ClinVar Miner

Submissions for variant NM_138413.4(HOGA1):c.221T>G (p.Val74Gly)

gnomAD frequency: 0.00001  dbSNP: rs796052084
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000186474 SCV000239833 likely pathogenic Primary hyperoxaluria type 3 2023-10-27 criteria provided, single submitter curation ACMG: PM2 PM3 PP3 PP4 PP5
Counsyl RCV000186474 SCV000800710 uncertain significance Primary hyperoxaluria type 3 2018-05-18 criteria provided, single submitter clinical testing
Invitae RCV001857598 SCV002174087 pathogenic not provided 2023-11-13 criteria provided, single submitter clinical testing This sequence change replaces valine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 74 of the HOGA1 protein (p.Val74Gly). This variant is present in population databases (rs796052084, gnomAD 0.002%). This missense change has been observed in individual(s) with primary hyperoxaluria type 3 (PMID: 22781098, 28711958). 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: 204267). 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 HOGA1 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

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