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NM_018129.4(PNPO):c.106C>T (p.Pro36Ser) AND Pyridoxal phosphate-responsive seizures

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 22, 2023
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV001208787.7

Allele description [Variation Report for NM_018129.4(PNPO):c.106C>T (p.Pro36Ser)]

NM_018129.4(PNPO):c.106C>T (p.Pro36Ser)

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.106C>T (p.Pro36Ser)
HGVS:
  • NC_000017.11:g.47941781C>T
  • NG_008744.1:g.5259C>T
  • NM_018129.4:c.106C>TMANE SELECT
  • NP_060599.1:p.Pro36Ser
  • NC_000017.10:g.46019147C>T
  • NM_018129.3:c.106C>T
Protein change:
P36S
Links:
dbSNP: rs2035939125
NCBI 1000 Genomes Browser:
rs2035939125
Molecular consequence:
  • NM_018129.4:c.106C>T - missense variant - [Sequence Ontology: SO:0001583]

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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001380194Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(May 22, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV001380194.5

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

Description

This sequence change replaces proline, which is neutral and non-polar, with serine, which is neutral and polar, at codon 36 of the PNPO protein (p.Pro36Ser). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PNPO-related conditions. ClinVar contains an entry for this variant (Variation ID: 939393). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Feb 28, 2024