ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.139G>C (p.Gly47Arg)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Clinical Biochemistry Laboratory, Health Services Laboratory RCV003468719 SCV004217830 likely pathogenic Primary hyperoxaluria, type I 2023-10-27 criteria provided, single submitter curation ACMG:PS1 PM2 PP3
Labcorp Genetics (formerly Invitae), Labcorp RCV005100267 SCV005737159 pathogenic not provided 2024-02-02 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 47 of the AGXT protein (p.Gly47Arg). This variant is present in population databases (rs180177173, gnomAD 0.003%). This missense change has been observed in individual(s) with primary hyperoxaluria type 1 (PMID: 17460142, 20564000). 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: 24718375, 26149463). For these reasons, this variant has been classified as Pathogenic.

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