ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.2989C>T (p.Arg997Trp)

gnomAD frequency: 0.00004  dbSNP: rs773926580
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001757252 SCV001996841 uncertain significance not provided 2019-11-11 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV001882904 SCV002111353 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2021-12-17 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 997 of the PIGO protein (p.Arg997Trp). 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 1310184). This variant has not been reported in the literature in individuals affected with PIGO-related conditions. This variant is present in population databases (rs773926580, gnomAD 0.003%).

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