ClinVar Miner

Submissions for variant NM_000284.4(PDHA1):c.482A>G (p.Tyr161Cys)

dbSNP: rs1569190962
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV000679874 SCV000807255 pathogenic Pyruvate dehydrogenase E1-alpha deficiency 2017-09-01 criteria provided, single submitter clinical testing This variant has been previously reported as disease-causing and was found once in our laboratory in a 6-year-old female with global delays, left-sided weakness, possible Leigh syndrome, leg length discrepancy, speech delay, ophthalmologic abnormalities
Elsea Laboratory, Baylor College of Medicine RCV000679874 SCV001424215 pathogenic Pyruvate dehydrogenase E1-alpha deficiency 2020-04-01 criteria provided, single submitter clinical testing
GeneDx RCV003313130 SCV004012647 pathogenic not provided 2023-01-09 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34052969, 17043409)
3billion RCV000679874 SCV004013462 pathogenic Pyruvate dehydrogenase E1-alpha deficiency criteria provided, single submitter clinical testing The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. Functional studies provide moderate evidence of having a damaging effect on the gene or gene product (PMID: 17043409). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.98; 3Cnet: 0.93). The same nucleotide change resulting in the same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000560929/PMID: 17043409/3billion dataset). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

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