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A very rare neonatal epileptic encephalopathy disorder characterized clinically by onset of severe seizures within hours of birth that are not responsive to anticonvulsants, but are responsive to treatment with pyridoxal phosphate.
Features include: Progressive microcephaly, Encephalopathy, Decreased CSF homovanillic acid concentration, and Axial hypotonia and 13 more.
Organ System | Phenotype Count | Example Features |
|---|---|---|
Brain and nerves | 5 | Encephalopathy, Seizure, Global developmental delay |
Head and neck | 1 | Progressive microcephaly |
Muscles | 1 | Axial hypotonia |
Eyes | 1 | Rotary nystagmus |
Lab test results | 1 | Increased circulating lactate concentration |
Growth and development | 1 | Failure to thrive |
Blood and immune system | 1 | Low red blood cell count (anemia) |
Digestive system | 1 | Feeding difficulties in infancy |
Metabolism | 1 | Metabolic acidosis |
As of 2022, approximately 90 individuals have been identified with pyridox(am)ine 5'-phosphate oxidase (PNPO) deficiency based on the identification of biallelic pathogenic variants in PNPO. The following description of the phenotypic features of PNPO deficiency is based on these reports [, , , , , , , , , , , , , , , , ]. includes a review of all publications up to 2015. also includes a review of all publications up to 2021; some affected individuals included in subsequent follow-up reports may have been counted more than once. Note that the clinical presentations of PNPO deficiency, ALDH7A1 deficiency, and PLPHP deficiency (also referred to as PLPBP or PROSC deficiency) are indistinguishable . The spectrum of the PNPO deficiency phenotype ranges from classic (i.e.
Source: GeneReviews — "PNPO Deficiency"
PNPO function has not been fully characterized.
Pyridoxal phosphate-responsive seizures is caused by mutations in the PNPO gene on chromosome 17.
No genotype-phenotype correlations have been reported. Nonetheless, the following observations about PN responsiveness may be helpful in guiding clinical management. See for details.
Seizures in individuals homozygous for the variant may respond to treatment with PN .
The seizures of four of the seven individuals reported to be homozygous or compound heterozygous for the variant responded to treatment with PN .
The majority of individuals who are homozygous for the variant , which may be present alongside other homozygous or compound heterozygous PNPO pathogenic variants (i.e., have a total of two or three pathogenic variants), have late-onset seizures that responded to treatment with PN . See also , PNPO-specific laboratory technical considerations.
Source: GeneReviews — "PNPO Deficiency"
Not all individuals homozygous for the variant develop seizures .
Source: GeneReviews — "PNPO Deficiency"
No consensus clinical diagnostic criteria for pyridox(am)ine 5'-phosphate oxidase (PNPO) deficiency have been published.
PNPO deficiency should be suspected in individuals with the following suggestive clinical phenotypes, positive response to a standardized vitamin B6 trial, supportive laboratory findings, and family history.
Clinical Findings
Classic PNPO deficiency (defined as neonatal onset) in premature infants and neonates
Source: GeneReviews — "PNPO Deficiency"
PNPO deficiency must be distinguished from ALDH7A1 deficiency and PLPHP deficiency (also referred to as PLPBP deficiency), as well as other disorders associated with pyridoxine (PN)- and pyridoxal 5'-phosphate (PLP)-responsive seizures . Table 3. Selected Disorders of Interest in the Differential Diagnosis of PNPO Deficiency
Gene | Disorder | Laboratory Features | Response to PN/PLP | Clinical Features |
|---|---|---|---|---|
ALDH7A1 | Pyridoxine-dependent epilepsy – ALDH7A1 (PDE-ALDH7A1)2 | -AASA levels irrespective of treatment w/PN or PLP. May also have levels of pipecolic acid. Low PLP levels in plasma CSF prior to vitamin B6 supplementation. |
Genetic testing for PNPO is available. Testing is considered confirmatory for diagnosis.
No approved treatments are currently available for pyridoxal phosphate-responsive seizures. The disease remains an area of unmet medical need.
No clinical practice guidelines for pyridox(am)ine 5'-phosphate oxidase (PNPO) deficiency have been published; however, these are currently being formulated by an international PNPO consortium [Author, personal observation].
To establish the extent of disease and needs in an individual diagnosed with PNPO deficiency, the evaluations summarized in this section (if not performed as part of the evaluation that led to the diagnosis) are recommended.
For classic and late-onset PNPO deficiency
Neurologic examination to evaluate eye movement and muscle tone (for hypotonia or rigidity), and to describe seizure semiology
EEG including sleep and wake cycles (preferably with a recording time of two hours) beginning at the time of seizure onset
Physical examination including measurement of weight, length, and head circumferenceand evaluation of liver involvement by determination of transaminases, liver function tests, and abdominal ultrasound
Consultation with a medical geneticist, certified genetic counselor, or certified advanced genetic nurse to inform affected individuals and their families about the nature, mode of inheritance, and implications of PNPO deficiency in order to facilitate medical and personal decision making
For late-onset PNPO deficiency
Developmental/educational assessment using age-appropriate standardized testing
Brain MRI in individuals with abnormal development
Treatment of Manifestations
Targeted Therapy
Source: GeneReviews — "PNPO Deficiency"
Several anti-seizure medications (such as carbamazepine, valproate, phenytoin, and phenobarbital) can cause a low plasma concentration of PLP .
Source: GeneReviews — "PNPO Deficiency"
Search ClinicalTrials.gov in the US and EU Clinical Trials Register in Europe for access to information on clinical studies for a wide range of diseases and conditions. Note: There may not be clinical trials for this disorder.
Source: GeneReviews — "PNPO Deficiency"
1 trial found
Table 4. Recommended Surveillance for Individuals with PNPO Deficiency
System/Concern | Evaluation | Frequency |
|---|---|---|
Seizure control | In outpatient epilepsy clinic | 1st yr of life: every 3-6 mos; Children adults: every 3-12 mos EEG |
Assessment of growth | Body weight, height, head circumference | Children: at each visit |
Neurologic findings | Neurologic exam (incl assessment of deep tendon reflexes) for emergence of new findings /or response to medications used in symptomatic treatment | At each visit Adverse effects |
of PLP therapy | Complete blood count | 1st yr of life: every 3-6 mos |
Liver assessment | Transaminases clotting factors; alpha-fetoprotein | Age 10 yrs: transaminases alpha-fetoprotein every 3-6 mos; If transaminases are 3x normal, also assess clotting factors Ultrasound |
Educational needs | Assessment | Children age 6 yrs: every 4-6 mos; Children age 6 yrs: annually |
Family/Community | Assess family need for social work support (e.g., palliative/respite care, home nursing, other local resources), care coordination, or follow-up genetic counseling if new questions arise (e.g., family planning). | At each visit PLP = pyridoxal 5'-phosphate |
Source: GeneReviews — "PNPO Deficiency"
Estimated prevalence: Unknown (Unknown prevalence).
1 clinical trial registered. Interventions under study include other interventions. Research is primarily sponsored by academic and government institutions.
13 publications have been identified in PubMed for pyridoxal phosphate-responsive seizures. Research spans Case Report / Case Series (31%), Other (23%), and Basic Science / Preclinical (23%).
Research Type | Count | % of Total |
|---|---|---|
Patient case studies | 4 | 31% |
Other research | 3 | 23% |
Laboratory research | 3 | 23% |
Research summaries | 2 | 15% |
Clinical study results | 1 | 8% |
Wang B (2026). [PMID: 42017538](https://pubmed.ncbi.nlm.nih.gov/42017538/). *Hum Mol Genet*. [Basic Science / Preclinical]
Webster R (2026). [PMID: 41527660](https://pubmed.ncbi.nlm.nih.gov/41527660/). *JIMD reports*. [Case Report / Case Series]
Brands MM (2026). [PMID: 41429136](https://pubmed.ncbi.nlm.nih.gov/41429136/). *Neuropediatrics*. [Case Report / Case Series]
Gowda VK (2026). [PMID: 41511620](https://pubmed.ncbi.nlm.nih.gov/41511620/). *Indian J Pediatr*. [Other]
de Puyraimond C (2026). [PMID: 42016347](https://pubmed.ncbi.nlm.nih.gov/42016347/). *JIMD Rep*. [Clinical Trial Publication]
Lee JZC (2025). [PMID: 40589945](https://pubmed.ncbi.nlm.nih.gov/40589945/). *Molecular genetics and metabolism reports*. [Case Report / Case Series]
Fu W (2025). [PMID: 41296493](https://pubmed.ncbi.nlm.nih.gov/41296493/). *J Neurogenet*. [Basic Science / Preclinical]
De Liso P (2025). [PMID: 41635634](https://pubmed.ncbi.nlm.nih.gov/41635634/). *Mol Genet Metab Rep*. [Other]
De Liso P (2025). [PMID: 40349651](https://pubmed.ncbi.nlm.nih.gov/40349651/). *Eur J Paediatr Neurol*. [Other]
Falsaperla R (2025). [PMID: 41149778](https://pubmed.ncbi.nlm.nih.gov/41149778/). *Neurology international*. [Review / Meta-Analysis]
Data assembled from 9 of 12 sources · Last updated Sep 17, 2026, 7:49 PM UTC
Online Mendelian Inheritance in Man
European rare disease database
Genetic and Rare Diseases Info Center
Szs in affected children respond to supraphysiologic doses of PN (or PLP).
While most newborns have szs soon after birth, some have late onset (i.e., age 2 mos, or as late as adolescence). DD/ID is common, w/more favorable outcome observed in those with late-onset szs. |
PLPBP | PLPBP (PLPHP) deficiency2 | Secondary biochemical abnormalities suggesting abnormal vitamin B6 metabolism may be present, as may lactic acidosis. | Szs in affected children respond to supraphysiologic doses of PN (or PLP). | Majority have sz onset w/in 1st wk of life; some children present as late as 6 mos.3 Acquired microcephaly, structural brain abnormalities, DD/ID are variable. Pyridoxine (vitamin B6)-responsive seizures4 |
PGAP3 | Hyperphosphatasia w/ID syndrome 42 (OMIM 615716) | serum ALP | Szs may respond to PN. | DD/ID, structural brain anomalies, dysmorphic facies, szs |
ALDH4A1 | Hyperprolinaemia type II2 (OMIM 239510) | Markedly plasma proline levels as well as P5C in urine | Szs may respond to ASM to PN. | Szs usually manifest beyond neonatal period, may occur w/febrile infections, may respond to common ASM. Persons may have ID or normal intellectual ability. |
ALPL | Infantile hypophosphatasia5 | Using appropriate pediatric normative reference values, this disorder is suspected w/low serum ALP enzyme activity. | Vitamin B6-responsive seizures may occur. | Clinical signs may be recognized between birth age 6 mos resemble rickets. Prior to availability of enzyme replacement therapy, ~50% succumbed to respiratory failure caused by undermineralization of ribs. Intractable szs may precede biochemical or radiographic manifestations of rickets. |
CACNA1A | Developmental epileptic encephalopathy 426 (OMIM 617106) | No assoc biochemical abnormalities | A female w/CACNA1A-related absence epilepsy ataxia responded dramatically to PN.7 | — |
KCNQ2 | KCNQ2-related disorders6 | No assoc biochemical abnormalities. | Some w/neonatal epilepsy are vitamin B6 responsive.8 | May present w/benign familial neonatal epilepsy or severe neonatal epileptic encephalopathy. |
Source: GeneReviews — "PNPO Deficiency"