ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.339T>G (p.Ile113Met)

gnomAD frequency: 0.00004  dbSNP: rs370330559
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001211929 SCV001383497 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2022-09-27 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 113 of the PIGO protein (p.Ile113Met). This variant is present in population databases (rs370330559, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with PIGO-related conditions. ClinVar contains an entry for this variant (Variation ID: 942025). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The methionine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
GeneDx RCV001586054 SCV001820613 uncertain significance not provided 2020-09-18 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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