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NM_018129.4(PNPO):c.674G>A (p.Arg225His) AND Pyridoxal phosphate-responsive seizures

Germline classification:
Pathogenic (6 submissions)
Last evaluated:
Aug 16, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000208779.14

Allele description [Variation Report for NM_018129.4(PNPO):c.674G>A (p.Arg225His)]

NM_018129.4(PNPO):c.674G>A (p.Arg225His)

Gene:
PNPO:pyridoxamine 5'-phosphate oxidase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q21.32
Genomic location:
Preferred name:
NM_018129.4(PNPO):c.674G>A (p.Arg225His)
HGVS:
  • NC_000017.11:g.47946670G>A
  • NG_008744.1:g.10148G>A
  • NM_018129.4:c.674G>AMANE SELECT
  • NP_060599.1:p.Arg225His
  • NC_000017.10:g.46024036G>A
  • NM_018129.3:c.674G>A
Protein change:
R225H; ARG225HIS
Links:
OMIM: 603287.0005
Molecular consequence:
  • NM_018129.4:c.674G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
2

Condition(s)

Name:
Pyridoxal phosphate-responsive seizures (PNPOD)
Synonyms:
EPILEPTIC ENCEPHALOPATHY, NEONATAL, PNPO-RELATED; SEIZURES, PYRIDOXINE-RESISTANT, PLP-SENSITIVE; Pyridoxal 5'-phosphate-dependent epilepsy; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0012407; MedGen: C1864723; Orphanet: 79096; OMIM: 610090

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000264658OMIM
no assertion criteria provided
Pathogenic
(Feb 9, 2022)
germlineliterature only

Plecko, B., Paul, K., Mills, P., Clayton, P., Paschke, E., Maier, O., Hasselmann, O., Schmiedel, G., Kanz, S., Connolly, M., Wolf, N., Struys, E., Stockler, S., Abela, L., Hofer, D. Pyridoxine responsiveness in novel mutations of the PNPO gene. Neurology 82: 1425-1433, 2014.,

SCV000644981Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Aug 16, 2023)
germlineclinical testing

PubMed (6)
[See all records that cite these PMIDs]

SCV001164129Génétique des Maladies du Développement, Hospices Civils de Lyon
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicunknownclinical testing

PubMed (3)
[See all records that cite these PMIDs]

SCV001370445Centre for Mendelian Genomics, University Medical Centre Ljubljana
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 1, 2016)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV001429012Institute of Human Genetics, University of Leipzig Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jul 3, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002802817Fulgent Genetics, Fulgent Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Nov 16, 2021)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineyes2not providednot providednot providednot providedclinical testing
not providedunknownyesnot providednot providednot providednot providednot providedclinical testing
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Typical and atypical phenotypes of PNPO deficiency with elevated CSF and plasma pyridoxamine on treatment.

Ware TL, Earl J, Salomons GS, Struys EA, Peters HL, Howell KB, Pitt JJ, Freeman JL.

Dev Med Child Neurol. 2014 May;56(5):498-502. doi: 10.1111/dmcn.12346. Epub 2013 Nov 23.

PubMed [citation]
PMID:
24266778

The genetic landscape of infantile spasms.

Michaud JL, Lachance M, Hamdan FF, Carmant L, Lortie A, Diadori P, Major P, Meijer IA, Lemyre E, Cossette P, Mefford HC, Rouleau GA, Rossignol E.

Hum Mol Genet. 2014 Sep 15;23(18):4846-58. doi: 10.1093/hmg/ddu199. Epub 2014 Apr 29.

PubMed [citation]
PMID:
24781210
See all PubMed Citations (7)

Details of each submission

From OMIM, SCV000264658.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided

Description

In 8 patients from 6 unrelated families with pyridoxamine 5-prime-phosphate oxidase deficiency (PNPOD; 610090), Plecko et al. (2014) identified a homozygous c.674G-A transition (c.674G-A, NM_001182.3) in exon 7 of the PNPO gene, resulting in an arg225-to-his (R225H) substitution at a conserved region in the PLP binding site. The mutation, which segregated with the disorder in the families, was not found in 100 control alleles. In vitro functional expression studies in CHO cells showed that the R225H mutant protein had no detectable enzyme activity. Most of the patients had a partial or even complete response to pyridoxine treatment. The 6 families derived from the former Yugoslavia.

In a 7-year-old Greek boy with PNPOD, Ware et al. (2014) identified a homozygous R225 substitution in the PNPO gene. Each unaffected parent was heterozygous for the mutation. Functional studies of the variant were not performed. The patient showed an initial response to treatment with pyridoxine, and later showed a sustained therapeutic response to monotherapy with high-dose pyridoxal 5-prime phosphate (PLP). Ware et al. (2014) hypothesized that some degree of pyridoxine 5-prime-phosphate binding was preserved in the mutant protein, resulting in pyridoxine responsiveness.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000644981.6

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 225 of the PNPO protein (p.Arg225His). This variant is present in population databases (rs550423482, gnomAD 0.007%). This missense change has been observed in individual(s) with pyridoxine-responsive epilepsy or neonatal onset epilepsy (PMID: 24266778, 24645144, 24658933, 24781210, 25762494). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 223153). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PNPO protein function. Experimental studies have shown that this missense change affects PNPO function (PMID: 24645144, 24658933). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Génétique des Maladies du Développement, Hospices Civils de Lyon, SCV001164129.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001370445.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant was classified as: Pathogenic. This variant was detected in homozygous state.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

From Institute of Human Genetics, University of Leipzig Medical Center, SCV001429012.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided2not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided2not providednot providednot provided

From Fulgent Genetics, Fulgent Genetics, SCV002802817.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: May 12, 2024