ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.265G>A (p.Val89Ile)

gnomAD frequency: 0.00003  dbSNP: rs534590083
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Baylor Genetics RCV001331223 SCV001523216 uncertain significance Kufor-Rakeb syndrome 2020-01-24 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
CeGaT Center for Human Genetics Tuebingen RCV001531614 SCV001746832 uncertain significance not provided 2021-03-01 criteria provided, single submitter clinical testing
Ambry Genetics RCV002431940 SCV002744114 uncertain significance Inborn genetic diseases 2017-12-16 criteria provided, single submitter clinical testing The p.V89I variant (also known as c.265G>A), located in coding exon 3 of the ATP13A2 gene, results from a G to A substitution at nucleotide position 265. The valine at codon 89 is replaced by isoleucine, an amino acid with highly similar 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV002546454 SCV003268151 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2023-06-29 criteria provided, single submitter clinical testing 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. 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. ClinVar contains an entry for this variant (Variation ID: 1029841). This variant has not been reported in the literature in individuals affected with ATP13A2-related conditions. This variant is present in population databases (rs534590083, gnomAD 0.004%). This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 89 of the ATP13A2 protein (p.Val89Ile).
GeneDx RCV001531614 SCV005375603 uncertain significance not provided 2023-11-13 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); 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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