ClinVar Genomic variation as it relates to human health

Published functional studies demonstrate decreased alpha galactosidase activity compared to wildtype (Lukas et al., 2013; Ishii et al., 2007); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 33204599, 30477121, 31956509, 11889412, 30386727, 27979989, 15776423, 20022777, 27657681, 25040344, 25382311, 27831900, 7531540, 24386359, 23935525, 21598360, 18205205, 23913314, 25026990, 17555407, 17532296)

The p.Arg112His variant in GLA has been reported in over 15 individuals with Fabry Disease, segregated with disease in three affected relatives from one family (PMID: 25040344, 27831900, 25040344, 25026990, 23913314, 7531540, 17532296, 18205205, 17555407), and has been identified in 0.0024% (2/81850) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs372966991). Although this variant has been seen in the general population, its frequency is low enough to be consistent with Fabry disease. Please note that for diseases with clinical variability, or reduced penetrance, pathogenic variants may be present at a low frequency in the general population. This variant has also been reported in ClinVar as pathogenic by EGL Genetic Diagnostics and Integrated Genetics (Variation ID: 195028). In vitro functional studies provide some evidence that the p.Arg112His variant may slightly impact protein function (PMID: 30386727, 27896103, 18205205, 23935525, 17532296, 17555407). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant will impact the protein, though this information is not predictive enough to determine pathogenicity. The phenotype of an individual hemizygous for this variant is highly specific for Fabry disease based on the classical phenotype consistent with disease (PMID: 27831900, 25040344, 25026990, 23913314, 7531540, 17532296, 18205205, 17555407). The p.Arg112His is located in a region of GLA that is essential to protein folding and stability, suggesting that this variant is in a functional domain and slightly supports pathogenicity (PMID: 27896103, 17555407). Two additional pathogenic variants, causing a different amino acid change at the same position, (p.Arg112Cys, p.Arg112Leu), have been reported in association with disease in the literature and ClinVar, supporting that a change at this position may not be tolerated (PMID: 1315715, 23935525, 14635108/Variation ID: 92550, 92551). In summary, this variant meets criteria to be classified as pathogenic for Fabry disease in an X-linked manner based on the prevalence of the variant in affected individuals, its absence from population databases, computational evidence suggesting the variant is deleterious, and functional studies with decreased enzyme activity. ACMG/AMP Criteria applied: PS4, PM5, PM2_supporting, PP3_moderate, PP1, PP4, PS3_supporting, PM1_supporting (Richards 2015).

Variant summary: GLA c.335G>A (p.Arg112His) 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 allele was found at a frequency of 1.1e-05 in 183395 control chromosomes. c.335G>A has been reported in the literature in many individuals affected with classical and non-classical, late onset Fabry Disease (example Schafer_2005, Shimotori_2007, Sirrs_2010, vanderTol_2016, Weidemann_2020, Nampoothiri_2020, Muto_2021). These data indicate that the variant is very likely to be associated with disease. Multiple publications report experimental evidence indicating that the variant severely impacts the enzymatic activity of the protein, resulting in <10% of normal activity (Ishii_2007, Shimotori_2007, Lukas_2013). Nine clinical diagnostic laboratories and three research groups have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All classified the variant as pathogenic (n=9) or likely pathogenic (n=3). Based on the evidence outlined above, the variant was classified as pathogenic.

This missense variant replaces arginine with histidine at codon 112 of the GLA protein. Computational prediction suggests that this variant may have a deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Functional studies have shown that this variant may cause the GLA protein to become unstable (PMID: 17555407, 18205205). This variant has been reported in hemizygous males affected with non-classical, variant Fabry disease (PMID: 17555407, 18205205, 25040344, 25026990, 33204599, 34803097; Zhiyon 2012); in many cases, GLA enzyme activity was significantly reduced and in the range observed with classical Fabry disease. A different variant occurring at the same codon, p.Arg112Cys, is a well documented pathogenic mutation (Clinvar variation ID: 92550), indicating that arginine at this position is important for GLA protein function. This variant has been identified in 2/183395 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic.

The p.R112H pathogenic mutation (also known as c.335G>A), located in coding exon 2 of the GLA gene, results from a G to A substitution at nucleotide position 335. The arginine at codon 112 is replaced by histidine, an amino acid with highly similar properties. This alteration has been detected in many individuals with Fabry disease and is described as being associated with later onset disease (Weidemann F et al. Mol. Genet. Metab., 2019 Feb;126:169-182; Sakuraba H et al. Mol Genet Metab Rep, 2018 Dec;17:73-79; Natarajan P et al. Sci Transl Med, 2016 11;8:364ra151; Riera C et al. Proteins, 2015 Jan;83:91-104; Smid BE et al. Clin. Genet., 2015 Aug;88:161-6; Nishida M et al. Eur. J. Pediatr., 2014 Aug;173:1111-4; Sechi A et al. BMC Cardiovasc Disord, 2014 Jul;14:86). In addition, several functional studies have shown reduced alpha-galactosidase protein function (Ishii S et al. Biochem. J., 2007 Sep;406:285-95; Lukas J et al. PLoS Genet., 2013 Aug;9:e1003632; Saito S et al. PLoS ONE, 2013 Dec;8:e84267; Shimotori M et al. Hum. Mutat., 2008 Feb;29:331; Shin SH et al. Biochem. Biophys. Res. Commun., 2007 Jul;359:168-73). 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 in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

The p.Arg112His variant in GLA has been reported in at least 8 individuals with either classic or atypical Fabry disease and segregated with disease in 2 affected male relatives from 2 families (Eng 1994, Shimotori 2008, Sirrs 2010, Gaggl 2013, Nishida 2014, Sechi 2014, Smid 2015, Arends 2017). This variant has been identified in 2/81850 European chromosomes by gnomAD (http://gnomad.broadinstitute.org/) and is reported by other clinical laboratories in ClinVar (Variation ID: 195028). Functional studies demonstrate that this variant is associated with reduced enzyme activity in patient samples (Nishida 2014) and in a transfected cell line (Shin 2007). Computational prediction tools and conservation analyses are consistent with pathogenicity. Additionally, a pathogenic variant at the same position, p.Arg112Cys, has been identified in patients with classic Fabry disease, suggesting that changes at this position may not be tolerated. In summary, this variant meets criteria to be classified as pathogenic for X-linked Fabry disease. ACMG/AMP Criteria applied: PS4, PM2, PM5, PS3_Moderate, PP1, PP3.

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 112 of the GLA protein (p.Arg112His). This variant is present in population databases (rs372966991, gnomAD 0.004%). This missense change has been observed in individual(s) with Fabry disease (PMID: 7531540, 17532296, 18205205, 25026990, 25040344). ClinVar contains an entry for this variant (Variation ID: 195028). 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 GLA protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change does not substantially affect GLA function (PMID: 17555407, 21598360, 23935525). For these reasons, this variant has been classified as Pathogenic.