ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.1171G>A (p.Val391Ile)

gnomAD frequency: 0.00012  dbSNP: rs113105667
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000595185 SCV000706630 uncertain significance not provided 2017-03-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV002317339 SCV000851627 uncertain significance Inborn genetic diseases 2018-12-29 criteria provided, single submitter clinical testing The p.V391I variant (also known as c.1171G>A), located in coding exon 12 of the ATP13A2 gene, results from a G to A substitution at nucleotide position 1171. The valine at codon 391 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.
Fulgent Genetics, Fulgent Genetics RCV000763771 SCV000894673 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2018-10-31 criteria provided, single submitter clinical testing
Invitae RCV000763771 SCV001545164 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2023-09-19 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 391 of the ATP13A2 protein (p.Val391Ile). This variant is present in population databases (rs113105667, gnomAD 0.05%). 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: 500604). 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 RCV000595185 SCV001995254 uncertain significance not provided 2019-11-13 criteria provided, single submitter clinical testing 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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