ClinVar Miner

Submissions for variant NM_005609.4(PYGM):c.517G>A (p.Gly173Arg) (rs141265458)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000523818 SCV000617959 uncertain significance not provided 2017-07-26 criteria provided, single submitter clinical testing The G173R variant in the PYGM gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The G173R variant is observed in 17/10398 (0.16%) alleles from individuals of African background in the ExAC dataset (Lek et al., 2016). The G173R variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved in mammals. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret G173R as a variant of uncertain significance.
Invitae RCV000812757 SCV000953080 uncertain significance Glycogen storage disease, type V 2018-12-26 criteria provided, single submitter clinical testing This sequence change replaces glycine with arginine at codon 173 of the PYGM protein (p.Gly173Arg). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and arginine. This variant is present in population databases (rs141265458, ExAC 0.2%). This variant has not been reported in the literature in individuals with PYGM-related conditions. ClinVar contains an entry for this variant (Variation ID: 449640). 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: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). 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.

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