ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.107G>A (p.Arg36His)

gnomAD frequency: 0.00001  dbSNP: rs180177162
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Mendelics RCV000186278 SCV001136273 pathogenic Primary hyperoxaluria, type I 2019-05-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001383728 SCV001582980 pathogenic not provided 2024-01-13 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 36 of the AGXT protein (p.Arg36His). This variant is present in population databases (rs180177162, gnomAD 0.003%). This missense change has been observed in individual(s) with AGXT-related conditions (PMID: 30341509). 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: 204072). 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: 19479957, 29110180, 30341509). This variant disrupts the p.Arg36 amino acid residue in AGXT. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 15356974, 17495019, 22923379, 24718375, 24988064). 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.
Arcensus RCV000186278 SCV002564578 likely pathogenic Primary hyperoxaluria, type I 2013-02-01 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000186278 SCV002809718 likely pathogenic Primary hyperoxaluria, type I 2022-03-23 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000186278 SCV003828220 likely pathogenic Primary hyperoxaluria, type I 2021-11-12 criteria provided, single submitter clinical testing
Baylor Genetics RCV000186278 SCV004194227 likely pathogenic Primary hyperoxaluria, type I 2024-03-02 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001383728 SCV005050616 pathogenic not provided 2024-05-01 criteria provided, single submitter clinical testing AGXT: PM3:Strong, PM2, PM5, PP4, PS3:Supporting
GeneDx RCV001383728 SCV005333569 likely pathogenic not provided 2024-03-27 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 34426522, 31589614, 30341509, 19479957, 34493867, 37464296, 36185032, 15356974, 17495019, 24988064, 37139236, 29110180)
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000186278 SCV000239604 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided in vitro

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