ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.116_117dup (p.Ala40fs) (rs180177166)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000186382 SCV000486452 likely pathogenic Primary hyperoxaluria, type I 2016-06-03 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001175458 SCV001339029 likely pathogenic Primary hyperoxaluria 2020-03-30 criteria provided, single submitter clinical testing Variant summary: AGXT c.116_117dupCA (p.Ala40GlnfsX7) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. The variant allele was found at a frequency of 4e-05 in 247578 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in AGXT causing Primary Hyperoxaluria Type 1 (4e-05 vs 0.0024), allowing no conclusion about variant significance. c.116_117dupCA has been reported in the literature in individuals affected with Primary Hyperoxaluria Type 1 (Coulter-Mackie_2005,Williams_2007,2015). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and cited the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Clinical Biochemistry Laboratory,Health Services Laboratory RCV000186382 SCV000239732 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided research

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