ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.976del (p.Val326fs) (rs180177301)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169587 SCV000221094 likely pathogenic Primary hyperoxaluria, type I 2015-01-28 criteria provided, single submitter literature only
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001328354 SCV001519444 pathogenic Primary hyperoxaluria 2021-03-12 criteria provided, single submitter clinical testing Variant summary: AGXT c.976delG (p.Val326TyrfsX15) 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. The variant allele was found at a frequency of 8e-06 in 249898 control chromosomes (gnomAD and publication data). c.976delG has been reported in the literature in multiple individuals affected with Primary Hyperoxaluria Type 1 (Pirulli_1999, van der Hoeven_2012, Kuhn_2014, Isiyel_2016). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One ClinVar submitter (evaluation after 2014) cites the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Invitae RCV001382061 SCV001580668 pathogenic not provided 2020-10-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Val326Tyrfs*15) in the AGXT gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with hyperoxaluria (PMID: 26383609, 22844106). ClinVar contains an entry for this variant (Variation ID: 189161). Loss-of-function variants in AGXT are known to be pathogenic (PMID: 19479957). For these reasons, this variant has been classified as Pathogenic.
Clinical Biochemistry Laboratory,Health Services Laboratory RCV000169587 SCV000239767 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided research

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