ClinVar Miner

Submissions for variant NM_012203.2(GRHPR):c.904C>T (p.Arg302Cys)

gnomAD frequency: 0.00001  dbSNP: rs180177322
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000794534 SCV000933948 pathogenic not provided 2024-01-11 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 302 of the GRHPR protein (p.Arg302Cys). This variant is present in population databases (rs180177322, gnomAD 0.02%). This missense change has been observed in individual(s) with primary hyperoxaluria type 2 (PMID: 14635115, 24116921, 31685312). 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: 162022). 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 GRHPR protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects GRHPR function (PMID: 14635115). This variant disrupts the p.Arg302 amino acid residue in GRHPR. Other variant(s) that disrupt this residue have been observed in individuals with GRHPR-related conditions (PMID: 25644115), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
MGZ Medical Genetics Center RCV000149443 SCV002581178 likely pathogenic Primary hyperoxaluria, type II 2022-07-26 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000149443 SCV002806312 likely pathogenic Primary hyperoxaluria, type II 2021-07-06 criteria provided, single submitter clinical testing
Baylor Genetics RCV000149443 SCV004191703 pathogenic Primary hyperoxaluria, type II 2023-09-26 criteria provided, single submitter clinical testing
OMIM RCV000149443 SCV000196081 pathogenic Primary hyperoxaluria, type II 2014-10-01 no assertion criteria provided literature only
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000149443 SCV000239798 pathogenic Primary hyperoxaluria, type II 2014-11-27 no assertion criteria provided in vitro
Natera, Inc. RCV000149443 SCV001462569 likely pathogenic Primary hyperoxaluria, type II 2020-09-16 no assertion criteria provided clinical testing

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