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PGD phosphogluconate dehydrogenase [ Homo sapiens (human) ]

Gene ID: 5226, updated on 7-Apr-2024

Summary

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Official Symbol
PGDprovided by HGNC
Official Full Name
phosphogluconate dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:8891
See related
Ensembl:ENSG00000142657 MIM:172200; AllianceGenome:HGNC:8891
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
6PGD
Summary
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]
Expression
Broad expression in esophagus (RPKM 163.6), bone marrow (RPKM 118.1) and 22 other tissues See more
Orthologs
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Genomic context

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Location:
1p36.22
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (10399064..10420511)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (9942673..9964125)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (10459121..10480568)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene kinesin family member 1B Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:10367507-10368007 Neighboring gene MPRA-validated peak67 silencer Neighboring gene RNA, U6 small nuclear 37, pseudogene Neighboring gene RNA, 7SL, cytoplasmic 731, pseudogene Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr1:10378039-10378580 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr1:10385546-10386745 Neighboring gene MPRA-validated peak69 silencer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10437772-10438272 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 147 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 245 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:10459711-10459887 Neighboring gene MPRA-validated peak70 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10485963-10486568 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:10486569-10487174 Neighboring gene Sharpr-MPRA regulatory region 15261 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 246 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:10493213-10493793 Neighboring gene CENPS-CORT readthrough Neighboring gene centromere protein S Neighboring gene cortistatin

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. 6PGD Upregulation is Associated with Chemo- and Immuno-Resistance of Renal Cell Carcinoma via AMPK Signaling-Dependent NADPH-Mediated Metabolic Reprograming. Cao J, et al. Am J Med Sci, 2020 Sep. PMID 32829780
  2. Inhibiting 6-phosphogluconate dehydrogenase enhances chemotherapy efficacy in cervical cancer via AMPK-independent inhibition of RhoA and Rac1. Guo H, et al. Clin Transl Oncol, 2019 Apr. PMID 30182212
  3. Inhibiting 6-phosphogluconate dehydrogenase reverses doxorubicin resistance in anaplastic thyroid cancer via inhibiting NADPH-dependent metabolic reprogramming. Ma L, et al. Biochem Biophys Res Commun, 2018 Apr 15. PMID 29534964
  4. 1p36.22 region containing PGD gene is frequently gained in human cervical cancer. Lee M, et al. J Obstet Gynaecol Res, 2014 Feb. PMID 24125036
  5. [Intensity of pentose phosphate metabolism of carbohydrates in various brain areas in normal and starved animals]. Kerimov BF. Vopr Med Khim, 2002 Sep-Oct. PMID 12498092

See all (99) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Critical Role of 6-Phosphogluconate Dehydrogenase in TAp73-Mediated Cancer Cell Proliferation.
    Title: Critical Role of 6-Phosphogluconate Dehydrogenase in TAp73-Mediated Cancer Cell Proliferation.
  2. HIF-1alpha regulates cellular metabolism, and Imatinib resistance by targeting phosphogluconate dehydrogenase in gastrointestinal stromal tumors.
    Title: HIF-1α regulates cellular metabolism, and Imatinib resistance by targeting phosphogluconate dehydrogenase in gastrointestinal stromal tumors.
  3. 6PGD Upregulation is Associated with Chemo- and Immuno-Resistance of Renal Cell Carcinoma via AMPK Signaling-Dependent NADPH-Mediated Metabolic Reprograming.
    Title: 6PGD Upregulation is Associated with Chemo- and Immuno-Resistance of Renal Cell Carcinoma via AMPK Signaling-Dependent NADPH-Mediated Metabolic Reprograming.
  4. 6-phosphogluconate dehydrogenase (6PGD) is aberrantly upregulated and activated in cervical cancer cells and patient tissues compared to normal counterparts. 6PGD inhibition decreases growth and migration, and enhances chemosensitivity in cervical cancer. Inhibition of 6PGD activates AMP-activated protein kinase and decreases rhoA GTP-binding protein and rac1 GTP-binding protein activities.
    Title: Inhibiting 6-phosphogluconate dehydrogenase enhances chemotherapy efficacy in cervical cancer via AMPK-independent inhibition of RhoA and Rac1.
  5. identified that 6-phosphogluconate dehydrogenase (6PGD) is critically involved in the development of anaplastic thyroid cancer (ATC) resistance to doxorubicin. 6PGD inhibition disrupts metabolic reprogramming in doxorubicin-resistant ATC cells.
    Title: Inhibiting 6-phosphogluconate dehydrogenase reverses doxorubicin resistance in anaplastic thyroid cancer via inhibiting NADPH-dependent metabolic reprogramming.
  6. Studies indicate link between the 6-phosphogluconate dehydrogenase, oxidative pentose phosphate pathway (PPP) and lipogenesis through Ru-5-P-dependent inhibition of serine/threonine protein kinase LKB1-AMPK signalling.
    Title: 6-Phosphogluconate dehydrogenase links oxidative PPP, lipogenesis and tumour growth by inhibiting LKB1-AMPK signalling.
  7. copy number gain of the PGD gene was consistently identified in cervical cancers but not in the normal tissues
    Title: 1p36.22 region containing PGD gene is frequently gained in human cervical cancer.
  8. Results show that 6PGD activity is upregulated with increased lysine acetylation in primary leukemia cells from human patients, providing mechanistic insights into 6PGD upregulation in cancer cells.
    Title: Lysine acetylation activates 6-phosphogluconate dehydrogenase to promote tumor growth.
  9. Expression of 6PGD positively correlates with advancing stage of lung carcinoma. Knockdown of 6PGD by shRNA potently inhibits c-Met tyrosine phosphorylation.
    Title: 6-Phosphogluconate dehydrogenase regulates tumor cell migration in vitro by regulating receptor tyrosine kinase c-Met.
  10. Glycolytic cancer cells lacking 6-phosphogluconate dehydrogenase metabolize glucose to induce senescence
    Title: Glycolytic cancer cells lacking 6-phosphogluconate dehydrogenase metabolize glucose to induce senescence.
Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study identifies 1p36.22 as a new susceptibility locus for hepatocellular carcinoma in chronic hepatitis B virus carriers.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables NADP binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphogluconate dehydrogenase (decarboxylating) activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables phosphogluconate dehydrogenase (decarboxylating) activity ISS
Inferred from Sequence or Structural Similarity
more info
  
Process Evidence Code Pubs
involved_in D-gluconate catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in pentose biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in pentose-phosphate shunt ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in pentose-phosphate shunt, oxidative branch IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in pentose-phosphate shunt, oxidative branch IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytosol IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in nucleus HDA PubMed 

General protein information

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Preferred Names
6-phosphogluconate dehydrogenase, decarboxylating
NP_001291380.1
NP_001291381.1
NP_002622.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001304451.2 → NP_001291380.1  6-phosphogluconate dehydrogenase, decarboxylating isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AK304423, AL139424, BC000368, HY049516, HY245069
    UniProtKB/TrEMBL
    B4E2U0
    Conserved Domains (3) summary
    COG0362
    Location:1 → 453
    Gnd; 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]
    pfam00393
    Location:158 → 447
    6PGD; 6-phosphogluconate dehydrogenase, C-terminal domain
    pfam03446
    Location:3 → 154
    NAD_binding_2; NAD binding domain of 6-phosphogluconate dehydrogenase

  2. NM_001304452.2 → NP_001291381.1  6-phosphogluconate dehydrogenase, decarboxylating isoform 3

    See identical proteins and their annotated locations for NP_001291381.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AK298830, AL139424, BC000368, HY245069
    UniProtKB/TrEMBL
    B4E2U0
    Conserved Domains (3) summary
    PRK09287
    Location:1 → 460
    PRK09287; 6-phosphogluconate dehydrogenase; Validated
    pfam00393
    Location:167 → 456
    6PGD; 6-phosphogluconate dehydrogenase, C-terminal domain
    pfam03446
    Location:1 → 163
    NAD_binding_2; NAD binding domain of 6-phosphogluconate dehydrogenase

  3. NM_002631.4 → NP_002622.2  6-phosphogluconate dehydrogenase, decarboxylating isoform 1

    See identical proteins and their annotated locations for NP_002622.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AL139424, BC000368, HY049516, HY245069
    Consensus CDS
    CCDS113.1
    UniProtKB/Swiss-Prot
    A8K2Y9, B4DQJ8, P52209, Q9BWD8
    UniProtKB/TrEMBL
    B4E2U0
    Related
    ENSP00000270776.8, ENST00000270776.13
    Conserved Domains (1) summary
    PRK09287
    Location:14 → 473
    PRK09287; 6-phosphogluconate dehydrogenase; Validated

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    10399064..10420511
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    9942673..9964125
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P52209.3 GenPept UniProtKB/Swiss-Prot:P52209

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