ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.1617G>T (p.Leu539=)

gnomAD frequency: 0.01259  dbSNP: rs61739752
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000116433 SCV000150358 benign not specified 2013-08-15 criteria provided, single submitter clinical testing
Eurofins Ntd Llc (ga) RCV000116433 SCV000226526 benign not specified 2014-11-08 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000116433 SCV000313950 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000273886 SCV000351389 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.
Labcorp Genetics (formerly Invitae), Labcorp RCV001080403 SCV000762693 benign Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2024-01-31 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000710704 SCV000840991 benign not provided 2017-09-06 criteria provided, single submitter clinical testing
Ambry Genetics RCV002313853 SCV000847449 benign Inborn genetic diseases 2016-03-21 criteria provided, single submitter clinical testing This alteration is classified as 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.
GeneDx RCV000710704 SCV001943093 benign not provided 2018-10-31 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000710704 SCV005285495 benign not provided criteria provided, single submitter not provided

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