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 transcri... See more...

Aliases for PGD Gene

Aliases for PGD Gene

  • Phosphogluconate Dehydrogenase 2 3 5
  • 6-Phosphogluconate Dehydrogenase, Decarboxylating 3 4
  • EC 1.1.1.44 4 51
  • 6PGD 3
  • PGDH 4
  • PGD 5

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-Phosphogluconolactonase Deficiency. Among its related pathways are Pentose phosphate pathway and NRF2 pathway. Gene Ontology (GO) annotations related to this gene include NADP binding and phosphogluconate dehydrogenase (decarboxylating) activity.

UniProtKB/Swiss-Prot Summary for PGD Gene

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

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

Genomics for PGD Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for PGD 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 PGD on the GeneHancer Hub at the UCSC Golden Path

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

Top Transcription factor binding sites by QIAGEN in the PGD gene promoter:
  • Bach1
  • C/EBPalpha
  • HOXA5
  • NF-1
  • NF-1/L
  • NF-AT
  • Sox5

Genomic Locations for PGD Gene

Genomic Locations for PGD Gene
chr1:10,398,592-10,420,511
(GRCh38/hg38)
Size:
21,920 bases
Orientation:
Plus strand
chr1:10,458,649-10,480,201
(GRCh37/hg19)
Size:
21,553 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 Lys38, Lys59, Lys119, Lys163, Lys265, and Lys377
  • Modification sites at PhosphoSitePlus

Domains & Families for PGD Gene

Gene Families for PGD Gene

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

Protein Domains for PGD Gene

InterPro:
Blocks:
  • 6-phosphogluconate dehydrogenase, NAD binding domain
ProtoNet:

Suggested Antigen Peptide Sequences for PGD Gene

GenScript: Design optimal peptide antigens:
  • 6-phosphogluconate dehydrogenase, decarboxylating (6PGD_HUMAN)
  • 6-phosphogluconate dehydrogenase, decarboxylating (A8K2Y9_HUMAN)
  • 6-phosphogluconate dehydrogenase, decarboxylating (B4DQJ8_HUMAN)
  • 6-phosphogluconate dehydrogenase, decarboxylating (B4DV68_HUMAN)
  • 6-phosphogluconate dehydrogenase, decarboxylating (F5H0L3_HUMAN)

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

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.
UniProtKB/Swiss-Prot CatalyticActivity:
Reaction=6-phospho-D-gluconate + NADP(+) = CO2 + D-ribulose 5-phosphate + NADPH; Xref=Rhea:RHEA:10116, ChEBI:CHEBI:16526, ChEBI:CHEBI:57783, ChEBI:CHEBI:58121, ChEBI:CHEBI:58349, ChEBI:CHEBI:58759; EC=1.1.1.44;.
GENATLAS Biochemistry:
phosphogluconate dehydrogenase,pentose phosphate pathway

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 IEA,ISS --
GO:0016491 oxidoreductase activity IEA --
GO:0050661 NADP binding IEA,IBA 21873635
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 Pgd<tm1a(EUCOMM)Wtsi>

Animal Model Products

CRISPR Products

Inhibitory RNA Products

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

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
cytosol 5
extracellular 4
nucleus 4
plasma membrane 3
mitochondrion 3
cytoskeleton 2
peroxisome 2
endoplasmic reticulum 2
endosome 1
lysosome 1
golgi apparatus 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 HDA 21630459
GO:0005737 cytoplasm IEA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome HDA 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:0046177 D-gluconate catabolic process IBA 21873635
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

(45) 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 193
Furosemide Approved, Vet_approved Pharma Agonist, Inhibitor, Inhibition, Enzyme, inhibitor GABAA receptors antagonist, Na+/2Cl-/K+ (NKCC) symporter inhibitor. Also antagonizes GABAA 263
Ketotifen Approved Pharma Target, inhibitor 29
Meloxicam Approved, Vet_approved Pharma Enzyme, inhibitor 103
Methotrexate Approved Pharma Enzyme, inhibitor Folate antagonist,inhibits DFHR 1825

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

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
D-Ribulose 5-phosphate
  • D-erythro-Pent-2-ulose 5-(dihydrogen phosphate)
  • D-erythro-Pent-2-ulose 5-(dihydrogen phosphoric acid)
  • D-Ribulose 5-phosphoric acid
4151-19-3
Hydrogen Ion
  • H+
  • H(+)
  • Hydrogen cation
  • Hydron
  • Proton
genes like me logo Genes that share compounds with PGD: view

Transcripts for PGD Gene

mRNA/cDNA for PGD Gene

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

CRISPR Products

Inhibitory RNA Products

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

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

Expression for PGD Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and 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, MaxQB, and MOPED for PGD Gene



Protein tissue co-expression partners for PGD Gene

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

SOURCE GeneReport for Unigene cluster for PGD Gene:

Hs.464071

Evidence on tissue expression from TISSUES for PGD Gene

  • Lung(4.9)
  • Blood(4.8)
  • Nervous system(4.8)
  • Liver(4.7)
  • Heart(4.6)
  • Eye(3.7)
  • Skin(3.6)
  • Intestine(3.4)
  • Kidney(3.2)
  • Bone marrow(2.8)
  • Muscle(2.7)
  • Thyroid gland(2.6)
  • Spleen(2.4)
  • Stomach(2.2)
  • Lymph node(2.2)
  • Pancreas(2.1)
genes like me logo Genes that share expression patterns with PGD: view

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 30 31
  • 94.55 (n)
OneToOne
Platypus
(Ornithorhynchus anatinus)
Mammalia PGD 31
  • 93 (a)
OneToOne
Oppossum
(Monodelphis domestica)
Mammalia PGD 31
  • 89 (a)
OneToOne
Dog
(Canis familiaris)
Mammalia PGD 30 31
  • 88.75 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia PGD 30 31
  • 88.34 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Pgd 30 17 31
  • 87.85 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia LOC100360180 30
  • 86.75 (n)
Chicken
(Gallus gallus)
Aves PGD 30 31
  • 80.43 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia PGD 31
  • 89 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia pgd 30
  • 74.43 (n)
Str.15342 30
African clawed frog
(Xenopus laevis)
Amphibia MGC68486 30
Zebrafish
(Danio rerio)
Actinopterygii pgd 30 31
  • 75.5 (n)
OneToOne
Dr.6619 30
Rainbow Trout
(Oncorhynchus mykiss)
Actinopterygii Omy.45 30
Fruit Fly
(Drosophila melanogaster)
Insecta Pgd 30 31 32
  • 67.15 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP004197 30
  • 66.81 (n)
Worm
(Caenorhabditis elegans)
Secernentea T25B9.9 30 31
  • 63.62 (n)
OneToOne
Baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes GND2 31
  • 64 (a)
OneToMany
GND1 30 31 33
  • 62.35 (n)
OneToMany
K. Lactis Yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0A09339g 30
  • 63.38 (n)
A. gosspyii yeast
(Eremothecium gossypii)
Saccharomycetes AGOS_AFR129W 30
  • 63.26 (n)
Thale Cress
(Arabidopsis thaliana)
eudicotyledons AT5G41670 30
  • 53.43 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.6832 30
Rice
(Oryza sativa)
Liliopsida Os11g0484500 30
  • 55.44 (n)
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 31
  • 76 (a)
OneToOne
Bread mold
(Neurospora crassa)
Ascomycetes NCU03100 30
  • 65.97 (n)
Fission Yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPBC660.16 30
  • 61.31 (n)
Sea Vase
(Ciona intestinalis)
Ascidiacea Cin.13189 30
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)
Aminode:
Evolutionary constrained regions (ECRs) for PGD: view image

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, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for PGD Gene

SNP ID Clinical significance and condition Chr 01 pos Variation AA Info Type
716657 Benign: not provided 10,413,142(+) C/T SYNONYMOUS_VARIANT
734224 Benign: not provided 10,417,384(+) C/T SYNONYMOUS_VARIANT
rs11547610 - p.Ala268Ser

Additional dbSNP identifiers (rs#s) for PGD Gene

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)

Additional Variant Information for PGD Gene

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

SNP Genotyping and Copy Number Assay Products

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

Disorders for PGD Gene

MalaCards: The human disease database

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

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

Additional Disease Information for PGD

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
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 23
  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 41
  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 41
  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
  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 23

Products for PGD Gene

Sources for PGD Gene