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    PDPR pyruvate dehydrogenase phosphatase regulatory subunit [ Homo sapiens (human) ]

    Gene ID: 55066, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PDPRprovided by HGNC
    Official Full Name
    pyruvate dehydrogenase phosphatase regulatory subunitprovided by HGNC
    Primary source
    HGNC:HGNC:30264
    See related
    Ensembl:ENSG00000090857 MIM:617835; AllianceGenome:HGNC:30264
    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
    PDP3
    Summary
    Pyruvate dehydrogenase complex (PDC) catalyzes the oxidative decarboxylation of pyruvate and links glycolysis to the tricarboxylic acid cycle and fatty acid synthesis. The dephosphorylation and reactivation of PDC is catalyzed by pyruvate dehydrogenase phosphatase (PDP). The dimeric PDP has a catalytic subunit and a regulatory subunit. This gene encodes the FAD-containing regulatory subunit of PDP. The encoded protein acts to decrease the sensitivity of the PDP catalytic subunit to magnesium ions. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jan 2017]
    Expression
    Ubiquitous expression in testis (RPKM 9.0), brain (RPKM 8.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See PDPR in Genome Data Viewer
    Location:
    16q22.1
    Exon count:
    23
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (70113626..70163427)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (75922058..75974584)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (70147529..70196440)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70099725-70100338 Neighboring gene uncharacterized LOC124903706 Neighboring gene ribosomal protein S10 pseudogene 24 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:70121188-70121409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11049 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70148769-70149711 Neighboring gene uncharacterized LOC400541 Neighboring gene H3K27ac hESC enhancer GRCh37_chr16:70200631-70201130 Neighboring gene C-type lectin domain family 18 member C Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:70221261-70222190 Neighboring gene uncharacterized LOC105371328

    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 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. PDPR Gene Variants Predisposing to Papillary Thyroid Cancer. Brock P, et al. Thyroid, 2024 May. PMID 38062777,
    2. Purification and properties of pyruvate dehydrogenase phosphatase from bovine heart and kidney. Teague WM, et al. Biochemistry, 1982 Oct 26. PMID 6293549
    3. Cloning, expression, and properties of the regulatory subunit of bovine pyruvate dehydrogenase phosphatase. Lawson JE, et al. J Biol Chem, 1997 Dec 12. PMID 9395502
    4. Novel association strategy with copy number variation for identifying new risk Loci of human diseases. Chen X, et al. PLoS One, 2010 Aug 20. PMID 20808825, Free PMC Article
    5. Recent advances in mechanisms regulating glucose oxidation at the level of the pyruvate dehydrogenase complex by PDKs. Sugden MC, et al. Am J Physiol Endocrinol Metab, 2003 May. PMID 12676647

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. PDPR Gene Variants Predisposing to Papillary Thyroid Cancer.
      Title: PDPR Gene Variants Predisposing to Papillary Thyroid Cancer.
    2. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    3. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Novel association strategy with copy number variation for identifying new risk Loci of human diseases.
    Submit: New GeneRIF Correction

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ10079, DKFZp686A088, DKFZp686D16130

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in mitochondrial matrix IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrial matrix TAS
    Traceable Author Statement
    more info
    		  
    located_in mitochondrion HTP PubMed 
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in mitochondrion NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    part_of pyruvate dehydrogenase (lipoamide) phosphatase complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial
    NP_001309046.1
    NP_001309047.1
    NP_001309048.1
    NP_060460.4
    XP_005256072.1
    XP_005256073.1
    XP_006721287.1
    XP_006721288.1
    XP_011521492.1
    XP_016878877.1
    XP_047290258.1
    XP_047290259.1
    XP_047290260.1
    XP_047290261.1
    XP_047290262.1
    XP_047290263.1
    XP_047290264.1
    XP_047290265.1
    XP_047290266.1
    XP_047302562.1
    XP_047302564.1
    XP_047302565.1
    XP_047302566.1
    XP_047302567.1
    XP_047302568.1
    XP_047302569.1
    XP_047302570.1
    XP_047302571.1
    XP_047302572.1
    XP_047302573.1

    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.

    Genomic

    1. NG_052842.1 RefSeqGene

      Range
      5707..53912
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001322117.1 → NP_001309046.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform 1 precursor

      Status: REVIEWED

      Source sequence(s)
      AC009022, AC009060
      Consensus CDS
      CCDS45520.1
      UniProtKB/Swiss-Prot
      A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
      UniProtKB/TrEMBL
      B4DZL5
      Related
      ENSP00000457916.1, ENST00000568530.5
      Conserved Domains (4) summary
      COG0665
      Location:39 → 426
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:463 → 736
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:786 → 852
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:405 → 459
      FAO_M; FAD dependent oxidoreductase central domain

    2. NM_001322118.1 → NP_001309047.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC009022, AC009060, AK302987
      Consensus CDS
      CCDS82007.1
      UniProtKB/TrEMBL
      A8MT40, B4DZL5
      Related
      ENSP00000381190.3, ENST00000398122.7
      Conserved Domains (5) summary
      COG0404
      Location:353 → 730
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:1 → 326
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:363 → 636
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:648 → 752
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:305 → 360
      FAO_M; FAD dependent oxidoreductase central domain

    3. NM_001322119.1 → NP_001309048.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC009022, AC009060
      Conserved Domains (4) summary
      COG0404
      Location:51 → 428
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      pfam01571
      Location:61 → 334
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:346 → 450
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:3 → 58
      FAO_M; FAD dependent oxidoreductase central domain

    4. NM_017990.5 → NP_060460.4  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform 1 precursor

      See identical proteins and their annotated locations for NP_060460.4

      Status: REVIEWED

      Source sequence(s)
      AC009022, AC009060
      Consensus CDS
      CCDS45520.1
      UniProtKB/Swiss-Prot
      A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
      UniProtKB/TrEMBL
      B4DZL5
      Related
      ENSP00000288050.5, ENST00000288050.9
      Conserved Domains (4) summary
      COG0665
      Location:39 → 426
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:463 → 736
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:786 → 852
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:405 → 459
      FAO_M; FAD dependent oxidoreductase central domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      70113626..70163427
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017023388.3 → XP_016878877.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X5

      Related
      ENST00000561920.5

    2. XM_047434302.1 → XP_047290258.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

      UniProtKB/Swiss-Prot
      A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
      Conserved Domains (4) summary
      COG0665
      Location:39 → 426
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:463 → 736
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:786 → 852
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:405 → 459
      FAO_M; FAD dependent oxidoreductase central domain

    3. XM_047434303.1 → XP_047290259.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X2

    4. XM_047434304.1 → XP_047290260.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X3

    5. XM_047434306.1 → XP_047290262.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X4

    6. XM_005256015.3 → XP_005256072.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_005256072.1

      UniProtKB/Swiss-Prot
      A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
      UniProtKB/TrEMBL
      B4DZL5
      Conserved Domains (4) summary
      COG0665
      Location:39 → 426
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:463 → 736
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:786 → 852
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:405 → 459
      FAO_M; FAD dependent oxidoreductase central domain

    7. XM_006721224.3 → XP_006721287.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X2

      UniProtKB/TrEMBL
      B4DZL5
      Conserved Domains (6) summary
      COG0404
      Location:453 → 769
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:39 → 426
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:463 → 684
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:687 → 791
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:405 → 460
      FAO_M; FAD dependent oxidoreductase central domain
      cl21454
      Location:5 → 74
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    8. XM_006721225.4 → XP_006721288.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X3

      UniProtKB/TrEMBL
      B4DZL5
      Conserved Domains (6) summary
      COG0404
      Location:373 → 750
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:39 → 346
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:383 → 656
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:668 → 772
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:325 → 380
      FAO_M; FAD dependent oxidoreductase central domain
      cl21454
      Location:5 → 74
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    9. XM_047434305.1 → XP_047290261.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X4

    10. XM_011523190.4 → XP_011521492.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X6

      Conserved Domains (5) summary
      COG0404
      Location:453 → 655
      GcvT; Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
      COG0665
      Location:39 → 426
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:463 → 655
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam16350
      Location:405 → 460
      FAO_M; FAD dependent oxidoreductase central domain
      cl21454
      Location:5 → 74
      NADB_Rossmann; Rossmann-fold NAD(P)(+)-binding proteins

    11. XM_047434310.1 → XP_047290266.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X9

      UniProtKB/TrEMBL
      H3BQG3
      Related
      ENSP00000455764.1, ENST00000565186.5

    12. XM_047434307.1 → XP_047290263.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X4

    13. XM_005256016.4 → XP_005256073.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

      See identical proteins and their annotated locations for XP_005256073.1

      UniProtKB/Swiss-Prot
      A7E298, A8K8Y7, B3KSE1, Q6AI20, Q6AWC9, Q8NCN5
      UniProtKB/TrEMBL
      B4DZL5
      Conserved Domains (4) summary
      COG0665
      Location:39 → 426
      DadA; Glycine/D-amino acid oxidase (deaminating) [Amino acid transport and metabolism]
      pfam01571
      Location:463 → 736
      GCV_T; Aminomethyltransferase folate-binding domain
      pfam08669
      Location:786 → 852
      GCV_T_C; Glycine cleavage T-protein C-terminal barrel domain
      pfam16350
      Location:405 → 459
      FAO_M; FAD dependent oxidoreductase central domain

    14. XM_047434308.1 → XP_047290264.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X7

    15. XM_047434309.1 → XP_047290265.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X8

    RNA

    1. XR_007064891.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      75922058..75974584
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047446613.1 → XP_047302569.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X5

    2. XM_047446609.1 → XP_047302565.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

    3. XM_047446611.1 → XP_047302567.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X2

    4. XM_047446606.1 → XP_047302562.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

    5. XM_047446610.1 → XP_047302566.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X2

    6. XM_047446612.1 → XP_047302568.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X3

    7. XM_047446614.1 → XP_047302570.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X6

    8. XM_047446617.1 → XP_047302573.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X9

    9. XM_047446608.1 → XP_047302564.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X1

    10. XM_047446615.1 → XP_047302571.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X7

    11. XM_047446616.1 → XP_047302572.1  pyruvate dehydrogenase phosphatase regulatory subunit, mitochondrial isoform X8

    RNA

    1. XR_007086598.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NCN5.2 GenPept UniProtKB/Swiss-Prot:Q8NCN5

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