ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.2T>C (p.Met1Thr)

gnomAD frequency: 0.00001  dbSNP: rs138584408
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000186271 SCV000788608 pathogenic Primary hyperoxaluria, type I 2017-05-18 criteria provided, single submitter clinical testing
Baylor Genetics RCV000186271 SCV001162941 likely pathogenic Primary hyperoxaluria, type I criteria provided, single submitter clinical testing
Invitae RCV001061218 SCV001225952 pathogenic not provided 2021-12-18 criteria provided, single submitter clinical testing This sequence change affects the initiator methionine of the AGXT mRNA. The next in-frame methionine is located at codon 38. This variant is present in population databases (rs138584408, gnomAD 0.05%). Disruption of the initiator codon has been observed in individuals with primary hyperoxaluria type 1 (PMID: 15365967, 24934730, 29456205). ClinVar contains an entry for this variant (Variation ID: 204065). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that disruption of the initiator codon affects AGXT function (PMID: 17495019). For these reasons, this variant has been classified as Pathogenic.
Clinical Biochemistry Laboratory,Health Services Laboratory RCV000186271 SCV000239596 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided research
Natera, Inc. RCV000186271 SCV002076446 pathogenic Primary hyperoxaluria, type I 2020-09-12 no assertion criteria provided clinical testing

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