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    PRODH2 proline dehydrogenase 2 [ Homo sapiens (human) ]

    Gene ID: 58510, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PRODH2provided by HGNC
    Official Full Name
    proline dehydrogenase 2provided by HGNC
    Primary source
    HGNC:HGNC:17325
    See related
    Ensembl:ENSG00000250799 MIM:616377; AllianceGenome:HGNC:17325
    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
    HYPDH; HSPOX1
    Summary
    The protein encoded by this gene catalyzes the first step in the catabolism of trans-4-hydroxy-L-proline, an amino acid derivative obtained through food intake and collagen turnover. One of the downstream products of this catabolism is glyoxylate, which in people with disorders of glyoxalate metabolism can lead to an increase in oxalate levels and the formation of calcium-oxalate kidney stones. Therefore, this gene may serve as a therapeutic target against primary hyperoxalurias (PH). This gene is similar to proline dehydrogenase (oxidase) 1, a mitochondrial enzyme that catalyzes the first step in proline catabolism. [provided by RefSeq, Jan 2017]
    Expression
    Restricted expression toward kidney (RPKM 100.5) See more
    Orthologs
    mouse all
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    Genomic context

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    See PRODH2 in Genome Data Viewer
    Location:
    19q13.12
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (35799988..35812845, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (38345290..38358148, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (36290890..36303747, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10539 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36268039-36268924 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36268925-36269809 Neighboring gene Rho GTPase activating protein 33 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36275082-36275900 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14503 Neighboring gene testis expressed 14B, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36297835-36298335 Neighboring gene NPHS1 adhesion molecule, nephrin Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36336236-36336488 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:36339012-36339187 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36342052-36342692 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:36342693-36343334 Neighboring gene kirre like nephrin family adhesion molecule 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:36351790-36352542 Neighboring gene uncharacterized LOC107985317 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10541 Neighboring gene amyloid beta precursor like protein 1

    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. A novel function for hydroxyproline oxidase in apoptosis through generation of reactive oxygen species. Cooper SK, et al. J Biol Chem, 2008 Apr 18. PMID 18287100, Free PMC Article
    2. Proline dehydrogenase 2 (PRODH2) is a hydroxyproline dehydrogenase (HYPDH) and molecular target for treating primary hyperoxaluria. Summitt CB, et al. Biochem J, 2015 Mar 1. PMID 25697095, Free PMC Article
    3. P53 family members modulate the expression of PRODH, but not PRODH2, via intronic p53 response elements. Raimondi I, et al. PLoS One, 2013. PMID 23861960, Free PMC Article
    4. Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression. Hendrickson SL, et al. PLoS One, 2010 Sep 21. PMID 20877624, Free PMC Article
    5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

    See all (6) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Data suggest that residues 157-515 of PRODH2 contain catalytic core with one FAD molecule; PRODH2 most likely utilizes coenzyme Q10 as terminal electron acceptor in vivo; PRODH2 exhibits substrate specificity for hydroxyproline over proline.
      Title: Proline dehydrogenase 2 (PRODH2) is a hydroxyproline dehydrogenase (HYPDH) and molecular target for treating primary hyperoxaluria.
    2. PRODH, but not PRODH2, expression is under the control of p53 family members, specifically p53 and p73.
      Title: P53 family members modulate the expression of PRODH, but not PRODH2, via intronic p53 response elements.
    3. Observational study of gene-disease association. (HuGE Navigator)
      Title: Genetic variants in nuclear-encoded mitochondrial genes influence AIDS progression.
    4. OH-POX plays a role analogous to POX in growth regulation, ROS generation, and activation of the apoptotic cascade
      Title: A novel function for hydroxyproline oxidase in apoptosis through generation of reactive oxygen species.
    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)

    Genotypes

    Pathways from PubChem

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    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables FAD binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables oxidoreductase activity, acting on the CH-NH group of donors IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables proline dehydrogenase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables proline dehydrogenase activity TAS
    Traceable Author Statement
    more info
    		  
    Process Evidence Code Pubs
    involved_in proline catabolic process TAS
    Traceable Author Statement
    more info
    		  
    involved_in proline catabolic process to glutamate IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in mitochondrial inner membrane TAS
    Traceable Author Statement
    more info
    		  
    is_active_in mitochondrion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    hydroxyproline dehydrogenase
    Names
    kidney and liver proline oxidase 1
    probable proline dehydrogenase 2
    probable proline oxidase 2
    proline dehydrogenase (oxidase) 2
    NP_001365221.1
    NP_001365222.1
    NP_001365223.1
    NP_067055.2

    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_001378292.1 → NP_001365221.1  hydroxyproline dehydrogenase isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC002398, U95090
      Conserved Domains (1) summary
      cl40683
      Location:10 → 400
      Pro_dh; Proline dehydrogenase

    2. NM_001378293.1 → NP_001365222.1  hydroxyproline dehydrogenase isoform 3

      Status: REVIEWED

      Source sequence(s)
      AC002398, U95090
      Conserved Domains (1) summary
      cl40683
      Location:10 → 375
      Pro_dh; Proline dehydrogenase

    3. NM_001378294.1 → NP_001365223.1  hydroxyproline dehydrogenase isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC002398, U95090
      Conserved Domains (1) summary
      cl40683
      Location:10 → 323
      Pro_dh; Proline dehydrogenase

    4. NM_021232.2 → NP_067055.2  hydroxyproline dehydrogenase isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC002398, U95090
      Consensus CDS
      CCDS12478.2
      UniProtKB/Swiss-Prot
      A0A590UKC3, Q9UF12
      Related
      ENSP00000499779.1, ENST00000653904.2
      Conserved Domains (1) summary
      PLN02681
      Location:10 → 452
      PLN02681; proline dehydrogenase

    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_000019.10 Reference GRCh38.p14 Primary Assembly

      Range
      35799988..35812845 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060943.1 Alternate T2T-CHM13v2.0

      Range
      38345290..38358148 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UF12.2 GenPept UniProtKB/Swiss-Prot:Q9UF12

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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