Pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate and links glycolysis to the tricarboxylic acid cycle and fatty acid synthesis. The dephosphorylation and reactivation of PDC is catalyzed by pyruvate dehydrogenase phosphatase (PDP). The dimeric PDP has a catalytic subunit and a regulatory subunit. This gene encodes the FAD-containing regul... See more...

Aliases for PDPR Gene

Aliases for PDPR Gene

  • Pyruvate Dehydrogenase Phosphatase Regulatory Subunit 2 3 5
  • Pyruvate Dehydrogenase Phosphatase Regulatory Subunit, Mitochondrial 3 4
  • PDP3 2 3
  • KIAA1990 4
  • PDPR 5
  • PDPr 4

External Ids for PDPR Gene

Previous GeneCards Identifiers for PDPR Gene

  • GC16P069883
  • GC16P069923
  • GC16P068705
  • GC16P070148
  • GC16P056002

Summaries for PDPR Gene

Entrez Gene Summary for PDPR Gene

  • Pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate and links glycolysis to the tricarboxylic acid cycle and fatty acid synthesis. The dephosphorylation and reactivation of PDC is catalyzed by pyruvate dehydrogenase phosphatase (PDP). The dimeric PDP has a catalytic subunit and a regulatory subunit. This gene encodes the FAD-containing regulatory subunit of PDP. The encoded protein acts to decrease the sensitivity of the PDP catalytic subunit to magnesium ions. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2017]

GeneCards Summary for PDPR Gene

PDPR (Pyruvate Dehydrogenase Phosphatase Regulatory Subunit) is a Protein Coding gene. Diseases associated with PDPR include Anismus and Spinocerebellar Ataxia 23. Among its related pathways are Metabolism and Pyruvate metabolism and Citric Acid (TCA) cycle. Gene Ontology (GO) annotations related to this gene include oxidoreductase activity and aminomethyltransferase activity. An important paralog of this gene is SARDH.

UniProtKB/Swiss-Prot Summary for PDPR Gene

  • Decreases the sensitivity of PDP1 to magnesium ions, and this inhibition is reversed by the polyamine spermine.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for PDPR Gene

Genomics for PDPR Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PDPR Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PDPR on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for PDPR

Top Transcription factor binding sites by QIAGEN in the PDPR gene promoter:
  • c-Myc
  • FOXI1
  • FOXO4
  • HFH-3
  • Max1
  • Pax-4a
  • USF-1
  • USF-1:USF-2
  • USF1
  • USF2

Genomic Locations for PDPR Gene

Latest Assembly
chr16:70,113,626-70,163,631
(GRCh38/hg38)
Size:
50,006 bases
Orientation:
Plus strand

Previous Assembly
chr16:70,147,529-70,196,440
(GRCh37/hg19 by Entrez Gene)
Size:
48,912 bases
Orientation:
Plus strand

chr16:70,147,529-70,195,203
(GRCh37/hg19 by Ensembl)
Size:
47,675 bases
Orientation:
Plus strand

Genomic View for PDPR Gene

Genes around PDPR on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PDPR Gene

Proteins for PDPR Gene

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

    Protein Symbol:
    Q8NCN5-PDPR_HUMAN
    Recommended name:
    Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
    Protein Accession:
    Q8NCN5
    Secondary Accessions:
    • A7E298
    • A8K8Y7
    • B3KSE1
    • Q6AI20
    • Q6AWC9

    Protein attributes for PDPR Gene

    Size:
    879 amino acids
    Molecular mass:
    99364 Da
    Quaternary structure:
    • Heterodimer of a catalytic (PDP1) and a regulatory (PDPR) subunit.
    SequenceCaution:
    • Sequence=BAC02699.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAF85191.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for PDPR Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PDPR Gene

Post-translational modifications for PDPR Gene

  • Ubiquitination at Lys100
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PDPR Gene

Domains & Families for PDPR Gene

Gene Families for PDPR Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PDPR Gene

InterPro:
Blocks:
  • Glycine cleavage T protein (aminomethyl transferase)

Suggested Antigen Peptide Sequences for PDPR Gene

GenScript: Design optimal peptide antigens:
  • cDNA FLJ36072 fis, clone TESTI2019669, highly similar to Homo sapiens pyruvate dehydrogenase phosphatase regulatory subunit (PDPR), mRNA (B3KSE1_HUMAN)
  • Pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial (PDPR_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q8NCN5

UniProtKB/Swiss-Prot:

PDPR_HUMAN :
  • Belongs to the GcvT family.
Family:
  • Belongs to the GcvT family.
genes like me logo Genes that share domains with PDPR: view

Function for PDPR Gene

Molecular function for PDPR Gene

UniProtKB/Swiss-Prot Function:
Decreases the sensitivity of PDP1 to magnesium ions, and this inhibition is reversed by the polyamine spermine.

Phenotypes From GWAS Catalog for PDPR Gene

Gene Ontology (GO) - Molecular Function for PDPR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
GO:0016491 oxidoreductase activity IEA,IBA 21873635
genes like me logo Genes that share ontologies with PDPR: view
genes like me logo Genes that share phenotypes with PDPR: view

Animal Models for PDPR Gene

MGI Knock Outs for PDPR:
  • Pdpr Pdpr<tm1b(EUCOMM)Wtsi>

Animal Models for research

  • Taconic Biosciences Mouse Models for PDPR

Inhibitory RNAs for research

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

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PDPR Gene

Localization for PDPR Gene

Subcellular locations from UniProtKB/Swiss-Prot for PDPR Gene

Mitochondrion matrix.

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 PDPR gene
Compartment Confidence
mitochondrion 4
cytosol 3
plasma membrane 1
extracellular 1
cytoskeleton 1
peroxisome 1
nucleus 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PDPR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IBA 21873635
GO:0005739 mitochondrion IBA 21873635
GO:0005759 mitochondrial matrix TAS --
genes like me logo Genes that share ontologies with PDPR: view

Pathways & Interactions for PDPR Gene

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

Gene Ontology (GO) - Biological Process for PDPR Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0010510 regulation of acetyl-CoA biosynthetic process from pyruvate TAS --
GO:0055114 oxidation-reduction process IEA --
genes like me logo Genes that share ontologies with PDPR: view

No data available for SIGNOR curated interactions for PDPR Gene

Drugs & Compounds for PDPR Gene

(4) Drugs for PDPR Gene - From: HMDB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Magnesium Approved, Experimental, Investigational Pharma 0
putrescine Experimental Pharma 0
spermidine Experimental Pharma 0
spermine Experimental Nutra 0

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
N1-acetylspermine
  • N'-acetylspermine
  • N'-monoacetylspermine
  • N(1)-Acetylspermine
  • N-(3-((4-((3-Aminopropyl)amino)butyl)amino)propyl)-acetamide
  • N-Acetylspermine
25593-72-0
Norspermidine
  • 1,7-Diamino-4-azaheptane
  • 3,3'-Iminobis(propylamine)
  • 3,3'-Iminobispropylamine
  • 3,3'-Iminodi(propylamine)
  • 3,3-Diaminodipropylamine
56-18-8
genes like me logo Genes that share compounds with PDPR: view

Transcripts for PDPR Gene

mRNA/cDNA for PDPR Gene

4 REFSEQ mRNAs :
18 NCBI additional mRNA sequence :
11 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

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

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

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c
SP1:
SP2: -
SP3: - -

Relevant External Links for PDPR Gene

GeneLoc Exon Structure for
PDPR

Expression for PDPR Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for PDPR Gene

This gene is overexpressed in Lymph node (8.8) and Uterus (7.7).

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



Protein tissue co-expression partners for PDPR Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for PDPR

SOURCE GeneReport for Unigene cluster for PDPR Gene:

Hs.744043

Evidence on tissue expression from TISSUES for PDPR Gene

  • Nervous system(4.8)
  • Kidney(2)
genes like me logo Genes that share expression patterns with PDPR: view

Primer products for research

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 PDPR Gene

Orthologs for PDPR Gene

This gene was present in the common ancestor of animals.

Orthologs for PDPR Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia PDPR 30
  • 100 (a)
OneToOne
LOC454207 29
  • 99.61 (n)
Dog
(Canis familiaris)
Mammalia PDPR 29 30
  • 91.25 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Pdpr 29
  • 88.65 (n)
Mouse
(Mus musculus)
Mammalia Pdpr 29 16 30
  • 88.61 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PDPR 29 30
  • 88.61 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PDPR 30
  • 86 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PDPR 30
  • 86 (a)
OneToOne
Chicken
(Gallus gallus)
Aves PDPR 29 30
  • 77.36 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PDPR 30
  • 84 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pdpr 29
  • 72.11 (n)
Str.18754 29
Zebrafish
(Danio rerio)
Actinopterygii pdpr 29
  • 71.2 (n)
PDPR 30
  • 70 (a)
OneToOne
zgc63662 29
Fruit Fly
(Drosophila melanogaster)
Insecta CG3626 29 30
  • 53.38 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004715 29
  • 52.31 (n)
Worm
(Caenorhabditis elegans)
Secernentea CELE_Y106G6H.5 29
  • 47.22 (n)
Y106G6H.5 30
  • 36 (a)
OneToOne
Species where no ortholog for PDPR was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (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 PDPR Gene

ENSEMBL:
Gene Tree for PDPR (if available)
TreeFam:
Gene Tree for PDPR (if available)
Aminode:
Evolutionary constrained regions (ECRs) for PDPR: view image
Alliance of Genome Resources:
Additional Orthologs for PDPR

Paralogs for PDPR Gene

(2) SIMAP similar genes for PDPR Gene using alignment to 9 proteins:

  • PDPR_HUMAN
  • A8MT40_HUMAN
  • B3KSE1_HUMAN
  • B7ZAR9_HUMAN
  • H3BQG3_HUMAN
  • H3BRS5_HUMAN
  • H3BU60_HUMAN
  • H3BUH3_HUMAN
  • H3BV59_HUMAN

Pseudogenes.org Pseudogenes for PDPR Gene

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

Variants for PDPR Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PDPR Gene

SNP ID Clinical significance and condition Chr 16 pos Variation AA Info Type
rs200469748 Not Provided: not provided 70,120,577(+) A/G
NM_017990.4(PDPR):c.85A>G (p.Thr29Ala)
MISSENSE_VARIANT,FIVE_PRIME_UTR_VARIANT,INTRON
rs202246074 Conflicting Interpretations: Joubert syndrome; not provided 70,142,278(+) G/T
NM_017990.5(PDPR):c.1360G>T
MISSENSE
rs2549532 Benign: not provided 70,127,360(+) T/Cp.Tyr109His
NM_017990.5(PDPR):c.328T>C (p.Tyr110His)
MISSENSE_VARIANT,FIVE_PRIME_UTR

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for PDPR Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

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

Variant ID Type Subtype PubMed ID
dgv1365n106 CNV duplication 24896259
dgv1626e59 CNV duplication 20981092
dgv1627e59 CNV duplication 20981092
dgv25e213 CNV gain 24956385
dgv2997n100 CNV loss 25217958
dgv2998n100 CNV gain 25217958
dgv3000n100 CNV gain+loss 25217958
dgv3002n100 CNV loss 25217958
dgv3003n100 CNV gain 25217958
dgv3004n100 CNV gain 25217958
dgv3005n100 CNV gain+loss 25217958
dgv3006n100 CNV loss 25217958
dgv3007n100 CNV loss 25217958
dgv3008n100 CNV gain 25217958
dgv3009n100 CNV gain 25217958
dgv3010n100 CNV gain 25217958
dgv3011n100 CNV gain+loss 25217958
dgv3012n100 CNV loss 25217958
dgv3013n100 CNV gain 25217958
dgv485n67 CNV loss 20364138
dgv486n67 CNV gain 20364138
dgv5178n54 CNV loss 21841781
dgv5179n54 CNV loss 21841781
dgv5180n54 CNV loss 21841781
dgv5181n54 CNV loss 21841781
dgv5182n54 CNV loss 21841781
dgv5183n54 CNV loss 21841781
dgv5184n54 CNV loss 21841781
dgv5185n54 CNV gain 21841781
dgv527e214 CNV gain 21293372
dgv848e212 CNV loss 25503493
dgv849e212 CNV gain 25503493
dgv850e212 CNV loss 25503493
dgv851e212 CNV loss 25503493
esv1007882 CNV loss 20482838
esv25519 CNV gain+loss 19812545
esv2577915 CNV gain 19546169
esv2657437 CNV deletion 23128226
esv2714669 CNV deletion 23290073
esv2758652 CNV gain+loss 17122850
esv2760404 CNV gain+loss 21179565
esv2762188 CNV gain+loss 21179565
esv29970 CNV loss 17803354
esv3333319 CNV duplication 20981092
esv33745 CNV gain+loss 17666407
esv3411986 CNV duplication 20981092
esv3426771 CNV duplication 20981092
esv3571454 CNV gain 25503493
esv3571465 CNV gain 25503493
esv3638943 CNV loss 21293372
esv3638944 CNV gain 21293372
esv3638945 CNV loss 21293372
esv3892879 CNV gain 25118596
esv3892880 CNV loss 25118596
esv997919 CNV loss 20482838
nsv1058068 CNV gain+loss 25217958
nsv1060953 CNV gain 25217958
nsv1062268 CNV gain+loss 25217958
nsv1077831 CNV duplication 25765185
nsv1127511 CNV deletion 24896259
nsv1131275 CNV deletion 24896259
nsv1149117 CNV duplication 26484159
nsv1160430 CNV duplication 26073780
nsv1853 CNV deletion 18451855
nsv428328 CNV gain+loss 18775914
nsv436059 CNV insertion 17901297
nsv442725 CNV gain 18776908
nsv469646 CNV gain 16826518
nsv471391 CNV gain 19718026
nsv471695 CNV loss 15918152
nsv482195 CNV gain 20164927
nsv514810 CNV gain+loss 21397061
nsv572912 CNV gain 21841781
nsv572913 CNV gain 21841781
nsv572916 CNV loss 21841781
nsv572918 CNV gain+loss 21841781
nsv572923 CNV loss 21841781
nsv572924 CNV loss 21841781
nsv572927 CNV loss 21841781
nsv572928 CNV loss 21841781
nsv572930 CNV loss 21841781
nsv572931 CNV loss 21841781
nsv572935 CNV loss 21841781
nsv7285 OTHER inversion 18451855
nsv820087 CNV loss 19587683
nsv820860 CNV duplication 20802225
nsv827719 CNV gain 20364138
nsv827723 CNV loss 20364138
nsv827728 CNV loss 20364138
nsv833269 CNV loss 17160897
nsv833271 CNV gain+loss 17160897
nsv9455 CNV gain+loss 18304495
nsv952048 CNV duplication 24416366
nsv960372 CNV duplication 23825009
nsv977991 CNV duplication 23825009
nsv977992 CNV duplication 23825009

Variation tolerance for PDPR Gene

Residual Variation Intolerance Score: 97.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.23; 81.07% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PDPR Gene

Human Gene Mutation Database (HGMD)
PDPR
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PDPR
Leiden Open Variation Database (LOVD)
PDPR

SNP Genotyping and Copy Number Assays for research

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

Disorders for PDPR Gene

MalaCards: The human disease database

(3) MalaCards diseases for PDPR Gene - From: COP

- elite association - COSMIC cancer census association via MalaCards
Search PDPR in MalaCards View complete list of genes associated with diseases

Additional Disease Information for PDPR

Human Genome Epidemiology Navigator
(HuGE)
Atlas
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
Open Targets Platform
genes like me logo Genes that share disorders with PDPR: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PDPR Gene

Publications for PDPR Gene

  1. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. (PMID: 20877624) Hendrickson SL … O'Brien SJ (PloS one 2010) 3 40
  2. Novel association strategy with copy number variation for identifying new risk Loci of human diseases. (PMID: 20808825) Chen X … Kong X (PloS one 2010) 3 40
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Characterization of size-fractionated cDNA libraries generated by the in vitro recombination-assisted method. (PMID: 12056414) Ohara O … Koseki H (DNA research : an international journal for rapid publication of reports on genes and genomes 2002) 3 4
  5. Cloning, expression, and properties of the regulatory subunit of bovine pyruvate dehydrogenase phosphatase. (PMID: 9395502) Lawson JE … Reed LJ (The Journal of biological chemistry 1997) 2 3

Products for PDPR Gene

Sources for PDPR Gene