one is predominantly expressed in skeletal muscle and another one is is much more abundant in the liver. The catalytic subunit, encoded by this gene, is the former, and belongs to the protein phosphatase 2C (PP2C) superfamily. Along with the pyruvate dehydrogenase complex and pyruvate dehydrogenase kinases, this enzyme is located in the mitochondrial matrix. Mutation in this gene causes pyruvate dehydrogenase phosphatase deficiency. Multiple alternatively spliced transcript variants encoding different isoforms have been identified.[provided by RefSeq, Jun 2009]

GeneCards Summary for PDP1 Gene

PDP1 (Pyruvate Dehyrogenase Phosphatase Catalytic Subunit 1) is a Protein Coding gene. Diseases associated with PDP1 include Pyruvate Dehydrogenase Phosphatase Deficiency and Atypical Autism. Among its related pathways are Development Dopamine D2 receptor transactivation of EGFR and Metabolism. Gene Ontology (GO) annotations related to this gene include protein serine/threonine phosphatase activity and [pyruvate dehydrogenase (lipoamide)] phosphatase activity. An important paralog of this gene is PDP2.

UniProtKB/Swiss-Prot for PDP1 Gene

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

Gene Wiki entry for PDP1 Gene

Additional gene information for PDP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PDP1 Gene

Genomics for PDP1 Gene

GeneHancer (GH) Regulatory Elements for PDP1 Gene

Promoters and enhancers for PDP1 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
GH08J093915 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE dbSUPER 665.4 +59.6 59554 3.8 HDGF PKNOX1 ARID4B NEUROD1 SIN3A DMAP1 ZNF2 YY1 ZNF213 ZNF207 PDP1 ENSG00000264448 MIR378D2 VIRMA LINC00535 FAM92A RBM12B ENSG00000253854 INTS8 PSMA2P2
GH08J093855 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE dbSUPER 650.7 -0.6 -590 2.5 JUN HLF CBFA2T3 ZNF644 TEAD3 ZNF121 FOSL1 JUND FOS PDP1 ENSG00000264448 MYL12AP1
GH08J093931 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 16.5 +76.8 76750 5.5 ELF3 PKNOX1 FOXA2 SMAD1 NFIB ZSCAN5C SCRT2 RCOR1 FOS IKZF2 PDP1 ENSG00000253722 GEM PSMA2P2 ENSG00000264448
GH08J093900 Enhancer 1.1 Ensembl ENCODE dbSUPER 17 +46.1 46061 6.7 PKNOX1 JUN MEF2B EP300 YY1 JUND MAFF FOXK2 POLR2A TARDBP LOC105375646 PDP1 LINC00535 FAM92A FSBP GC08M093861
GH08J093878 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.8 +22.7 22723 3.5 KLF14 BATF RAD21 ZEB1 ZSCAN5C RCOR1 ETV6 FOS IKZF2 RUNX3 PDP1 ENSG00000264448 GC08M093861 LOC105375646
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDP1 on UCSC Golden Path with GeneCards custom track

Genomic Locations for PDP1 Gene

Genomic Locations for PDP1 Gene
68,262 bases
Plus strand
68,262 bases
Plus strand

Genomic View for PDP1 Gene

Genes around PDP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PDP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PDP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PDP1 Gene

Proteins for PDP1 Gene

  • Protein details for PDP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial
    Protein Accession:
    Secondary Accessions:
    • B3KX71
    • J3KPU0
    • Q5U5K1

    Protein attributes for PDP1 Gene

    537 amino acids
    Molecular mass:
    61054 Da
    Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
    Quaternary structure:
    • Heterodimer of a catalytic (PDP1) and a regulatory (PDPR) subunit.
    • Sequence=AAF67480.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PDP1 Gene


neXtProt entry for PDP1 Gene

Post-translational modifications for PDP1 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

  • R&D Systems Antibodies for PDP1 (Pyruvate Dehydrogenase Phosphatase/PDP1)
  • Abcam antibodies for PDP1
  • Santa Cruz Biotechnology (SCBT) Antibodies for PDP1

No data available for DME Specific Peptides for PDP1 Gene

Domains & Families for PDP1 Gene

Gene Families for PDP1 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Plasma proteins
  • Potential drug targets
  • Predicted intracellular proteins

Protein Domains for PDP1 Gene

Suggested Antigen Peptide Sequences for PDP1 Gene

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 PDP1: view

Function for PDP1 Gene

Molecular function for PDP1 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 PDP1 Gene

Phenotypes From GWAS Catalog for PDP1 Gene

Gene Ontology (GO) - Molecular Function for PDP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004721 phosphoprotein phosphatase activity IEA --
GO:0004722 protein serine/threonine phosphatase activity IDA 20801214
GO:0004741 [pyruvate dehydrogenase (lipoamide)] phosphatase activity IEA,EXP 9651365
GO:0005515 protein binding IPI 25416956
GO:0016787 hydrolase activity IEA --
genes like me logo Genes that share ontologies with PDP1: view
genes like me logo Genes that share phenotypes with PDP1: view

Human Phenotype Ontology for PDP1 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDP1

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PDP1 Gene

Localization for PDP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDP1 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 PDP1 gene
Compartment Confidence
mitochondrion 5
nucleus 3
cytosol 2
extracellular 1
peroxisome 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Mitochondria (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PDP1 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 PDP1: view

Pathways & Interactions for PDP1 Gene

genes like me logo Genes that share pathways with PDP1: view

SIGNOR curated interactions for PDP1 Gene


Gene Ontology (GO) - Biological Process for PDP1 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 --
GO:0035970 peptidyl-threonine dephosphorylation IDA 20801214
genes like me logo Genes that share ontologies with PDP1: view

Drugs & Compounds for PDP1 Gene

(31) Drugs for PDP1 Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved Nutra 0
Phosphoric acid Approved Pharma 0
Water Approved Pharma 0
Alpha-Hydroxy-Beta-Phenyl-Propionic Acid Experimental Pharma Target 0
Phenylpyruvic acid Experimental Pharma Target 0

(30) Additional Compounds for PDP1 Gene - From: Novoseek and 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 PDP1: view

Transcripts for PDP1 Gene

Unigene Clusters for PDP1 Gene

Pyruvate dehyrogenase phosphatase catalytic subunit 1:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for PDP1

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PDP1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b · 8c · 8d · 8e
SP1: -
SP2: - - - - - - -
SP3: - - - - - - - -
SP4: - - - - - -
SP5: - - - - -
SP6: - - -

Relevant External Links for PDP1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PDP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PDP1 Gene

mRNA differential expression in normal tissues according to GTEx for PDP1 Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x5.0).

Protein differential expression in normal tissues from HIPED for PDP1 Gene

This gene is overexpressed in Liver (14.8) and Nasal epithelium (8.9).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for PDP1 Gene

Protein tissue co-expression partners for PDP1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PDP1 Gene:


SOURCE GeneReport for Unigene cluster for PDP1 Gene:


Evidence on tissue expression from TISSUES for PDP1 Gene

  • Nervous system(4.9)
  • Adrenal gland(4.3)
  • Heart(2.2)
  • Muscle(2.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PDP1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • digestive
  • nervous
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • eye
  • head
  • mouth
  • pharynx
  • esophagus
  • stomach
  • lower limb
  • peripheral nerve
  • peripheral nervous system
genes like me logo Genes that share expression patterns with PDP1: view

No data available for mRNA Expression by UniProt/SwissProt for PDP1 Gene

Orthologs for PDP1 Gene

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

Orthologs for PDP1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia PDP1 34 33
  • 99.64 (n)
(Rattus norvegicus)
Mammalia Pdp1 33
  • 92.65 (n)
(Bos Taurus)
Mammalia PDP1 34 33
  • 92.43 (n)
(Mus musculus)
Mammalia Pdp1 16 34 33
  • 92.17 (n)
(Monodelphis domestica)
Mammalia PDP1 34
  • 92 (a)
(Canis familiaris)
Mammalia PDP1 34 33
  • 90.75 (n)
(Ornithorhynchus anatinus)
Mammalia PDP1 34
  • 88 (a)
(Gallus gallus)
Aves PDP1 34 33
  • 80.08 (n)
(Anolis carolinensis)
Reptilia PDP1 34
  • 90 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pdp1 33
  • 75.02 (n)
(Danio rerio)
Actinopterygii pdp1 34 33
  • 69.33 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008349 33
  • 51.4 (n)
fruit fly
(Drosophila melanogaster)
Insecta Pdp 34 33
  • 50.98 (n)
(Caenorhabditis elegans)
Secernentea pdp-1 34 33
  • 47.03 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PTC5 36 34
  • 22 (a)
Species where no ortholog for PDP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • 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 PDP1 Gene

Gene Tree for PDP1 (if available)
Gene Tree for PDP1 (if available)
Evolutionary constrained regions (ECRs) for PDP1: view image

Paralogs for PDP1 Gene

Paralogs for PDP1 Gene

(2) SIMAP similar genes for PDP1 Gene using alignment to 6 proteins:

  • E5RI96_HUMAN
genes like me logo Genes that share paralogs with PDP1: view

Variants for PDP1 Gene

Sequence variations from dbSNP and Humsavar for PDP1 Gene

SNP ID Clin Chr 08 pos Variation AA Info Type
rs111728711 uncertain-significance, Pyruvate dehydrogenase phosphatase deficiency 93,925,237(+) C/A 3_prime_UTR_variant
rs116788695 likely-benign, Pyruvate dehydrogenase phosphatase deficiency 93,925,409(+) G/C 3_prime_UTR_variant
rs137975172 uncertain-significance, Pyruvate dehydrogenase phosphatase deficiency 93,923,505(+) C/A/T coding_sequence_variant, synonymous_variant
rs138488258 benign, uncertain-significance, not specified, Pyruvate dehydrogenase phosphatase deficiency 93,922,965(+) C/T coding_sequence_variant, synonymous_variant
rs147477305 benign, uncertain-significance, not specified, Pyruvate dehydrogenase phosphatase deficiency 93,923,490(+) C/T coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for PDP1 Gene

Variant ID Type Subtype PubMed ID
nsv1022473 CNV loss 25217958

Variation tolerance for PDP1 Gene

Residual Variation Intolerance Score: 8.98% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.78; 16.50% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDP1 Gene

Human Gene Mutation Database (HGMD)
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 PDP1 Gene

Disorders for PDP1 Gene

MalaCards: The human disease database

(7) MalaCards diseases for PDP1 Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
pyruvate dehydrogenase phosphatase deficiency
  • pdhpd
atypical autism
  • pdd
  • sarcos
lactic acidosis
  • acidosis lactic
  • deerfly fever
- elite association - COSMIC cancer census association via MalaCards
Search PDP1 in MalaCards View complete list of genes associated with diseases


  • Pyruvate dehydrogenase phosphatase deficiency (PDP deficiency) [MIM:608782]: Results in lactic acidosis leading to neurological dysfunction. {ECO:0000269 PubMed:15855260}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PDP1

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PDP1: view

No data available for Genatlas for PDP1 Gene

Publications for PDP1 Gene

  1. Pyruvate dehydrogenase phosphatase deficiency: identification of the first mutation in two brothers and restoration of activity by protein complementation. (PMID: 15855260) Maj MC … Cameron JM (The Journal of clinical endocrinology and metabolism 2005) 3 4 22 58
  2. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 44 58
  3. Crystallization and preliminary crystallographic studies of the catalytic subunits of human pyruvate dehydrogenase phosphatase isoforms 1 and 2. (PMID: 20208177) Kato J … Kato M (Acta crystallographica. Section F, Structural biology and crystallization communications 2010) 3 22 58
  4. Pyruvate dehydrogenase phosphatase 1 (PDP1) null mutation produces a lethal infantile phenotype. (PMID: 19184109) Cameron JM … Robinson BH (Human genetics 2009) 3 22 58
  5. Decreased PDH activation and glycogenolysis during exercise following fat adaptation with carbohydrate restoration. (PMID: 16188909) Stellingwerff T … Burke LM (American journal of physiology. Endocrinology and metabolism 2006) 3 22 58

Products for PDP1 Gene

Sources for PDP1 Gene

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