ClinVar Miner

Submissions for variant NM_022089.4(ATP13A2):c.*130C>T

gnomAD frequency: 0.00217  dbSNP: rs189334432
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV000317055 SCV000351353 likely 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
CeGaT Center for Human Genetics Tuebingen RCV000513062 SCV000608461 likely benign not provided 2024-07-01 criteria provided, single submitter clinical testing ATP13A2: PP3, BS2
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago RCV000768152 SCV000898531 uncertain significance Kufor-Rakeb syndrome; Autosomal recessive spastic paraplegia type 78 2021-03-30 criteria provided, single submitter clinical testing ATP13A2 NM_001141974 exon 27 p.Pro1124Leu (c.3371C>T): This variant has not been reported in the literature but is present in 0.5% (460/81050) of European alleles, including 2 homozygotes in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs189334432). This variant is present in ClinVar (Variation ID:293762). Evolutionary conservation and computational predictive tools for this variant are limited or unavailable. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.
GeneDx RCV000513062 SCV001753062 likely benign not provided 2020-08-13 criteria provided, single submitter clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000513062 SCV001740354 likely benign not provided no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000513062 SCV001800518 likely benign not provided no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000513062 SCV001975814 likely benign not provided no assertion criteria provided clinical testing

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