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    PNPO pyridoxamine 5'-phosphate oxidase [ Homo sapiens (human) ]

    Gene ID: 55163, updated on 17-Jun-2019

    Summary

    Official Symbol
    PNPOprovided by HGNC
    Official Full Name
    pyridoxamine 5'-phosphate oxidaseprovided by HGNC
    Primary source
    HGNC:HGNC:30260
    See related
    Ensembl:ENSG00000108439 MIM:603287
    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
    PDXPO; HEL-S-302
    Summary
    The enzyme encoded by this gene catalyzes the terminal, rate-limiting step in the synthesis of pyridoxal 5'-phosphate, also known as vitamin B6. Vitamin B6 is a required co-factor for enzymes involved in both homocysteine metabolism and synthesis of neurotransmitters such as catecholamine. Mutations in this gene result in pyridoxamine 5'-phosphate oxidase (PNPO) deficiency, a form of neonatal epileptic encephalopathy. [provided by RefSeq, Oct 2008]
    Expression
    Ubiquitous expression in liver (RPKM 22.0), kidney (RPKM 16.0) and 23 other tissues See more
    Orthologs

    Genomic context

    See PNPO in Genome Data Viewer
    Location:
    17q21.32
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 17 NC_000017.11 (47941524..47949308)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (46018889..46026674)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC102724532 Neighboring gene SP2 antisense RNA 1 Neighboring gene Sp2 transcription factor Neighboring gene proline rich 15 like Neighboring gene CDK5 regulatory subunit associated protein 3

    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 FunctionsWhat's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Pyridoxal 5'-phosphate-dependent epilepsy
    MedGen: C1864723 OMIM: 610090 GeneReviews: Not available
    not available

    NHGRI GWAS Catalog

    Description
    Genome-wide association analysis of genetic generalized epilepsies implicates susceptibility loci at 1q43, 2p16.1, 2q22.3 and 17q21.32
    NHGRI GWA Catalog

    Pathways from BioSystems

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • FLJ10535

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    FMN binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    pyridoxal phosphate binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    pyridoxamine-phosphate oxidase activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    pyridoxamine-phosphate oxidase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    oxidation-reduction process IEA
    Inferred from Electronic Annotation
    more info
     
    pyridoxal phosphate biosynthetic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    pyridoxal phosphate biosynthetic process IDA
    Inferred from Direct Assay
    more info
    PubMed 
    pyridoxine biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
     
    vitamin B6 metabolic process TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    cytosol IDA
    Inferred from Direct Assay
    more info
     
    cytosol TAS
    Traceable Author Statement
    more info
     
    nucleoplasm IDA
    Inferred from Direct Assay
    more info
     

    General protein information

    Preferred Names
    pyridoxine-5'-phosphate oxidase
    Names
    epididymis secretory protein Li 302
    epididymis secretory sperm binding protein
    pyridoxal 5'-phosphate synthase
    pyridoxamine-phosphate oxidase
    pyridoxine 5'-phosphate oxidase
    NP_060599.1
    XP_005257557.1
    XP_011523270.1
    XP_016880302.1

    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.

    Genomic

    1. NG_008744.1 RefSeqGene

      Range
      5001..12786
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_018129.4NP_060599.1  pyridoxine-5'-phosphate oxidase

      See identical proteins and their annotated locations for NP_060599.1

      Status: REVIEWED

      Source sequence(s)
      AC018521, AK001397, BC006525, CB853441
      Consensus CDS
      CCDS11522.1
      UniProtKB/Swiss-Prot
      Q9NVS9
      UniProtKB/TrEMBL
      V9HW45
      Related
      ENSP00000493302.1, ENST00000642017.1
      Conserved Domains (1) summary
      TIGR00558
      Location:57261
      pdxH; pyridoxamine-phosphate oxidase

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p13 Primary Assembly

      Range
      47941524..47949308
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017024813.1XP_016880302.1  pyridoxine-5'-phosphate oxidase isoform X1

      Related
      ENSP00000463919.2, ENST00000583599.6
      Conserved Domains (2) summary
      pfam01243
      Location:173
      Pyridox_oxidase; Pyridoxamine 5'-phosphate oxidase
      pfam10590
      Location:126181
      PNPOx_C; Pyridoxine 5'-phosphate oxidase C-terminal dimerization region
    2. XM_005257500.3XP_005257557.1  pyridoxine-5'-phosphate oxidase isoform X1

      See identical proteins and their annotated locations for XP_005257557.1

      Conserved Domains (2) summary
      pfam01243
      Location:173
      Pyridox_oxidase; Pyridoxamine 5'-phosphate oxidase
      pfam10590
      Location:126181
      PNPOx_C; Pyridoxine 5'-phosphate oxidase C-terminal dimerization region
    3. XM_011524968.2XP_011523270.1  pyridoxine-5'-phosphate oxidase isoform X2

      See identical proteins and their annotated locations for XP_011523270.1

      UniProtKB/Swiss-Prot
      Q9NVS9
      Conserved Domains (2) summary
      pfam01243
      Location:158
      Pyridox_oxidase; Pyridoxamine 5'-phosphate oxidase
      pfam10590
      Location:111166
      PNPOx_C; Pyridoxine 5'-phosphate oxidase C-terminal dimerization region
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