ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.1658G>A (p.Arg553Gln)

gnomAD frequency: 0.00007  dbSNP: rs376011760
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001203112 SCV001374259 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2021-09-01 criteria provided, single submitter clinical testing This sequence change replaces arginine with glutamine at codon 553 of the ATP13A2 protein (p.Arg553Gln). The arginine residue is weakly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs376011760, ExAC 0.02%). This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest 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.
GeneDx RCV001773453 SCV001993001 uncertain significance not provided 2019-07-01 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 that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

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