ClinVar Miner

Submissions for variant NM_033109.5(PNPT1):c.1528G>C (p.Ala510Pro)

gnomAD frequency: 0.00001  dbSNP: rs879255657
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine RCV000239707 SCV000298031 pathogenic Combined oxidative phosphorylation defect type 13 criteria provided, single submitter research
Labcorp Genetics (formerly Invitae), Labcorp RCV002518548 SCV003524590 likely pathogenic not provided 2022-12-18 criteria provided, single submitter clinical testing In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. Studies have shown that this missense change alters PNPT1 gene expression (PMID: 27759031). 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 PNPT1 protein function. ClinVar contains an entry for this variant (Variation ID: 253224). This missense change has been observed in individual(s) with combined oxidative phosphorylation deficiency (PMID: 27759031). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces alanine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 510 of the PNPT1 protein (p.Ala510Pro).
OMIM RCV000239707 SCV002546569 pathogenic Combined oxidative phosphorylation defect type 13 2022-07-11 no assertion criteria provided literature only

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