ClinVar Miner

Submissions for variant NM_000282.4(PCCA):c.1558A>T (p.Ser520Cys) (rs112237881)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000493022 SCV000581973 uncertain significance not provided 2018-11-01 criteria provided, single submitter clinical testing The S520C variant has not been published as a pathogenic variant, nor has it been reported as a benignvariant to our knowledge. The S520C variant is observed in 0.4%-1.6% of alleles from individuals ofAfrican background in the 1000 Genomes Project and in the ExAC dataset (1000 GenomesConsortium et al., 2015; Lek et al., 2016). The S520C variant is a non-conservative amino acidsubstitution, which is likely to impact secondary protein structure as these residues differ in polarity,charge, size and/or other properties. This substitution occurs at a position that is not conserved. Insilico analysis is inconsistent in its predictions as to whether or not the variant is damaging to theprotein structure/function. In summary, based on the currently available information, it is unclearwhether this variant is a pathogenic variant or a rare benign variant.
Invitae RCV001083571 SCV001057872 likely benign Propionic acidemia 2020-12-04 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001083571 SCV001269314 uncertain significance Propionic acidemia 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

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