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Aliases for PNPO Gene

Aliases for PNPO Gene

  • Pyridoxamine 5'-Phosphate Oxidase 2 3
  • Pyridoxamine-Phosphate Oxidase 3 4
  • Pyridoxine 5-Phosphate Oxidase 2 3
  • Epididymis Secretory Protein Li 302 3
  • Pyridoxamine 5-Phosphate Oxidase 5
  • Pyridoxal 5-Phosphate Synthase 3
  • Pyridoxine-5-Phosphate Oxidase 3
  • EC 4
  • 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-Prime-Phosphate Oxidase Deficiency and Pyridoxal 5'-Phosphate-Dependent Epilepsy. Among its related pathways are Metabolism and Vitamin B6 metabolism. Gene Ontology (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

Additional gene information for PNPO Gene

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

Genomics for PNPO Gene

GeneHancer (GH) Regulatory Elements for PNPO Gene

Promoters and enhancers for PNPO Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH17J047941 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 650.7 +0.4 351 2 CLOCK MLX DMAP1 YBX1 YY1 SLC30A9 ZNF213 E2F8 ZNF416 SP3 SP2-AS1 PNPO SP6 MRPL45P2 SP2 UBE2Z EFCAB13 ENSG00000264701 ENSG00000266601 CDK5RAP3
GH17J047943 Enhancer 0.3 dbSUPER 650.7 +1.9 1908 0.2 POLR2A PNPO PRR15L SP2 SCRN2 SNX11 CBX1 NFE2L1 ENSG00000263798
GH17J047940 Enhancer 0.2 Ensembl 650.7 -1.0 -1005 0.2 PNPO SP2-AS1 LOC102724532 ENSG00000266601
GH17J047970 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 20.4 +29.8 29816 2.1 CLOCK ZFP64 YBX1 DMAP1 YY1 E2F8 ZNF143 SP3 NFYC SSRP1 CDK5RAP3 SP2 ENSG00000266601 KPNB1 SCRN2 MRPL45P2 PNPO EFCAB13 PRR15L SP2-AS1
GH17J047964 Enhancer 1.4 FANTOM5 Ensembl ENCODE dbSUPER 21.8 +25.5 25524 4.6 ELF3 MLX ARID4B RAD21 YY1 ZNF121 FOS THAP11 RXRA SP5 CDK5RAP3 SCRN2 PNPO PRR15L SKAP1 SP2-AS1 SP2 MIR152 COPZ2 SNX11
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around PNPO on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PNPO gene promoter:
  • deltaCREB
  • CREB
  • Spz1
  • NF-1
  • ZIC2
  • E47
  • NF-1/L
  • IRF-2
  • Max1

Genomic Locations for PNPO Gene

Genomic Locations for PNPO Gene
7,803 bases
Plus strand
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.
    • Sequence=BAG64562.1; Type=Erroneous translation; Note=Wrong choice of frame.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PNPO Gene

    Alternative splice isoforms for PNPO Gene


neXtProt entry for PNPO Gene

Post-translational modifications for PNPO Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for PNPO Gene

Domains & Families for PNPO Gene

Gene Families for PNPO Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Enzymes
  • Potential drug targets
  • Predicted intracellular proteins

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

Function for PNPO Gene

Molecular function for PNPO Gene

UniProtKB/Swiss-Prot Function:
Catalyzes the oxidation of either pyridoxine 5-phosphate (PNP) or pyridoxamine 5-phosphate (PMP) into pyridoxal 5-phosphate (PLP).
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).

Enzyme Numbers (IUBMB) for PNPO Gene

Phenotypes From GWAS Catalog 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:0005515 protein binding IPI 25910212
GO:0010181 FMN binding IEA,IDA 12824491
GO:0016491 oxidoreductase activity IEA --
GO:0016638 oxidoreductase activity, acting on the CH-NH2 group of donors IEA --
genes like me logo Genes that share ontologies with PNPO: view
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 Model Products

Clone Products

No data available for Animal Models , Transcription Factor Targets and HOMER Transcription for PNPO Gene

Localization for PNPO Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PNPO gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
mitochondrion 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for PNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA --
GO:0005829 cytosol TAS --
GO:0070062 extracellular exosome HDA --
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.

Gene Ontology (GO) - Biological Process for PNPO Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0008615 pyridoxine biosynthetic process IEA --
GO:0042816 vitamin B6 metabolic process TAS --
GO:0042823 pyridoxal phosphate biosynthetic process IEA,IDA 12824491
GO:0055114 oxidation-reduction process IEA --
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

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

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Flavin Mononucleotide Approved, Investigational Pharma Target 8
Pyridoxal Phosphate Approved, Investigational Nutra Target, cofactor 17
Pyridoxal Approved Nutra 197
Pyridoxine Approved, Investigational, Vet_approved Nutra 198,198
Ammonia Approved Pharma 0

(4) Additional Compounds for PNPO Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with PNPO: view

Transcripts for PNPO Gene

mRNA/cDNA for PNPO Gene

Unigene Clusters for PNPO Gene

Pyridoxamine 5-phosphate oxidase:
Representative Sequences:

Clone Products

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 from GTEx, Illumina, BioGPS, and CGAP SAGE 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, MaxQB, and MOPED for PNPO Gene

Protein tissue co-expression partners for PNPO Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PNPO Gene:


SOURCE GeneReport for Unigene cluster for PNPO Gene:


Evidence on tissue expression from TISSUES for PNPO Gene

  • Nervous system(4.8)
  • Liver(4.6)
  • Thyroid gland(4.2)
  • Kidney(2.4)
  • Muscle(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PNPO Gene

Germ Layers:
  • ectoderm
  • mesoderm
  • cardiovascular
  • endocrine
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
Head and neck:
  • brain
  • cerebrospinal fluid
  • ear
  • head
  • meninges
  • neck
  • chest wall
  • heart
  • abdominal wall
  • adrenal gland
  • blood
  • peripheral nerve
  • peripheral nervous system
  • red blood cell
  • skin
  • sweat gland
genes like me logo Genes that share expression patterns with PNPO: view

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
(Pan troglodytes)
Mammalia PNPO 34 33
  • 99.87 (n)
(Canis familiaris)
Mammalia PNPO 34 33
  • 90.42 (n)
(Bos Taurus)
Mammalia PNPO 34 33
  • 90.04 (n)
(Mus musculus)
Mammalia Pnpo 16 34 33
  • 89.02 (n)
(Rattus norvegicus)
Mammalia Pnpo 33
  • 88.76 (n)
(Monodelphis domestica)
Mammalia PNPO 34
  • 80 (a)
(Ornithorhynchus anatinus)
Mammalia PNPO 34
  • 80 (a)
(Gallus gallus)
Aves PNPO 34 33
  • 74.79 (n)
(Anolis carolinensis)
Reptilia PNPO 34
  • 69 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia pnpo 33
  • 67.11 (n)
Str.20417 33
(Danio rerio)
Actinopterygii pnpo 34 33
  • 64.65 (n)
Dr.14932 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002227 33
  • 54.38 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG31472 34 33
  • 51.72 (n)
CG31473 34
  • 26 (a)
(Caenorhabditis elegans)
Secernentea F57B9.1 34 33
  • 52.62 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAR186W 33
  • 50.79 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0B07062g 33
  • 47.35 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes PDX3 36 34 33
  • 46.89 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU08269 33
  • 50.81 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC1093.02 33
  • 47.78 (n)
Species where no ortholog for PNPO was found in the sources mined by GeneCards:
  • 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)
Evolutionary constrained regions (ECRs) for PNPO: view image

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 Variation AA Info Type
rs104894629 pathogenic, Pyridoxal 5'-phosphate-dependent epilepsy, Pyridoxine-5'-phosphate oxidase deficiency (PNPOD) [MIM:610090] 47,946,681(+) C/T coding_sequence_variant, missense_variant
rs104894631 pathogenic, Pyridoxal 5'-phosphate-dependent epilepsy 47,946,780(+) T/C stop_lost, terminator_codon_variant
rs1060504669 likely-benign, Pyridoxal 5'-phosphate-dependent epilepsy 47,943,335(+) T/G 5_prime_UTR_variant, coding_sequence_variant, intron_variant, synonymous_variant
rs11079804 conflicting-interpretations-of-pathogenicity, benign, not specified, Pyridoxal 5'-phosphate-dependent epilepsy 47,943,332(+) C/T 5_prime_UTR_variant, coding_sequence_variant, intron_variant, synonymous_variant
rs114087393 likely-benign, Pyridoxal 5'-phosphate-dependent epilepsy 47,947,830(+) C/T 3_prime_UTR_variant

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

Variant ID Type Subtype PubMed ID
esv1000014 CNV deletion 20482838
nsv2072 CNV deletion 18451855
nsv518892 CNV loss 19592680

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)

Additional Variant Information for PNPO Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

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

Disorders for PNPO Gene

MalaCards: The human disease database

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

- 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 (PNPOD) [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, ECO:0000269 PubMed:23708187, ECO:0000269 PubMed:27864847}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Additional Disease Information for PNPO

Genetic Association Database
Human Genome Epidemiology 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. Association between PNPO and schizophrenia in the Japanese population. (PMID: 17851041) Song H … Ohmori T (Schizophrenia research 2007) 3 22 44 58
  2. Neonatal epileptic encephalopathy caused by mutations in the PNPO gene encoding pyridox(am)ine 5'-phosphate oxidase. (PMID: 15772097) Mills PB … Clayton PT (Human molecular genetics 2005) 3 4 22 58
  3. Genomic organization, tissue distribution and deletion mutation of human pyridoxine 5'-phosphate oxidase. (PMID: 15182361) Kang JH … Kwon OS (European journal of biochemistry 2004) 2 3 22 58
  4. Absence of pyridoxine-5'-phosphate oxidase (PNPO) activity in neoplastic cells: isolation, characterization, and expression of PNPO cDNA. (PMID: 9601034) Ngo EO … Nutter LM (Biochemistry 1998) 2 3 22 58
  5. PNPO deficiency: an under diagnosed inborn error of pyridoxine metabolism. (PMID: 18485777) Khayat M … Falik-Zaccai TC (Molecular genetics and metabolism 2008) 3 22 58

Products for PNPO Gene

Sources for PNPO Gene

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