Submissions for variant NM_022089.4(ATP13A2):c.1926G>A (p.Ala642=)

gnomAD frequency: 0.00034  dbSNP: rs200916673

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Illumina Laboratory Services, Illumina	RCV000263146	SCV000351386	uncertain significance	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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
CeGaT Center for Human Genetics Tuebingen	RCV000658498	SCV000780266	likely benign	not provided	2022-10-01	criteria provided, single submitter	clinical testing	ATP13A2: BP4, BP7
Athena Diagnostics	RCV000658498	SCV000840994	benign	not provided	2017-12-19	criteria provided, single submitter	clinical testing
Ambry Genetics	RCV002317826	SCV000851428	likely benign	Inborn genetic diseases	2016-12-27	criteria provided, single submitter	clinical testing	This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, 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.
Labcorp Genetics (formerly Invitae), Labcorp	RCV001080875	SCV001015656	likely benign	Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78	2024-01-15	criteria provided, single submitter	clinical testing
GeneDx	RCV000658498	SCV001767455	likely benign	not provided	2020-02-06	criteria provided, single submitter	clinical testing
Mayo Clinic Laboratories, Mayo Clinic	RCV000658498	SCV000801626	likely benign	not provided	2015-12-16	no assertion criteria provided	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004549647	SCV004772621	likely benign	ATP13A2-related disorder	2019-11-26	no assertion criteria provided	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).