ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.302T>C (p.Leu101Pro)

dbSNP: rs180177195
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169219 SCV000220484 likely pathogenic Primary hyperoxaluria, type I 2014-07-07 criteria provided, single submitter literature only
Centogene AG - the Rare Disease Company RCV000169219 SCV001424358 pathogenic Primary hyperoxaluria, type I criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001850392 SCV002137677 pathogenic not provided 2024-01-22 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 101 of the AGXT protein (p.Leu101Pro). This variant is present in population databases (rs180177195, gnomAD 0.03%). This missense change has been observed in individual(s) with primary hyperoxaluria, type 1 (PMID: 23439734, 25013605). ClinVar contains an entry for this variant (Variation ID: 188866). 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 AGXT protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV000169219 SCV002790068 likely pathogenic Primary hyperoxaluria, type I 2022-01-10 criteria provided, single submitter clinical testing
Revvity Omics, Revvity RCV000169219 SCV003809037 pathogenic Primary hyperoxaluria, type I 2022-09-01 criteria provided, single submitter clinical testing
Neuberg Centre For Genomic Medicine, NCGM RCV000169219 SCV004176561 likely pathogenic Primary hyperoxaluria, type I 2023-02-14 criteria provided, single submitter clinical testing The missense c.302T>C(p.Leu101Pro) variant in AGXT gene has been reported in homozygous state in individuals affected with primary Hyperoxaluria (Siegal D, et. al., 2011;Chanchlani R, et. al., 2012). The p.Leu101Pro variant is reported with an allele frequency of 0.003% in the gnomAD exomes database and is novel (not in any individuals) in 1000 Genomes database. The amino acid Leu at position 101 is changed to a Pro changing protein sequence and it might alter its composition and physico-chemical properties. This variant has been reported to the ClinVar database as Likely Pathogenic/ Pathogenic. The amino acid change p.Leu101Pro in AGXT is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. Additional studies will be required to prove the pathogenicity of this variant. For these reasons, this variant has been classified as Likely Pathogenic.
Baylor Genetics RCV000169219 SCV004194760 pathogenic Primary hyperoxaluria, type I 2024-02-08 criteria provided, single submitter clinical testing
Clinical Biochemistry Laboratory, Health Services Laboratory RCV000169219 SCV000239624 pathogenic Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided in vitro

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