ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.473C>T (p.Ser158Leu)

dbSNP: rs180177225
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000186309 SCV000485635 likely pathogenic Primary hyperoxaluria, type I 2016-01-20 criteria provided, single submitter clinical testing
GenePathDx, GenePath diagnostics RCV000186309 SCV000616342 likely pathogenic Primary hyperoxaluria, type I 2017-07-07 criteria provided, single submitter clinical testing
Invitae RCV001233993 SCV001406618 pathogenic not provided 2023-12-14 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with leucine, which is neutral and non-polar, at codon 158 of the AGXT protein (p.Ser158Leu). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with primary hyperoxaluria type 1 (PMID: 15849466, 17460142, 17495019, 23430879, 25629080, 30541997). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 204103). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt AGXT protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects AGXT function (PMID: 18782763, 22018727, 22923379). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV000186309 SCV004196514 pathogenic Primary hyperoxaluria, type I 2023-10-17 criteria provided, single submitter clinical testing
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000186309 SCV000239644 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided in vitro
Yale Center for Mendelian Genomics, Yale University RCV000186309 SCV002106578 pathogenic Primary hyperoxaluria, type I 2019-01-17 no assertion criteria provided literature only

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