ClinVar Miner

Submissions for variant NM_012203.2(GRHPR):c.139C>T (p.Arg47Ter)

gnomAD frequency: 0.00007  dbSNP: rs774654020
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001042856 SCV001206563 pathogenic not provided 2024-01-18 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg47*) in the GRHPR gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in GRHPR are known to be pathogenic (PMID: 25644115). This variant is present in population databases (rs774654020, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with GRHPR-related conditions. ClinVar contains an entry for this variant (Variation ID: 632541). For these reasons, this variant has been classified as Pathogenic.
PreventionGenetics, part of Exact Sciences RCV003392593 SCV004120498 likely pathogenic GRHPR-related disorder 2023-09-22 criteria provided, single submitter clinical testing The GRHPR c.139C>T variant is predicted to result in premature protein termination (p.Arg47*). This variant has been reported homozygous in a male individual with primary hyperoxaluria type 2 (Dhondup et al. 2018. PubMed ID: 28681512). Additional protein truncating variants in the GRHPR gene have also been reported to be associated with hyperoxaluria (Williams et al. 2015. PubMed ID: 25629080, Hopp et al. 2015. PubMed ID: 25644115). This variant is reported in 0.0080% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/9-37424897-C-T). Nonsense variants in GRHPR are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000779582 SCV004174336 pathogenic Primary hyperoxaluria, type II 2023-10-27 criteria provided, single submitter curation ACMG:PVS1 PM2 PP3
Baylor Genetics RCV000779582 SCV004191702 likely pathogenic Primary hyperoxaluria, type II 2023-09-26 criteria provided, single submitter clinical testing
Natera, Inc. RCV000779582 SCV001458445 pathogenic Primary hyperoxaluria, type II 2020-09-16 no assertion criteria provided clinical testing

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