ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.3144C>G (p.Thr1048=)

gnomAD frequency: 0.03793  dbSNP: rs56126202
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 9
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000116441 SCV000313956 likely benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000359787 SCV000351365 benign Kufor-Rakeb syndrome 2018-01-12 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 RCV000538915 SCV000640196 benign Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2025-02-03 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000675892 SCV000841004 benign not provided 2017-11-17 criteria provided, single submitter clinical testing
Ambry Genetics RCV002312031 SCV000845999 benign Inborn genetic diseases 2016-03-02 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 RCV000675892 SCV001865548 benign not provided 2018-07-05 criteria provided, single submitter clinical testing
Breakthrough Genomics, Breakthrough Genomics RCV000675892 SCV005257084 likely benign not provided criteria provided, single submitter not provided
Genetic Services Laboratory, University of Chicago RCV000116441 SCV000150366 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Mayo Clinic Laboratories, Mayo Clinic RCV000675892 SCV000801618 benign not provided 2017-09-26 no assertion criteria provided clinical testing

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.