ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.3059A>G (p.Tyr1020Cys)

gnomAD frequency: 0.00003  dbSNP: rs372182128
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 3
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000710712 SCV000841003 uncertain significance not provided 2017-10-05 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001861952 SCV002181882 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2022-08-04 criteria provided, single submitter clinical testing This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 1020 of the ATP13A2 protein (p.Tyr1020Cys). This variant is present in population databases (rs372182128, gnomAD 0.006%). 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: 585470). 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.
Ambry Genetics RCV002442545 SCV002754164 uncertain significance Inborn genetic diseases 2018-02-14 criteria provided, single submitter clinical testing The p.Y1020C variant (also known as c.3059A>G), located in coding exon 26 of the ATP13A2 gene, results from an A to G substitution at nucleotide position 3059. The tyrosine at codon 1020 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.