ClinVar Miner

Submissions for variant NM_000282.4(PCCA):c.1593_1595del (p.Leu532del)

gnomAD frequency: 0.00001  dbSNP: rs937519016
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000670118 SCV000794934 uncertain significance Propionic acidemia 2017-10-19 criteria provided, single submitter clinical testing
GeneDx RCV001565479 SCV001788833 likely pathogenic not provided 2019-08-16 criteria provided, single submitter clinical testing Reported in an individual reported to have propionic acidemia who also had a second variant identified in the PCCA gene; although, no information was provided about how the diagnosis of propionic acidemia was established (Perez et al., 2003); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 12559849, 15464417)
Invitae RCV000670118 SCV002302089 likely pathogenic Propionic acidemia 2024-01-21 criteria provided, single submitter clinical testing This variant, c.1593_1595del, results in the deletion of 1 amino acid(s) of the PCCA protein (p.Leu532del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has been observed in individual(s) with propionic acidemia (PMID: 12559849; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 554477). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.
Baylor Genetics RCV000670118 SCV004202848 likely pathogenic Propionic acidemia 2023-09-24 criteria provided, single submitter clinical testing
Natera, Inc. RCV000670118 SCV002094979 likely pathogenic Propionic acidemia 2020-06-18 no assertion criteria provided clinical testing

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