ClinVar Miner

Submissions for variant NM_000282.4(PCCA):c.1268C>T (p.Pro423Leu)

gnomAD frequency: 0.00001  dbSNP: rs1443858896
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000669921 SCV000794721 likely pathogenic Propionic acidemia 2017-10-16 criteria provided, single submitter clinical testing
Invitae RCV000669921 SCV001222394 pathogenic Propionic acidemia 2023-11-07 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 423 of the PCCA protein (p.Pro423Leu). This variant is present in population databases (no rsID available, gnomAD 0.01%). This missense change has been observed in individual(s) with propionic acidemia (PMID: 10518292, 20549364, 22033733). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as 1193C>T; P398L. ClinVar contains an entry for this variant (Variation ID: 554310). 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 PCCA protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects PCCA function (PMID: 2037281, 22033733). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV000669921 SCV003813205 likely pathogenic Propionic acidemia 2022-05-24 criteria provided, single submitter clinical testing

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