ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.1876C>T (p.His626Tyr)

gnomAD frequency: 0.00001  dbSNP: rs778267471
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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 RCV000801923 SCV000941726 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2022-02-24 criteria provided, single submitter clinical testing This sequence change replaces histidine, which is basic and polar, with tyrosine, which is neutral and polar, at codon 626 of the ATP13A2 protein (p.His626Tyr). This variant is present in population databases (rs778267471, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 647413). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt ATP13A2 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 RCV001759525 SCV001996627 uncertain significance not provided 2019-11-07 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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