ClinVar Miner

Submissions for variant NM_018129.4(PNPO):c.784T>C (p.Ter262Gln)

dbSNP: rs104894631
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Neuberg Centre For Genomic Medicine, NCGM RCV000006898 SCV004047196 pathogenic Pyridoxal phosphate-responsive seizures criteria provided, single submitter clinical testing The stop lost p.*262Qext*28 in PNPO (NM_018129.4) has been previously reported in homozygous form in individuals affected with Pyridoxamine 5'-phosphate oxidase deficiency. Expression studies in Chinese hamster ovary cells showed that the stop codon (X262Q) mutation was null activity mutation (Mills et al, 2005). The p.*262Qext*28 variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.Ter262GlnextTer28 variant in the stop codon (Ter/*) at position 262, changing it to a Glutamine-codon (a no-stop variant) and adding a tail of new amino acids to the protein’s C-terminus, ending at a new stop codon (Ter/*) at position 28. The nucleotide c.784 in PNPO is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic. The observed variant was also detected in the spouse.
OMIM RCV000006898 SCV000027094 pathogenic Pyridoxal phosphate-responsive seizures 2005-04-15 no assertion criteria provided literature only

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