ClinVar Miner

Submissions for variant NM_033109.5(PNPT1):c.1453A>G (p.Met485Val)

dbSNP: rs767310806
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000195745 SCV000252110 likely pathogenic not provided 2019-06-12 criteria provided, single submitter clinical testing Not observed at a significant frequency and not observed in the homozygous state in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 26633542)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV004689670 SCV005184901 uncertain significance not specified 2024-05-10 criteria provided, single submitter clinical testing Variant summary: PNPT1 c.1453A>G (p.Met485Val) results in a conservative amino acid change located in the Exoribonuclease, phosphorolytic domain 1 (IPR001247) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 250782 control chromosomes. c.1453A>G has been reported in the literature in at-least two individuals affected with mitochondrion disease using WES (HosseiniBereshneh_2021, Retterer_2016). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 33812062, 26633542). ClinVar contains an entry for this variant (Variation ID: 215009). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
OMIM RCV002273982 SCV002559883 pathogenic Combined oxidative phosphorylation defect type 13 2022-08-11 no assertion criteria provided literature only

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