Gene Gene information from NCBI Gene database.
Entrez ID 55163
Gene name Pyridoxamine 5'-phosphate oxidase
Gene symbol PNPO
Synonyms (NCBI Gene)
HEL-S-302PDXPO
Chromosome 17
Chromosome location 17q21.32
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 neuro
SNPs SNP information provided by dbSNP.
15
SNP ID Visualize variation Clinical significance Consequence
rs104894629 C>T Pathogenic Missense variant, coding sequence variant
rs104894631 T>C Pathogenic Stop lost, terminator codon variant
rs138727329 G>A Conflicting-interpretations-of-pathogenicity, uncertain-significance Coding sequence variant, missense variant
rs144362146 C>G Conflicting-interpretations-of-pathogenicity, benign Coding sequence variant, synonymous variant
rs146027425 C>G,T Likely-pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
1007
miRTarBase ID miRNA Experiments Reference
MIRT028520 hsa-miR-30a-5p Proteomics 18668040
MIRT050711 hsa-miR-18a-5p CLASH 23622248
MIRT720170 hsa-miR-4770 HITS-CLIP 19536157
MIRT720169 hsa-miR-143-3p HITS-CLIP 19536157
MIRT720168 hsa-miR-6088 HITS-CLIP 19536157
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
18
GO ID Ontology Definition Evidence Reference
GO:0004733 Function Pyridoxamine phosphate oxidase activity IBA
GO:0004733 Function Pyridoxamine phosphate oxidase activity IDA 12824491, 15772097
GO:0004733 Function Pyridoxamine phosphate oxidase activity IEA
GO:0005515 Function Protein binding IPI 25910212, 28514442, 32296183, 33961781
GO:0005739 Component Mitochondrion HTP 34800366
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
603287 30260 ENSG00000108439
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9NVS9
Protein name Pyridoxine-5'-phosphate oxidase (EC 1.4.3.5) (Pyridoxamine-phosphate oxidase)
Protein function Catalyzes the oxidation of either pyridoxine 5'-phosphate (PNP) or pyridoxamine 5'-phosphate (PMP) into pyridoxal 5'-phosphate (PLP).
PDB 1NRG , 3HY8 , 6H00 , 8QYT , 8QYW , 8ROS
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF01243 Putative_PNPOx 59 153 Domain
PF10590 PNP_phzG_C 206 261 Domain
Tissue specificity TISSUE SPECIFICITY: Ubiquitous. Expressed in liver, brain, lung, prostate and stomach (at protein level). {ECO:0000269|PubMed:15182361}.
Sequence
MTCWLRGVTATFGRPAEWPGYLSHLCGRSAAMDLGPMRKSYRGDREAFEETHLTSLDPVK
QFAAWFEEAVQCPDIGEANAMCLATCTRDGKPSARMLLLKGFGKDGFRFFTNFESRKGKE
LDSNPFASLVFYWEPLNRQVRVEGPVKKLPEEE
AECYFHSRPKSSQIGAVVSHQSSVIPD
REYLRKKNEELEQLYQDQEVPKPKSWGGYVLYPQVMEFWQGQTNRLHDRIVFRRGLPTGD
SPLGPMTHRGEEDWLYERLAP
Sequence length 261
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  KEGG  Reactome
  Vitamin B6 metabolism
Metabolic pathways
Biosynthesis of cofactors
  Vitamins B6 activation to pyridoxal phosphate
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
15
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Fetal growth restriction Pathogenic rs550423482 RCV000414812
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Growth delay Pathogenic rs550423482 RCV000414812
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Neuronopathy, distal hereditary motor, type 5A Pathogenic rs550423482 RCV000825022
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PNPO-related disorder Likely pathogenic; Pathogenic rs769266169, rs773450573 RCV004537581
RCV004539748
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Cholangiocarcinoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
NEURONOPATHY, DISTAL HEREDITARY MOTOR, TYPE V Disgenet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
PYRIDOXAMINE-5-PHOSPHATE DEFICIENCY-DEVELOPMENTAL AND EPILEPTIC ENCEPHALOPATHY Orphanet
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Sarcoma Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Anemia Anemia Pubtator 28985901 Associate
★☆☆☆☆
Found in Text Mining only
Anemia Anemia HPO_DG
★☆☆☆☆
Found in Text Mining only
Brain Diseases Brain disease Pubtator 28133863, 28985901, 32788630 Associate
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma BEFREE 30982780
★☆☆☆☆
Found in Text Mining only
Carcinoma, Ovarian Epithelial Ovarian Epithelial carcinoma BEFREE 29238081
★☆☆☆☆
Found in Text Mining only
Cardiomyopathy, Familial Idiopathic Cardiomyopathy BEFREE 30982780
★☆☆☆☆
Found in Text Mining only
Complex Partial Status Epilepticus Status Epilepticus CTD_human_DG 19356691
★☆☆☆☆
Found in Text Mining only
Congenital chromosomal disease Congenital Chromosomal Disease BEFREE 31506944
★☆☆☆☆
Found in Text Mining only
Encephalopathies Epileptic encephalopathy HPO_DG
★☆☆☆☆
Found in Text Mining only
Epilepsy Epilepsy BEFREE 24114605, 24645144, 26535729, 28818555
★☆☆☆☆
Found in Text Mining only