ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.346G>A (p.Gly116Arg)

gnomAD frequency: 0.00002  dbSNP: rs180177207
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169408 SCV000220811 likely pathogenic Primary hyperoxaluria, type I 2014-10-16 criteria provided, single submitter literature only
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University RCV000169408 SCV000891624 likely pathogenic Primary hyperoxaluria, type I 2017-12-30 criteria provided, single submitter curation
Labcorp Genetics (formerly Invitae), Labcorp RCV001236818 SCV001409555 pathogenic not provided 2024-03-13 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 116 of the AGXT protein (p.Gly116Arg). This variant is present in population databases (rs180177207, gnomAD 0.003%). This missense change has been observed in individual(s) with primary hyperoxaluria (PMID: 10453743, 17460142, 25629080, 26252291, 33691640). 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: 189021). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on AGXT protein function. For these reasons, this variant has been classified as Pathogenic.
Kariminejad - Najmabadi Pathology & Genetics Center RCV001814082 SCV001755665 likely pathogenic Abnormality of metabolism/homeostasis 2021-07-10 criteria provided, single submitter clinical testing
Baylor Genetics RCV000169408 SCV004192761 pathogenic Primary hyperoxaluria, type I 2024-02-24 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000169408 SCV005651599 likely pathogenic Primary hyperoxaluria, type I 2023-12-27 criteria provided, single submitter clinical testing
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000169408 SCV000239632 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided in vitro
Natera, Inc. RCV000169408 SCV002076457 likely pathogenic Primary hyperoxaluria, type I 2020-11-03 no assertion criteria provided clinical testing

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