ClinVar Miner

Submissions for variant NM_138413.4(HOGA1):c.907C>T (p.Arg303Cys)

gnomAD frequency: 0.00003  dbSNP: rs149150736
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001379332 SCV001577118 pathogenic not provided 2024-01-29 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 303 of the HOGA1 protein (p.Arg303Cys). This variant is present in population databases (rs149150736, gnomAD 0.004%). This missense change has been observed in individual(s) with primary hyperoxaluria type 3 (PMID: 21896830, 22391140). 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: 204279). 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 80%. Experimental studies have shown that this missense change affects HOGA1 function (PMID: 22771891). For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000186486 SCV002810935 likely pathogenic Primary hyperoxaluria type 3 2022-02-15 criteria provided, single submitter clinical testing
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000186486 SCV000239848 pathogenic Primary hyperoxaluria type 3 2014-11-27 no assertion criteria provided in vitro Prediction programme. Found in conjunction with c.700+5G>T.
Natera, Inc. RCV000186486 SCV002094649 likely pathogenic Primary hyperoxaluria type 3 2021-04-01 no assertion criteria provided clinical testing

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