ClinVar Miner

Submissions for variant NM_032634.4(PIGO):c.2506A>G (p.Met836Val)

gnomAD frequency: 0.00006  dbSNP: rs752108320
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000689194 SCV000816834 uncertain significance Hyperphosphatasia with intellectual disability syndrome 2 2021-08-27 criteria provided, single submitter clinical testing This sequence change replaces methionine with valine at codon 836 of the PIGO protein (p.Met836Val). The methionine residue is moderately conserved and there is a small physicochemical difference between methionine and valine. This variant is present in population databases (rs752108320, ExAC 0.01%). This variant has not been reported in the literature in individuals affected with PIGO-related conditions. 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 valine 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 RCV001771943 SCV002001328 uncertain significance not provided 2021-10-26 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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