ClinVar Genomic variation as it relates to human health

Variant summary: GLA c.901C>G (p.Arg301Gly) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 183457 control chromosomes. c.901C>G has been reported in the literature in multiple individuals affected with Fabry Disease, and in some patients specifically with reported Anderson-Fabry disease (Calcagnino_2011, Romani_2015, Liguori_2017, Shabeer_2002, Spinelli_2020). These data indicate that the variant is very likely to be associated with disease. Experimental studies have shown the variant to have reduced alpha-Gal activity in vitro: enzyme activity was 19.3% of wild-type, which increased to 56.5% with the addition of Migalastat (Lukas_2013); similarly the variant was reported with in vitro activity of 19.1% of wild-type, which increased to 64.7% of with the addition of Migalastat (Benjamin_2016). One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 301 of the GLA protein (p.Arg301Gly). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Fabry disease (PMID: 12175777, 28672034; Invitae). ClinVar contains an entry for this variant (Variation ID: 179546). 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 not expected to disrupt GLA protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects GLA function (PMID: 23935525, 27657681). This variant disrupts the p.Arg301 amino acid residue in GLA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 2171331, 8738659, 9395081, 11688386, 15702404, 20505683, 21598360, 22241068, 23378663). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

The p.R301G pathogenic mutation (also known as c.901C>G), located in coding exon 6 of the GLA gene, results from a C to G substitution at nucleotide position 901. The arginine at codon 301 is replaced by glycine, an amino acid with dissimilar properties. This alteration has been reported in numerous individuals with Fabry disease, having low enzyme activity observed (Shabbeer J et al. Mol Genet Metab, 2002 May;76:23-30; Calcagnino M et al. J Am Coll Cardiol, 2011 Jun;58:88-9; Romani I et al. J Stroke Cerebrovasc Dis, 2015 Nov;24:2588-95; Esposito R et al. Eur Heart J Cardiovasc Imaging, 2019 Apr;20:438-445; Citro R et al. Front Cardiovasc Med, 2022 Apr;9:838200; Di Risi T et al. Int J Mol Sci, 2022 Oct;23:[ePub ahead of print]). Another alteration at the same codon, p.R301Q (c.902G>A), has been detected in individuals with Fabry disease, who had reduced enzyme activity (Sakuraba H et al. Am J Hum Genet. 1990;47:784-789; Shin SH et al Biochem. Biophys. Res. Commun. 2007 Jul;359(1):168-73; Sawada K et al. Clin. Nephrol. 1996 May;45:289-294). In vitro studies showed this alteration impacts protein function (Lukas J et al. PLoS Genet, 2013 Aug;9:e1003632; Benjamin ER et al. Genet Med, 2017 Apr;19:430-438). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by BayesDel in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

Variant classified as Uncertain Significance - Favor Pathogenic. The Arg301Gly v ariant in GLA has been listed in HGMD as reported in an individual with Fabry di sease, though that publication could not be found. Studies have shown that this variant leads to reduce, but residual GLA function (Lukas 2013); however, this i n vitro assay may not accurately represent biological function. This variant was absent from large population studies. Other missense variants at this position (Arg301Gln, Arg301Pro) have been reported in individuals with Fabry disease (Sak uraba 1990, Ashley 2001), suggesting that variation at this position may not be tolerated, though additional studies are needed. Computational prediction tools and conservation analysis suggest that the Arg301Gly variant may impact the prot ein, though this information is not predictive enough to determine pathogenicity . Although this data supports that this variant may be pathogenic, additional st udies are needed to fully assess its clinical significance.