ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.2836A>T (p.Ile946Phe)

gnomAD frequency: 0.00091  dbSNP: rs55708915
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 8
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000116438 SCV000150363 uncertain significance not provided 2014-02-07 criteria provided, single submitter clinical testing
Invitae RCV000550501 SCV000640194 likely benign Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2024-01-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV002313855 SCV000848291 benign Inborn genetic diseases 2021-02-03 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Genomic Research Center, Shahid Beheshti University of Medical Sciences RCV000785011 SCV000923563 uncertain significance Autosomal recessive spastic paraplegia type 78 2019-01-01 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001097255 SCV001253516 uncertain significance Kufor-Rakeb syndrome 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Mayo Clinic Laboratories, Mayo Clinic RCV000116438 SCV001715510 uncertain significance not provided 2023-01-09 criteria provided, single submitter clinical testing
GeneDx RCV000116438 SCV001759516 likely benign not provided 2021-01-08 criteria provided, single submitter clinical testing Reported in the heterozygous state in an individual with Parkinson disease; however, a second ATP13A2 variant was not detected and I946F was observed in an unaffected control (Djarmati et al., 2009); This variant is associated with the following publications: (PMID: 19458722, 18075584, 12169656, 19705361, 19085912, 18075585)
GenomeConnect - Invitae Patient Insights Network RCV003483485 SCV004228802 not provided Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78; Parkinsonism due to ATP13A2 deficiency no assertion provided phenotyping only Variant interpreted as Uncertain significance and reported on 12-28-2020 by Lab Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.

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.