Submissions for variant NM_022089.4(ATP13A2):c.3192C>T (p.Ala1064=)

gnomAD frequency: 0.40884  dbSNP: rs9435659

Total submissions: 14

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Genetic Services Laboratory, University of Chicago	RCV000116442	SCV000150367	benign	not specified	2013-08-15	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000116442	SCV000313957	benign	not specified		criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000309613	SCV000351364	benign	Kufor-Rakeb syndrome	2018-01-13	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Athena Diagnostics Inc	RCV000675891	SCV000841005	benign	not provided	2017-04-20	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002312032	SCV000845982	benign	Inborn genetic diseases	2016-01-08	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.
Invitae	RCV001511874	SCV001719189	benign	Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78	2024-02-01	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV000309613	SCV001775314	benign	Kufor-Rakeb syndrome	2021-07-14	criteria provided, single submitter	clinical testing
Genome-Nilou Lab	RCV001554137	SCV001775315	benign	Autosomal recessive spastic paraplegia type 78	2021-07-14	criteria provided, single submitter	clinical testing
GeneDx	RCV000675891	SCV001902809	benign	not provided	2018-07-05	criteria provided, single submitter	clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	RCV000309613	SCV000733950	benign	Kufor-Rakeb syndrome		no assertion criteria provided	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000675891	SCV000801617	benign	not provided	2015-10-22	no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center	RCV000116442	SCV001809377	benign	not specified		no assertion criteria provided	clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	RCV000116442	SCV001959883	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000116442	SCV001973827	benign	not specified		no assertion criteria provided	clinical testing