ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.447_454del (p.Leu151fs)

dbSNP: rs180177221
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000186392 SCV000485620 pathogenic Primary hyperoxaluria, type I 2016-01-18 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001192773 SCV001361101 pathogenic Primary hyperoxaluria 2019-06-30 criteria provided, single submitter clinical testing Variant summary: AGXT c.447_454delGCTGCTGT (p.Leu151AsnfsX14) 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 was absent in 213810 control chromosomes (gnomAD) but has been reported in the literature in multiple individuals (primarily of Asian origin) affected with Primary Hyperoxaluria Type 1 (Williams_2007, Dutta_2016). These data indicate that the variant is very likely to be associated with disease. Enzymatic activity measured from a homozygous individual harboring this variant show 6% of mean control activity (Williams_2007). A ClinVar submission (evaluation after 2014) cites the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000186392 SCV002811683 pathogenic Primary hyperoxaluria, type I 2022-02-11 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000186392 SCV003809048 pathogenic Primary hyperoxaluria, type I 2023-01-24 criteria provided, single submitter clinical testing
Baylor Genetics RCV000186392 SCV004192850 pathogenic Primary hyperoxaluria, type I 2022-12-28 criteria provided, single submitter clinical testing
Invitae RCV003556230 SCV004292184 pathogenic not provided 2023-09-05 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu151Asnfs*14) in the AGXT gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in AGXT are known to be pathogenic (PMID: 19479957). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with primary hyperoxaluria (PMID: 17495019, 27512303). This variant is also known as c.445_452delGTGCTGCT. ClinVar contains an entry for this variant (Variation ID: 204185). For these reasons, this variant has been classified as Pathogenic.
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000186392 SCV000239742 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided research

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