IEMbase 0076: PNPO-related pyridoxamine 5-phosphate oxidase deficiency
Scope
| Field | Value |
|---|---|
| IEMbase ID | 76 |
| Nosology | 21.6.01.01 |
| Gene | PNPO |
| External IDs | OMIM:610090 |
| Generated mapping | UNMAPPED |
| Candidate DisMech targets | Best fuzzy candidate COA3-Related_COX_Deficiency.yaml |
| Review date | 2026-07-07 |
IEMbase phenotype signal
IEMbase represents this as autosomal recessive PNPO-related pyridoxamine 5-phosphate oxidase deficiency, with alternate labels pyridoxal 5-phosphate dependent seizures and PNPO deficiency. Treatability is marked yes.
The characteristic biochemical signal includes abnormal CSF 5-hydroxyindoleacetic acid, CSF pyridoxal 5-phosphate, and plasma pyridoxamine. Additional biochemical rows include CSF 3-methoxytyrosine, CSF HVA, plasma and CSF threonine, plasma glycine, plasma lactate and glucose, vanillactic acid in urine, and the pyridoxamine/pyridoxic acid ratio.
The characteristic clinical row is pharmacoresistant seizures. Additional clinical rows include developmental delay, hypotonia, low Apgar scores, prematurity, and vomiting. The treatment row is pyridoxal 5-phosphate.
DisMech phenotype coverage
No valid local DisMech target was found for PNPO deficiency or pyridoxamine 5-phosphate oxidase deficiency.
The best fuzzy candidate, COA3-Related_COX_Deficiency.yaml, is a false
positive. COA3-related COX deficiency is a mitochondrial complex IV assembly
factor disorder with COA3/CCDC56, not a vitamin B6 cofactor-synthesis disorder.
Local hypophosphatasia mentions extracellular pyridoxal 5-phosphate, but it is
not PNPO deficiency.
Concordance and completeness
Judgement: true local gap.
This record is a treatable PLP-biosynthesis/cofactor disorder with pharmacoresistant neonatal or early-life seizures. It requires a separate PNPO entry rather than mapping to a mitochondrial COX assembly disease.
Curation actions
- Keep this IEMbase record unmapped for now.
- Add a future standalone PNPO deficiency entry.
- Prioritize PLP-dependent seizure mechanism, CSF PLP and biogenic amine abnormalities, pyridoxamine/pyridoxic acid ratio, pharmacoresistant seizures, prematurity/low Apgar presentation, and PLP treatment.