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    PGD phosphogluconate dehydrogenase [ Homo sapiens (human) ]

    Gene ID: 5226, updated on 5-May-2024

    Summary

    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
    NEW
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    Genomic context

    See PGD in Genome Data Viewer
    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

    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

    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

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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/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/TrEMBL
      B4E2U0
      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
      A8K2Y9, B4DQJ8, P52209, Q9BWD8
      UniProtKB/TrEMBL
      B4E2U0
      Related
      ENSP00000270776.8, ENST00000270776.13
      Conserved Domains (1) summary
      PRK09287
      Location:14473
      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)