ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.698G>A (p.Arg233His)

gnomAD frequency: 0.00006  dbSNP: rs121908527
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000006002 SCV000486360 likely pathogenic Primary hyperoxaluria, type I 2016-05-24 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001385647 SCV001585584 pathogenic not provided 2024-02-16 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 233 of the AGXT protein (p.Arg233His). This variant is present in population databases (rs121908527, gnomAD 0.008%). This missense change has been observed in individual(s) with primary hyperoxaluria (PMID: 9192270, 17495019, 25629080). ClinVar contains an entry for this variant (Variation ID: 5648). 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: 17495019, 18448374). This variant disrupts the p.Arg233 amino acid residue in AGXT. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 9192270, 17495019, 18282470, 18448374, 25629080). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000006002 SCV002810968 pathogenic Primary hyperoxaluria, type I 2024-04-05 criteria provided, single submitter clinical testing
Baylor Genetics RCV000006002 SCV004192275 pathogenic Primary hyperoxaluria, type I 2024-02-26 criteria provided, single submitter clinical testing
OMIM RCV000006002 SCV000026184 pathogenic Primary hyperoxaluria, type I 1997-06-01 no assertion criteria provided literature only
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000006002 SCV000239671 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided in vitro

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