ClinVar Miner

Submissions for variant NM_033109.5(PNPT1):c.1676C>G (p.Ala559Gly)

gnomAD frequency: 0.00038  dbSNP: rs149843729
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001332753 SCV001525160 uncertain significance Combined oxidative phosphorylation defect type 13 2019-11-13 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
GeneDx RCV001760432 SCV002008443 uncertain significance not provided 2024-06-18 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV001760432 SCV002011200 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001760432 SCV002308404 uncertain significance not provided 2024-01-19 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 559 of the PNPT1 protein (p.Ala559Gly). This variant is present in population databases (rs149843729, gnomAD 0.1%). This variant has not been reported in the literature in individuals affected with PNPT1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1031031). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Baylor Genetics RCV003333153 SCV004040673 uncertain significance Autosomal recessive nonsyndromic hearing loss 70 2023-03-07 criteria provided, single submitter clinical testing

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