ClinVar Genomic variation as it relates to human health

A variant of uncertain significance has been identified in the GLA gene. The I242V variant has been reported in one patient referred for Fabry disease testing who had slightly elevated levels of Globotriaosylceramide (Lukas et al., 2016). This variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. However, the I242V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is not conserved across species and where Valine is the wild type in several species. In silico analysis predicts this variant likely does not alter the protein structure/function. Finally, while missense variants affecting the same residue (I242N, I242F) have been reported in the Human Gene Mutation Database in association with Fabry disease (Stenson et al., 2014), the pathogencity of these variants has not been definitively determined.

Variant of Uncertain Significance due to insufficient evidence: This missense variant replaces isoleucine with valine at codon 242 of the GLA protein. Computational prediction tools and conservation analyses are inconclusive regarding the impact of this variant on the protein function. Computational splicing tools suggest that this variant may not impact RNA splicing. To our knowledge, functional assays have not been performed for this variant. This variant has been reported in two individuals referred for Fabry disease testing (PMID: 26415523, 27356758). One of these individuals showed up to 89% of normal GLA enzyme activity in vitro (PMID: 26415523). This variant is rare in the general population and has been identified in 0/277264 chromosomes by the Genome Aggregation Database (gnomAD). Available evidence is insufficient to determine the role of this variant in disease conclusively.

This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 242 of the GLA protein (p.Ile242Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GLA-related conditions. ClinVar contains an entry for this variant (Variation ID: 217396). 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 are conflicting or provide insufficient evidence to determine the effect of this variant on GLA function (PMID: 26415523). This variant disrupts the p.Ile242 amino acid residue in GLA. Other variant(s) that disrupt this residue have been observed in individuals with GLA-related conditions (PMID: 9105656, 23935525, 30386727, 33016649), which suggests that this may be a clinically significant amino acid residue. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

The p.Ile242Val variant in GLA has been reported in 1 individual referred for Fabry testing with mildly elevated Globotriaosylceramide (Lukas 2016), was absent from large population studies. It has also been reported by other clinical laboratories in ClinVar (Variation ID: 217396). In vitro functional studies provide some evidence that the p.Ile242Val variant may mildly impact protein function (Lukas 2016). Isoleucine (Ile) at position 242 is not conserved in mammals or evolutionarily distant species and 6 species (including 4 mammals) carry a valine (Val) at this position, supporting that this change may be tolerated. Additional computational prediction tools suggest that the p.Ile242Val variant may not impact the protein. In summary, while the clinical significance of the p.Ile242Val variant is uncertain, these data suggest that it is more likely to be benign. ACMG/AMP Criteria applied: PM2; PS3_Supporting; BP4.

The p.I242V variant (also known as c.724A>G), located in coding exon 5 of the GLA gene, results from an A to G substitution at nucleotide position 724. The isoleucine at codon 242 is replaced by valine, an amino acid with highly similar properties. This alteration has been reported in Fabry disease cohorts (Lenders M et al. Orphanet J Rare Dis, 2016 May;11:54; Xiao K et al. Sci Rep, 2019 Oct;9:15277). An in vitro assay showed this alteration has >50% enzyme activity compared to wild-type (Lukas J et al. Hum Mutat, 2016 Jan;37:43-51). This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.