ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.2970G>A (p.Val990=)

gnomAD frequency: 0.41522  dbSNP: rs761421
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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000116439 SCV000150364 benign not specified 2013-08-15 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000116439 SCV000313954 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000360410 SCV000351368 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 RCV000675895 SCV000841002 benign not provided 2017-04-20 criteria provided, single submitter clinical testing
Ambry Genetics RCV002312029 SCV000845976 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: 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 RCV001511875 SCV001719190 benign Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2024-02-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000360410 SCV001775398 benign Kufor-Rakeb syndrome 2021-07-14 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001554184 SCV001775399 benign Autosomal recessive spastic paraplegia type 78 2021-07-14 criteria provided, single submitter clinical testing
GeneDx RCV000675895 SCV001900460 benign not provided 2018-07-06 criteria provided, single submitter clinical testing
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan RCV000116439 SCV005087432 benign not specified 2024-07-15 criteria provided, single submitter clinical testing This variant is classified as Benign based on local population frequency. This variant was detected in 71% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 66. Only high quality variants are reported.
Breakthrough Genomics, Breakthrough Genomics RCV000675895 SCV005285489 benign not provided criteria provided, single submitter not provided
Mayo Clinic Laboratories, Mayo Clinic RCV000675895 SCV000801621 benign not provided 2015-10-19 no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000116439 SCV001807338 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000116439 SCV001958916 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000116439 SCV001966062 benign not specified no assertion criteria provided clinical testing

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