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Aliases for PNPO Gene

Aliases for PNPO Gene

  • Pyridoxamine 5'-Phosphate Oxidase 2
  • Pyridoxamine 5-Phosphate Oxidase 2 3 5
  • Pyridoxine 5-Phosphate Oxidase 2 3
  • Pyridoxamine-Phosphate Oxidase 3 4
  • EC 4 63
  • Epididymis Secretory Protein Li 302 3
  • Pyridoxal 5-Phosphate Synthase 3
  • HEL-S-302 3
  • PDXPO 3

External Ids for PNPO Gene

Previous GeneCards Identifiers for PNPO Gene

  • GC17U990158
  • GC17P046361
  • GC17P046493
  • GC17P043373
  • GC17P046018
  • GC17P041387

Summaries for PNPO Gene

Entrez Gene Summary for PNPO Gene

  • 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]

GeneCards Summary for PNPO Gene

PNPO (Pyridoxamine 5'-Phosphate Oxidase) is a Protein Coding gene. Diseases associated with PNPO include pyridoxamine 5'-phosphate oxidase deficiency and pyridoxal phosphate-responsive seizures. Among its related pathways are Metabolism and Metabolism of water-soluble vitamins and cofactors. GO annotations related to this gene include oxidoreductase activity and oxidoreductase activity, acting on the CH-NH2 group of donors.

UniProtKB/Swiss-Prot for PNPO Gene

  • Catalyzes the oxidation of either pyridoxine 5-phosphate (PNP) or pyridoxamine 5-phosphate (PMP) into pyridoxal 5-phosphate (PLP).

Gene Wiki entry for PNPO Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PNPO Gene

Genomics for PNPO Gene

Regulatory Elements for PNPO Gene

Promoters for PNPO Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around PNPO on UCSC Golden Path with GeneCards custom track

Genomic Location for PNPO Gene

47,941,506 bp from pter
47,949,308 bp from pter
7,803 bases
Plus strand

Genomic View for PNPO Gene

Genes around PNPO on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PNPO Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PNPO Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PNPO Gene

Proteins for PNPO Gene

  • Protein details for PNPO Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Pyridoxine-5-phosphate oxidase
    Protein Accession:
    Secondary Accessions:
    • B4E0V0
    • B4E152
    • B4E1D7
    • D3DTT9

    Protein attributes for PNPO Gene

    261 amino acids
    Molecular mass:
    29988 Da
    Name=FMN; Xref=ChEBI:CHEBI:58210;
    Quaternary structure:
    • Homodimer.

    Three dimensional structures from OCA and Proteopedia for PNPO Gene

    Alternative splice isoforms for PNPO Gene


neXtProt entry for PNPO Gene

Proteomics data for PNPO Gene at MOPED

Selected DME Specific Peptides for PNPO Gene

Post-translational modifications for PNPO Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PNPO Gene

Antibody Products

Domains & Families for PNPO Gene

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the pyridoxamine 5-phosphate oxidase family.
  • Belongs to the pyridoxamine 5-phosphate oxidase family.
genes like me logo Genes that share domains with PNPO: view

No data available for Gene Families for PNPO Gene

Function for PNPO Gene

Molecular function for PNPO Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Pyridoxamine 5-phosphate + H(2)O + O(2) = pyridoxal 5-phosphate + NH(3) + H(2)O(2).
UniProtKB/Swiss-Prot CatalyticActivity:
Pyridoxine 5-phosphate + O(2) = pyridoxal 5-phosphate + H(2)O(2).
UniProtKB/Swiss-Prot Function:
Catalyzes the oxidation of either pyridoxine 5-phosphate (PNP) or pyridoxamine 5-phosphate (PMP) into pyridoxal 5-phosphate (PLP).

Enzyme Numbers (IUBMB) for PNPO Gene

genes like me logo Genes that share phenotypes with PNPO: view

Human Phenotype Ontology for PNPO Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PNPO Gene

MGI Knock Outs for PNPO:
  • Pnpo tm1a(KOMP)Wtsi

Animal Model Products

No data available for Gene Ontology (GO) - Molecular Function , Transcription Factor Targets and HOMER Transcription for PNPO Gene

Localization for PNPO Gene

Subcellular locations from

Jensen Localization Image for PNPO Gene COMPARTMENTS Subcellular localization image for PNPO gene
Compartment Confidence
cytosol 5
extracellular 5
nucleus 5
mitochondrion 2
chloroplast 1

Gene Ontology (GO) - Cellular Components for PNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IDA --
GO:0070062 extracellular exosome IDA 23376485
genes like me logo Genes that share ontologies with PNPO: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for PNPO Gene

Pathways & Interactions for PNPO Gene

genes like me logo Genes that share pathways with PNPO: view

UniProtKB/Swiss-Prot Q9NVS9-PNPO_HUMAN

  • Pathway: Cofactor metabolism; pyridoxal 5-phosphate salvage; pyridoxal 5-phosphate from pyridoxamine 5-phosphate: step 1/1.
  • Pathway: Cofactor metabolism; pyridoxal 5-phosphate salvage; pyridoxal 5-phosphate from pyridoxine 5-phosphate: step 1/1.

Interacting Proteins for PNPO Gene

Gene Ontology (GO) - Biological Process for PNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0002230 positive regulation of defense response to virus by host IMP 22020285
GO:0006766 vitamin metabolic process TAS --
GO:0006767 water-soluble vitamin metabolic process TAS --
GO:0042823 pyridoxal phosphate biosynthetic process IEA,IBA --
GO:0044281 small molecule metabolic process TAS --
genes like me logo Genes that share ontologies with PNPO: view

No data available for SIGNOR curated interactions for PNPO Gene

Drugs & Compounds for PNPO Gene

(9) Drugs for PNPO Gene - From: DrugBank, HMDB, and Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Pyridoxal Approved Nutra 163
Pyridoxine Approved Nutra 165,165
Flavin Mononucleotide Experimental Pharma Target 6
Pyridoxine-5'-Phosphate Experimental Pharma Enzyme 0
Beta-Mercaptoethanol Experimental Pharma Target 0

(7) Additional Compounds for PNPO Gene - From: Novoseek and HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
  • Ammonia anhydrous
  • Ammonia inhalant
  • Ammonia solution strong [usan]
  • Ammonia water
  • Ammoniak
  • Dioxygen
  • Molecular oxygen
  • O2
  • Oxygen
  • Oxygen molecule
  • Dihydrogen oxide
  • Steam
genes like me logo Genes that share compounds with PNPO: view

Transcripts for PNPO Gene

Unigene Clusters for PNPO Gene

Pyridoxamine 5-phosphate oxidase:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for PNPO Gene

ExUns: 1a · 1b · 1c · 1d ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c ^ 6 ^ 7a · 7b · 7c
SP1: - -
SP2: - - - -
SP3: - - - - -
SP4: - - -
SP5: - - -
SP6: - - - - - - - -
SP8: - - -

Relevant External Links for PNPO Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for PNPO Gene

mRNA expression in normal human tissues for PNPO Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PNPO Gene

This gene is overexpressed in Liver (x5.3).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for PNPO Gene

SOURCE GeneReport for Unigene cluster for PNPO Gene Hs.631742

genes like me logo Genes that share expression patterns with PNPO: view

Protein tissue co-expression partners for PNPO Gene

- Elite partner

Primer Products

In Situ Assay Products

No data available for Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for PNPO Gene

Orthologs for PNPO Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PNPO Gene

Organism Taxonomy Gene Similarity Type Details
(Bos Taurus)
Mammalia PNPO 35
  • 90.04 (n)
  • 91.95 (a)
  • 92 (a)
(Canis familiaris)
Mammalia PNPO 35
  • 90.42 (n)
  • 92.34 (a)
  • 92 (a)
(Mus musculus)
Mammalia Pnpo 35
  • 89.02 (n)
  • 90.04 (a)
Pnpo 16
Pnpo 36
  • 90 (a)
(Pan troglodytes)
Mammalia PNPO 35
  • 99.87 (n)
  • 100 (a)
  • 100 (a)
(Rattus norvegicus)
Mammalia Pnpo 35
  • 88.76 (n)
  • 89.66 (a)
(Monodelphis domestica)
Mammalia PNPO 36
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia PNPO 36
  • 80 (a)
(Gallus gallus)
Aves PNPO 35
  • 74.79 (n)
  • 78.85 (a)
  • 79 (a)
(Anolis carolinensis)
Reptilia PNPO 36
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pnpo 35
  • 67.11 (n)
  • 71.93 (a)
Str.20417 35
(Danio rerio)
Actinopterygii Dr.14932 35
pnpo 35
  • 64.65 (n)
  • 63.64 (a)
pnpo 36
  • 64 (a)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002227 35
  • 54.38 (n)
  • 51.69 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG31472 35
  • 51.72 (n)
  • 45.26 (a)
CG31472 36
  • 43 (a)
CG31473 36
  • 26 (a)
(Caenorhabditis elegans)
Secernentea F57B9.1 35
  • 52.62 (n)
  • 46.76 (a)
F57B9.1 36
  • 44 (a)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR186W 35
  • 50.79 (n)
  • 42.93 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B07062g 35
  • 47.35 (n)
  • 41.54 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PDX3 35
  • 46.89 (n)
  • 41.15 (a)
PDX3 36
  • 37 (a)
PDX3 38
bread mold
(Neurospora crassa)
Ascomycetes NCU08269 35
  • 50.81 (n)
  • 44.17 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC1093.02 35
  • 47.78 (n)
  • 45.32 (a)
Species with no ortholog for PNPO:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PNPO Gene

Gene Tree for PNPO (if available)
Gene Tree for PNPO (if available)

Paralogs for PNPO Gene

No data available for Paralogs for PNPO Gene

Variants for PNPO Gene

Sequence variations from dbSNP and Humsavar for PNPO Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
VAR_029358 -
rs17679445 - 47,944,699(+) GAGTC(A/G)AAAAG reference, missense
rs104894629 Pyridoxine-5-phosphate oxidase deficiency (PNPO deficiency) 47,946,681(+) ATGAC(C/T)GGATA reference, missense
rs1962201 -- 47,947,686(+) ACCAC(A/G)CCCAA utr-variant-3-prime
rs1986693 -- 47,948,790(+) CCGCT(A/G)ACCAG utr-variant-3-prime

Structural Variations from Database of Genomic Variants (DGV) for PNPO Gene

Variant ID Type Subtype PubMed ID
nsv518892 CNV Loss 19592680
nsv908575 CNV Loss 21882294
nsv2072 CNV Loss 18451855
esv1000014 CNV Deletion 20482838

Variation tolerance for PNPO Gene

Residual Variation Intolerance Score: 65.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.43; 54.66% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PNPO Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PNPO Gene

Disorders for PNPO Gene

MalaCards: The human disease database

(6) MalaCards diseases for PNPO Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
pyridoxamine 5'-phosphate oxidase deficiency
  • pyridoxamine 5'-phosphate oxidase
pyridoxal phosphate-responsive seizures
  • pnpo deficiency
  • brain diseases
seizure disorder
  • epilepsy
benign familial infantile epilepsy
  • benign familial infantile convulsion
- elite association - COSMIC cancer census association via MalaCards
Search PNPO in MalaCards View complete list of genes associated with diseases


  • Pyridoxine-5-phosphate oxidase deficiency (PNPO deficiency) [MIM:610090]: The main feature of neonatal epileptic encephalopathy is the onset within hours of birth of a severe seizure disorder that does not respond to anticonvulsant drugs and can be fatal. Seizures can cease with the administration of PLP, being resistant to treatment with pyridoxine,. {ECO:0000269 PubMed:15772097}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for PNPO

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with PNPO: view

No data available for Genatlas for PNPO Gene

Publications for PNPO Gene

  1. Absence of pyridoxine-5'-phosphate oxidase (PNPO) activity in neoplastic cells: isolation, characterization, and expression of PNPO cDNA. (PMID: 9601034) Ngo E.O. … Nutter L.M. (Biochemistry 1998) 2 3 23 67
  2. Neonatal epileptic encephalopathy caused by mutations in the PNPO gene encoding pyridox(am)ine 5'-phosphate oxidase. (PMID: 15772097) Mills P.B. … Clayton P.T. (Hum. Mol. Genet. 2005) 3 23 25
  3. Genomic organization, tissue distribution and deletion mutation of human pyridoxine 5'-phosphate oxidase. (PMID: 15182361) Kang J.H. … Kwon O.S. (Eur. J. Biochem. 2004) 2 3 23
  4. PNPO deficiency: an under diagnosed inborn error of pyridoxine metabolism. (PMID: 18485777) Khayat M. … Falik-Zaccai T.C. (Mol. Genet. Metab. 2008) 3 23
  5. Association between PNPO and schizophrenia in the Japanese population. (PMID: 17851041) Song H. … Ohmori T. (Schizophr. Res. 2007) 3 23

Products for PNPO Gene

Sources for PNPO Gene

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