ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.568G>A (p.Gly190Arg)

gnomAD frequency: 0.00004  dbSNP: rs180177239
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169439 SCV000220856 likely pathogenic Primary hyperoxaluria, type I 2014-11-06 criteria provided, single submitter literature only
Invitae RCV000816747 SCV000957270 pathogenic not provided 2023-10-11 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 190 of the AGXT protein (p.Gly190Arg). This variant is present in population databases (rs180177239, gnomAD 0.01%). This missense change has been observed in individuals with primary hyperoxaluria (PMID: 9604803, 15849466, 15961946, 27568336, 27935012). It has also been observed to segregate with disease in related individuals. This variant is also known as c.690G>A. ClinVar contains an entry for this variant (Variation ID: 189047). 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. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000169439 SCV001752663 pathogenic Primary hyperoxaluria, type I 2021-06-30 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000169439 SCV003809004 pathogenic Primary hyperoxaluria, type I 2022-09-02 criteria provided, single submitter clinical testing
GeneDx RCV000816747 SCV003845926 pathogenic not provided 2022-09-25 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: 27935012, 27568336, 18282470, 15849466, 31589614, 24988064, 23810941, 30341509, 10541294, 25629080, 19571789, 17460142, 9604803)
Baylor Genetics RCV000169439 SCV004196492 pathogenic Primary hyperoxaluria, type I 2023-10-19 criteria provided, single submitter clinical testing
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000169439 SCV000239656 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided in vitro
Natera, Inc. RCV000169439 SCV002076464 pathogenic Primary hyperoxaluria, type I 2020-10-05 no assertion criteria provided clinical testing

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