ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.3429C>T (p.Pro1143=)

gnomAD frequency: 0.00024  dbSNP: rs377703085
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000403466 SCV000351357 uncertain significance 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, 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.
Invitae RCV000875471 SCV001017804 likely benign Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2024-01-31 criteria provided, single submitter clinical testing
GeneDx RCV001660565 SCV001873901 likely benign not provided 2021-02-18 criteria provided, single submitter clinical testing
Ambry Genetics RCV002450840 SCV002614746 likely benign Inborn genetic diseases 2017-06-29 criteria provided, single submitter clinical testing This alteration is classified as likely 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.
PreventionGenetics, part of Exact Sciences RCV003409441 SCV004115961 uncertain significance ATP13A2-related condition 2023-01-17 criteria provided, single submitter clinical testing The ATP13A2 c.3127C>T variant is predicted to result in the amino acid substitution p.Arg1043Cys. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.054% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-17312830-G-A). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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