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PGD phosphogluconate dehydrogenase [ Homo sapiens (human) ]

Gene ID: 5226, updated on 11-Sep-2019

Summary

Official Symbol
PGDprovided by HGNC
Official Full Name
phosphogluconate dehydrogenaseprovided by HGNC
Primary source
HGNC:HGNC:8891
See related
Ensembl:ENSG00000142657 MIM:172200
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

Genomic context

See PGD in Genome Data Viewer
Location:
1p36.22
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (10399064..10420511)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (10458884..10480565)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene kinesin family member 1B Neighboring gene RNA, 7SL, cytoplasmic 731, pseudogene Neighboring gene uncharacterized LOC105376725 Neighboring gene CENPS-CORT readthrough Neighboring gene centromere protein S Neighboring gene cortistatin

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

Pathways from BioSystems

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

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

General protein information

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

NCBI Reference Sequences (RefSeq)

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_001304451.2NP_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/Swiss-Prot
    P52209
    UniProtKB/TrEMBL
    B4E2U0
    Conserved Domains (3) summary
    COG0362
    Location:1453
    Gnd; 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]
    pfam00393
    Location:158447
    6PGD; 6-phosphogluconate dehydrogenase, C-terminal domain
    pfam03446
    Location:3154
    NAD_binding_2; NAD binding domain of 6-phosphogluconate dehydrogenase
  2. NM_001304452.2NP_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/Swiss-Prot
    P52209
    Conserved Domains (3) summary
    PRK09287
    Location:1460
    PRK09287; 6-phosphogluconate dehydrogenase; Validated
    pfam00393
    Location:167456
    6PGD; 6-phosphogluconate dehydrogenase, C-terminal domain
    pfam03446
    Location:1163
    NAD_binding_2; NAD binding domain of 6-phosphogluconate dehydrogenase
  3. NM_002631.4NP_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
    P52209
    Related
    ENSP00000270776.8, ENST00000270776.13
    Conserved Domains (1) summary
    PRK09287
    Location:14473
    PRK09287; 6-phosphogluconate dehydrogenase; Validated

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

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