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Aliases for PNPO Gene

Aliases for PNPO Gene

  • Pyridoxamine 5'-Phosphate Oxidase 2
  • Pyridoxamine 5-Phosphate Oxidase 2 3
  • 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
  • Pyridoxine-5-Phosphate Oxidase 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 5'-phosphate-dependent epilepsy. Among its related pathways are Disease and Metabolism. GO annotations related to this gene include FMN binding and pyridoxamine-phosphate oxidase activity.

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

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

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
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; Note=Binds 1 FMN per subunit.;
    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 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

Gene Ontology (GO) - Molecular Function for PNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0004733 pyridoxamine-phosphate oxidase activity TAS --
GO:0010181 FMN binding IEA --
GO:0016491 oxidoreductase activity --
GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors --
genes like me logo Genes that share ontologies with PNPO: view
genes like me logo Genes that share phenotypes with PNPO: view

Animal Model Products

miRNA for PNPO Gene

miRTarBase miRNAs that target PNPO

No data available for Animal Models , 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 4
nucleus 4
mitochondrion 2
chloroplast 1
cytoskeleton 1

Gene Ontology (GO) - Cellular Components for PNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005737 cytoplasm IDA --
GO:0005829 cytosol TAS --
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 for PNPO Gene

SuperPathways for PNPO Gene

Superpath Contained pathways
1 Defective BTD causes biotidinase deficiency
2 Vitamin B6 metabolism
3 Metabolism
4 Disease
5 Selenium Pathway
genes like me logo Genes that share pathways with PNPO: view

UniProtKB/Swiss-Prot Q9NVS9-PNPO_HUMAN

  • Pathway: Cofactor biosynthesis; B6 vitamer interconversion; pyridoxal 5-phosphate from pyridoxamine 5-phosphate: step 1/1
  • Pathway: Cofactor biosynthesis; B6 vitamer interconversion; 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:0008615 pyridoxine biosynthetic process IEA --
GO:0042816 vitamin B6 metabolic process TAS --
genes like me logo Genes that share ontologies with PNPO: view

Drugs for PNPO Gene

(4) Drugbank Compounds for PNPO Gene

Compound Status Synonyms Cas Number PubChem ID Type Actions PubMed IDs
  • 2-Sulfhydryl-Ethanol
60-24-2 1567 Target experimental
447-05-2 1055 Enzyme experimental
Riboflavin Monophosphate
146-17-8 5702760 Target experimental
Pyridoxal Phosphate
  • Codecarboxylase
54-47-7 1051 Target cofactor nutraceutical

(11) HMDB Compounds for PNPO Gene

Compound Synonyms Cas Number PubMed IDs
  • Ammonia anhydrous
Flavin Mononucleotide
  • Flanin
Hydrogen peroxide
  • Adeka Super EL
  • Dioxygen
  • 3-Hydroxy-5-(hydroxymethyl)-2-methylpyridine-4-carboxaldehyde

(6) Novoseek inferred chemical compound relationships for PNPO Gene

Compound -log(P) Hits PubMed IDs
pyridoxine 5-phosphate 96.3 9
pyridoxamine 5-phosphate 96.2 13
pyridoxal 5-phosphate 86.2 17
pyridoxal 79.7 5
vitamin b6 77.5 9
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 (5.3).

Integrated Proteomics: protein expression 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 expressions with PNPO: view

Expression partners for PNPO Gene

* - Elite partner

Primer Products

  • QuantiTect SYBR Green Assays in human,mouse,rat
  • Pre-validated RT² qPCR Primer Assay in human,mouse,rat
  • QuantiFast Probe-based Assays in human,mouse,rat

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 MAF
rs2325750 -- 47,944,964(-) GCCTT(C/T)CTGAG intron-variant
rs56185758 -- 47,944,236(+) TGTGT(-/GTGT/GTGTGT/GTGTGTGTGTGT)TGTGG intron-variant
rs61165779 -- 47,945,459(+) TCTGC(-/T)GTGGG intron-variant
rs73985445 -- 47,945,794(+) GGAAC(A/G)GGGCC intron-variant
rs77495459 -- 47,949,495(+) TCATC(A/G)GCTTG downstream-variant-500B

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

Relevant External Links for PNPO Gene

HapMap Linkage Disequilibrium report
Human Gene Mutation Database (HGMD)
Locus Specific Mutation Databases (LSDB)

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

Disorders for PNPO Gene

(1) OMIM Diseases for PNPO Gene (603287)


  • 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.

(1) University of Copenhagen DISEASES for PNPO Gene

(1) Novoseek inferred disease relationships for PNPO Gene

Disease -log(P) Hits PubMed IDs
encephalopathy 44.1 4

Relevant External Links for PNPO

Genetic Association Database (GAD)
Human Genome Epidemiology (HuGE) Navigator
genes like me logo Genes that share disorders with PNPO: view

No data available for Genatlas for PNPO Gene

Publications for PNPO Gene

  1. 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 4 23 25
  2. Association between PNPO and schizophrenia in the Japanese population. (PMID: 17851041) Song H. … Ohmori T. (Schizophr. Res. 2007) 3 23 48
  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. 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
  5. PNPO deficiency: an under diagnosed inborn error of pyridoxine metabolism. (PMID: 18485777) Khayat M. … Falik-Zaccai T.C. (Mol. Genet. Metab. 2008) 3 23

Products for PNPO Gene

Sources for PNPO Gene

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