ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.146G>T (p.Gly49Val)

gnomAD frequency: 0.00001  dbSNP: rs372254666
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001048775 SCV001212795 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2021-09-02 criteria provided, single submitter clinical testing This sequence change replaces glycine with valine at codon 49 of the ATP13A2 protein (p.Gly49Val). The glycine residue is weakly conserved and there is a moderate physicochemical difference between glycine and valine. This variant is present in population databases (rs372254666, ExAC 0.002%). 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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). 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.
Mayo Clinic Laboratories, Mayo Clinic RCV001509026 SCV001715513 uncertain significance not provided 2019-06-09 criteria provided, single submitter clinical testing
Ambry Genetics RCV002393239 SCV002697503 uncertain significance Inborn genetic diseases 2019-02-08 criteria provided, single submitter clinical testing The p.G49V variant (also known as c.146G>T), located in coding exon 3 of the ATP13A2 gene, results from a G to T substitution at nucleotide position 146. The glycine at codon 49 is replaced by valine, an amino acid with dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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