PNPO

Chr 17AR

pyridoxamine 5'-phosphate oxidase

Also known as: HEL-S-302, PDXPO

This enzyme catalyzes the oxidation of pyridoxine 5'-phosphate and pyridoxamine 5'-phosphate into pyridoxal 5'-phosphate (vitamin B6), which serves as an essential cofactor for neurotransmitter synthesis and homocysteine metabolism. Mutations cause pyridoxamine 5'-phosphate oxidase deficiency, a form of neonatal epileptic encephalopathy with autosomal recessive inheritance. The gene shows minimal constraint against loss-of-function variants, consistent with the recessive disease pattern.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 1.441 OMIM phenotype
Clinical SummaryPNPO
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Gene-Disease Validity (ClinGen)
pyridoxal phosphate-responsive seizures · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint
1.44LOEUF
pLI 0.000
Z-score 0.33
OE 0.90 (0.591.44)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.78Z-score
OE missense 0.82 (0.700.95)
120 obs / 146.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.90 (0.591.44)
00.351.4
Missense OE0.82 (0.700.95)
00.61.4
Synonymous OE0.93
01.21.6
LoF obs/exp: 13 / 14.4Missense obs/exp: 120 / 146.6Syn Z: 0.37

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

PNPO · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold
Clinical Literature
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