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Aliases for PGD Gene

Aliases for PGD Gene

  • Phosphogluconate Dehydrogenase 2 3 5
  • EC 1.1.1.44 4 58
  • 6-Phosphogluconate Dehydrogenase, Decarboxylating 3
  • PGDH 4
  • 6PGD 3

External Ids for PGD Gene

Previous GeneCards Identifiers for PGD Gene

  • GC01P010420
  • GC01P010302
  • GC01P010068
  • GC01P010168
  • GC01P010393
  • GC01P009613
  • GC01P010458

Summaries for PGD Gene

Entrez Gene Summary for PGD Gene

  • 6-phosphogluconate dehydrogenase is the second dehydrogenase in the pentose phosphate shunt. Deficiency of this enzyme is generally asymptomatic, and the inheritance of this disorder is autosomal dominant. Hemolysis results from combined deficiency of 6-phosphogluconate dehydrogenase and 6-phosphogluconolactonase suggesting a synergism of the two enzymopathies. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2015]

GeneCards Summary for PGD Gene

PGD (Phosphogluconate Dehydrogenase) is a Protein Coding gene. Diseases associated with PGD include Cutaneous Leishmaniasis and 6-Phosphogluconate Dehydrogenase Deficiency. Among its related pathways are Metabolism and Pentose phosphate pathway. GO annotations related to this gene include NADP binding and phosphogluconate dehydrogenase (decarboxylating) activity.

UniProtKB/Swiss-Prot for PGD Gene

  • Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH.

Additional gene information for PGD Gene

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

Genomics for PGD Gene

Regulatory Elements for PGD Gene

Enhancers for PGD 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
GH01H010386 1.4 Ensembl ENCODE dbSUPER 77 -10.1 -10130 3 HDAC1 PKNOX1 NFIB ARID4B YY1 ZNF766 FOS ATF7 ZNF362 SMAD5 PGD ENSG00000284735 GC01P010390
GH01H010398 1.4 ENCODE dbSUPER 76.1 +1.4 1366 3 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1 PGD UBIAD1 TARDBP EXOSC10 CENPS-CORT CENPS
GH01H010376 1.5 Ensembl ENCODE dbSUPER 68.2 -19.5 -19454 4 FOXA2 ARID4B SIN3A ZNF2 GATA2 ZNF143 FOS ATF7 RUNX3 DEK PGD EXOSC10 MTOR TARDBP ENSG00000271895 KIF1B PIR46417 PIR47129
GH01H010413 1.5 Ensembl ENCODE dbSUPER 67.2 +16.8 16844 3 HDGF PKNOX1 ATF1 ARNT ZNF766 ELK1 ATF7 PAF1 ZNF592 MEF2D PGD CORT PEX14 DFFA CENPS-CORT CENPS
GH01H010250 1.1 Ensembl ENCODE 59.3 -145.2 -145172 5 HDAC1 PKNOX1 KLF1 TAL1 INSM2 FEZF1 ZBTB40 ZNF664 ZNF121 GATA3 PGD KIF1B RNU6-37P RNU6-828P CTNNBIP1 NMNAT1 GC01M010233 GC01P010298
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PGD on UCSC Golden Path with GeneCards custom track

Promoters for PGD Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000001268 908 2601 HDGF PKNOX1 MLX ARNT ARID4B SIN3A DMAP1 ZNF2 ZBTB7B YY1

Genomic Location for PGD Gene

Chromosome:
1
Start:
10,398,592 bp from pter
End:
10,420,511 bp from pter
Size:
21,920 bases
Orientation:
Plus strand

Genomic View for PGD Gene

Genes around PGD on UCSC Golden Path with GeneCards custom track

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

RefSeq DNA sequence for PGD Gene

Proteins for PGD Gene

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

    Protein Symbol:
    P52209-6PGD_HUMAN
    Recommended name:
    6-phosphogluconate dehydrogenase, decarboxylating
    Protein Accession:
    P52209
    Secondary Accessions:
    • A8K2Y9
    • B4DQJ8
    • Q9BWD8

    Protein attributes for PGD Gene

    Size:
    483 amino acids
    Molecular mass:
    53140 Da
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PGD Gene

    Alternative splice isoforms for PGD Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PGD Gene

Selected DME Specific Peptides for PGD Gene

P52209:
  • GQKGTGKWT
  • LSFYDGYR
  • AGQKGTG
  • LDSFLIEIT
  • NLLLDDFF
  • SGGEEGA
  • RDYFGAH
  • PCCDWVG
  • GDIIIDGGN
  • IIDGGNS
  • QAQRDYFG
  • LSSLKDER
  • PVTLIGEAV
  • SYAQGFML
  • GPSLMPGG
  • FIEKLVPLLD
  • NWTGHGG
  • LNYGGIALMWRGGCIIRSVFLG
  • LQNLLLD
  • IGLAVMG
  • KMVHNGIEY
  • ALYASKIISY

Post-translational modifications for PGD Gene

  • Ubiquitination at Lys119, Lys163, Lys265, and Lys377
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for PGD (PGD)
  • Santa Cruz Biotechnology (SCBT) Antibodies for PGD

Domains & Families for PGD Gene

Gene Families for PGD Gene

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

Graphical View of Domain Structure for InterPro Entry

P52209

UniProtKB/Swiss-Prot:

6PGD_HUMAN :
  • Belongs to the 6-phosphogluconate dehydrogenase family.
Family:
  • Belongs to the 6-phosphogluconate dehydrogenase family.
genes like me logo Genes that share domains with PGD: view

Function for PGD Gene

Molecular function for PGD Gene

GENATLAS Biochemistry:
phosphogluconate dehydrogenase,pentose phosphate pathway
UniProtKB/Swiss-Prot CatalyticActivity:
6-phospho-D-gluconate + NADP(+) = D-ribulose 5-phosphate + CO(2) + NADPH.
UniProtKB/Swiss-Prot Function:
Catalyzes the oxidative decarboxylation of 6-phosphogluconate to ribulose 5-phosphate and CO(2), with concomitant reduction of NADP to NADPH.

Enzyme Numbers (IUBMB) for PGD Gene

Phenotypes From GWAS Catalog for PGD Gene

Gene Ontology (GO) - Molecular Function for PGD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004616 phosphogluconate dehydrogenase (decarboxylating) activity ISS --
GO:0016491 oxidoreductase activity IEA --
genes like me logo Genes that share ontologies with PGD: view
genes like me logo Genes that share phenotypes with PGD: view

Animal Models for PGD Gene

MGI Knock Outs for PGD:
  • Pgd tm1a(EUCOMM)Wtsi

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PGD
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for PGD Gene

Localization for PGD Gene

Subcellular locations from UniProtKB/Swiss-Prot for PGD Gene

Cytoplasm.

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 PGD gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
mitochondrion 3
plasma membrane 2
cytoskeleton 2
peroxisome 2
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (2)
  • Intermediate filaments (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PGD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 21630459
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome IDA 19056867
genes like me logo Genes that share ontologies with PGD: view

Pathways & Interactions for PGD Gene

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

UniProtKB/Swiss-Prot P52209-6PGD_HUMAN

  • Pathway: Carbohydrate degradation; pentose phosphate pathway; D-ribulose 5-phosphate from D-glucose 6-phosphate (oxidative stage): step 3/3.

Gene Ontology (GO) - Biological Process for PGD Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006098 pentose-phosphate shunt IEA,TAS --
GO:0009051 pentose-phosphate shunt, oxidative branch IDA 3858849
GO:0019322 pentose biosynthetic process IEA --
GO:0019521 D-gluconate metabolic process IEA --
GO:0055114 oxidation-reduction process IEA,IDA 3858849
genes like me logo Genes that share ontologies with PGD: view

No data available for SIGNOR curated interactions for PGD Gene

Drugs & Compounds for PGD Gene

(54) Drugs for PGD Gene - From: DrugBank, ClinicalTrials, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Dacarbazine Approved, Investigational Pharma Target, inhibitor 702
Furosemide Approved, Vet_approved Pharma Agonist, Enzyme, inhibitor GABAA receptors antagonist, Na+/2Cl-/K+ (NKCC) symporter inhibitor. Also antagonizes GABAA 201
Gadopentetate dimeglumine Approved Pharma Target, inhibitor 0
Ketotifen Approved Pharma Target, inhibitor 22
Meloxicam Approved, Vet_approved Pharma Enzyme, inhibitor 82

(32) Additional Compounds for PGD Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
nadph
  • 2'-(Dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) Adenosine 5'-ester with 1,4-dihydro-1-b-D-ribofuranosylnicotinamide
  • 2'-(Dihydrogen phosphate) 5'-(trihydrogen pyrophosphate) Adenosine 5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosylnicotinamide
  • Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) P'-5'-ester with 1,4-dihydro-1-beta-D-ribofuranosyl-3-pyridinecarboxamide
  • Adenosine 5'-(trihydrogen diphosphate) 2'-(dihydrogen phosphate) P'-5'-ester with 1,4-dihydro-1-beta-delta-ribofuranosyl-3-pyridinecarboxamide
  • b-NADPH
53-57-6
D-Ribulose 5-phosphate
  • alpha-D-Ribose 5-phosphate
  • D-Ribulose 5-phosphate
  • Erythro-Pentulose 5-phosphate
  • Ribulose 5-phosphate
  • Ribulose phosphate
4151-19-3
Hydrogen Ion
  • Hydrogen cation
  • Hydron
  • Proton
NADP
  • Adenine-nicotinamide dinucleotide phosphate
  • b-NADP
  • b-Nicotinamide adenine dinucleotide phosphate
  • b-TPN
  • beta-NADP
53-59-8
genes like me logo Genes that share compounds with PGD: view

Transcripts for PGD Gene

Unigene Clusters for PGD Gene

Phosphogluconate dehydrogenase:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PGD
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

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

ExUns: 1 ^ 2a · 2b · 2c · 2d · 2e ^ 3a · 3b · 3c · 3d ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c ^ 10a · 10b · 10c ^
SP1: - -
SP2: - - -
SP3: -
SP4: - - - -
SP5: - - -
SP6: - - - - - - -
SP7: - - -
SP8: -
SP9: - - - - - - - - - - -
SP10: - - - - - - - - - - -
SP11: - - - - - - - -
SP12:
SP13:

ExUns: 11a · 11b · 11c ^ 12 ^ 13a · 13b · 13c ^ 14a · 14b
SP1: - - -
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11: -
SP12: -
SP13: -

Relevant External Links for PGD Gene

GeneLoc Exon Structure for
PGD
ECgene alternative splicing isoforms for
PGD

Expression for PGD Gene

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

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

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

This gene is overexpressed in Whole Blood (x19.2) and Esophagus - Mucosa (x5.5).

Protein differential expression in normal tissues from HIPED for PGD Gene

This gene is overexpressed in Neutrophil (6.4).

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



Protein tissue co-expression partners for PGD Gene

NURSA nuclear receptor signaling pathways regulating expression of PGD Gene:

PGD

SOURCE GeneReport for Unigene cluster for PGD Gene:

Hs.464071

Evidence on tissue expression from TISSUES for PGD Gene

  • Blood(4.8)
  • Lung(4.8)
  • Liver(4.7)
  • Nervous system(4.7)
  • Heart(4.3)
  • Eye(3.5)
  • Intestine(3)
  • Skin(2.9)
  • Kidney(2.8)
  • Bone marrow(2.2)
  • Thyroid gland(2.2)
  • Muscle(2.1)
genes like me logo Genes that share expression patterns with PGD: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PGD Gene

Orthologs for PGD Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for PGD Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PGD 33 34
  • 94.55 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PGD 34
  • 93 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PGD 34
  • 89 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PGD 33 34
  • 88.75 (n)
cow
(Bos Taurus)
Mammalia PGD 33 34
  • 88.34 (n)
mouse
(Mus musculus)
Mammalia Pgd 33 16 34
  • 87.85 (n)
rat
(Rattus norvegicus)
Mammalia LOC100360180 33
  • 86.75 (n)
chicken
(Gallus gallus)
Aves PGD 33 34
  • 80.43 (n)
lizard
(Anolis carolinensis)
Reptilia PGD 34
  • 89 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia pgd 33
  • 74.43 (n)
Str.15342 33
African clawed frog
(Xenopus laevis)
Amphibia MGC68486 33
zebrafish
(Danio rerio)
Actinopterygii pgd 33 34
  • 75.5 (n)
Dr.6619 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.45 33
fruit fly
(Drosophila melanogaster)
Insecta Pgd 35 33 34
  • 67.15 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004197 33
  • 66.81 (n)
worm
(Caenorhabditis elegans)
Secernentea T25B9.9 33 34
  • 63.62 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GND2 34
  • 64 (a)
OneToMany
GND1 33 34 36
  • 62.35 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A09339g 33
  • 63.38 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AFR129W 33
  • 63.26 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT5G41670 33
  • 53.43 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6832 33
rice
(Oryza sativa)
Liliopsida Os11g0484500 33
  • 55.44 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 76 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU03100 33
  • 65.97 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC660.16 33
  • 61.31 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.13189 33
Species where no ortholog for PGD was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • 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)
  • 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)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PGD Gene

ENSEMBL:
Gene Tree for PGD (if available)
TreeFam:
Gene Tree for PGD (if available)

Paralogs for PGD Gene

Pseudogenes.org Pseudogenes for PGD Gene

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

No data available for Paralogs for PGD Gene

Variants for PGD Gene

Sequence variations from dbSNP and Humsavar for PGD Gene

SNP ID Clin Chr 01 pos Sequence Context AA Info Type
rs1000240584 -- 10,416,525(+) TTTTC(A/C)TGCGC intron-variant
rs1000284724 -- 10,410,715(+) GGGCC(A/G)GAATG intron-variant
rs1000292932 -- 10,416,699(+) TTTCT(C/T)TTACG intron-variant
rs1000521546 -- 10,410,376(+) GGCAG(G/T)TGTTG intron-variant
rs1000530304 -- 10,411,844(+) GTTGT(C/G)CCACA intron-variant

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

Variant ID Type Subtype PubMed ID
esv1010529 CNV deletion 20482838
esv2758920 CNV gain+loss 17122850
esv2764192 CNV gain 21179565
nsv8213 CNV gain 18304495

Variation tolerance for PGD Gene

Residual Variation Intolerance Score: 11.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.01; 60.32% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PGD Gene

Human Gene Mutation Database (HGMD)
PGD
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PGD

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

Disorders for PGD Gene

MalaCards: The human disease database

(5) MalaCards diseases for PGD Gene - From: HGMD, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
cutaneous leishmaniasis
  • asian desert cutaneous leishmaniasis
6-phosphogluconate dehydrogenase deficiency
  • 6-phosphogluconate dehydrogenase
visceral leishmaniasis
  • infection by visceral leishmaniasis
glucosephosphate dehydrogenase deficiency
  • deficiency of g-6pd
sleeping sickness
  • african sleeping sickness
- elite association - COSMIC cancer census association via MalaCards
Search PGD in MalaCards View complete list of genes associated with diseases

Relevant External Links for PGD

Genetic Association Database (GAD)
PGD
Human Genome Epidemiology (HuGE) Navigator
PGD
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PGD
genes like me logo Genes that share disorders with PGD: view

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

Publications for PGD Gene

  1. Identification of a cDNA encoding 6-phosphogluconate dehydrogenase from a human heart cDNA library. (PMID: 8978909) Tsui SK … Lee CY (Biochemical genetics 1996) 3 4 22 60
  2. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. (PMID: 20628086) Bailey SD … DREAM investigators (Diabetes care 2010) 3 45 60
  3. Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers. (PMID: 20676096) Zhang H … Zhou G (Nature genetics 2010) 3 45 60
  4. 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 60
  5. 6-Phosphogluconate dehydrogenase: the mechanism of action investigated by a comparison of the enzyme from different species. (PMID: 9920387) Rippa M … Hanau S (Biochimica et biophysica acta 1998) 3 22 60

Products for PGD Gene

Sources for PGD Gene

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