ClinVar Genomic variation as it relates to human health

This variant, c.655G>A (p.Gly219Arg), has been reported in at least eight individuals with Pompe disease and residual GAA activity meeting the ClinGen LSD VCEP's specifications for PP4. Of these individuals, four are compound heterozygous for the variant and another pathogenic variant in GAA, including c.-32-13T>G (PMID 21550241, 24844452), c.169C>T (p.Gln57Ter) (PMID 29124014), or c.2560C>T (p.Arg854Ter)(PMID 23266370), and one is homozygous for the variant (PMID 25139343). This in trans data meets PM3_Strong. A further three individuals are compound heterozygous for the variant and either c.1735G>A (p.Glu579Lys) (PMIDs 23601496, 31193175), c.546G>A (PMID 25037089), or c.784G>A (p.Glu262Lys) (PMID 11738358). However, the in trans data for these patients will be used in the assessment of those respective variants and was not included here in order to avoid a circular argument. Additional patients have been reported but were not included because the residual GAA activity was not reported and therefore PP4 cannot be assessed, patients with the same genotype had already been included, or no cDNA sequence change was provided for the variant (PMIDs 14695532, 18429042, 20033296, 21550241, 23787031, 25139343, 27711114, 30023291, 30155607). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00004024 in the African population, meeting PM2. When it was expressed in COS cells, this variant results in <2% wild type GAA activity and it is abnormally processed (PMIDs 14695532; 19862843), meeting PS3. The score for the REVEL in silico meta-predictor, 0.872, also supports that the variant has a deleterious impact on GAA function, meeting PP3. There is a ClinVar entry for this variant (Variation ID 189065; 2 star review status) with four submitters classifying the variant as pathogenic and one as likely pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease. ACMG/AMP criteria met, based on the specifications of the ClinGen LSD VCEP: PS3, PM2, PM3_Strong, PP3, PP4.

Variant summary: The GAA c.655G>A (p.Gly219Arg) variant located in the Galactose mutarotase, N-terminal barrel domain (via InterPro) involves the alteration of a conserved nucleotide and 5/5 in silico tools predict a damaging outcome for this variant. This variant was found in 2/120140 control chromosomes at a frequency of 0.0000166, which does not exceed the estimated maximal expected allele frequency of a pathogenic GAA variant (0.0042205). Multiple publications have cited the variant in both compound heterozygous and homozygous Pompe disease patients, which were found to have very little GAA activity. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as "likely pathogenic/pathogenic." Taken together, this variant is classified as pathogenic.

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 219 of the GAA protein (p.Gly219Arg). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with Pompe disease, including individuals with low alpha-glucosidase enzyme activity (less than 40% of normal) (PMID: 11738358, 14695532, 18429042, 21550241, 23266370, 23601496, 23787031, 29124014). ClinVar contains an entry for this variant (Variation ID: 189065). 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 GAA protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects GAA function (PMID: 14695532). For these reasons, this variant has been classified as Pathogenic.

The p.Gly219Arg variant in GAA has been reported in 22 individuals (including 10 French, 3 Saudi, 1 Italian, 1 Spanish, 1 Japanese, and 3 other Caucasian individuals) with Glycogen Storage Disease II (PMID: 23787031, 30023291, 18995995, 23266370, 11738358, 21550241, 25037089, 23601496, 21637107, 29124014, 30155607, 18429042, 24844452, 14695532), and has also been reported pathogenic (by EGL, GeneDx, Invitae, and Integrated Genetics) and likely pathogenic (by Counsyl) in ClinVar (Variation ID: 189065). This variant has been identified in 0.004% (1/24848) of African chromosomes and 0.003% (1/35388) of Latino chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs370950728). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. In vitro functional studies with COS cells transfected with this variant provide some evidence that the p.Gly219Arg variant may reduce GAA activity by more than 98% (PMID: 14695532, 19862843). However, these types of assays may not accurately represent biological function. Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. The presence of this variant in combination with pathogenic and likely pathogenic variants, and in individuals with Glycogen Storage Disease II increases the likelihood that the p.Gly219Arg variant is pathogenic (PMID: 21637107, 21550241, 11738358). The phenotype of individuals heterozygous for this variant is highly specific for Glycogen Storage Disease II with very low GAA activity detected in relevant tissues (PMID: 23601496, 24844452, 21550241, 29124014, 11738358, 21637107). In summary, this variant meets criteria to be classified as pathogenic for Glycogen Storage Disease II in an autosomal recessive manner based on in vitro functional studies with COS cells transfected with this variant and multiple occurrences with pathogenic GAA variants in individuals with Glycogen Storage Disease II. ACMG/AMP Criteria applied: PS3, PM2, PM3, PP3, PP4 (Richards 2015).

Published functional studies demonstrate a damaging effect with significant reduction of enzyme activity (PMID: 33560568, 14695532); Not observed at a significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 18429042, 34501319, 33301762, 30564623, 14695532, 21550241, 23601496, 21392261, 23266370, 20033296, 11738358, 24844452, 28648663, 31086307, 29122469, 32870709, 19343043, 22253258, 33560568, 23787031)

The GAA c.655G>A variant is predicted to result in the amino acid substitution p.Gly219Arg. This variant was reported in the homozygous and compound heterozygous state in multiple patients with clinical and biochemical features consistent with Pompe disease (Sacconi et al. 2014. PubMed ID: 24844452, Fernandez-Hojas et al. 2002. PubMed ID: 11738358, Prakalapakorn et al. 2014. PubMed ID: 25139343, Hermans et al. 2004. PubMed ID: 14695532). Functional characterization of the variant suggests it is deleterious (Hermans et al. 2004. PubMed ID: 14695532). This variant is reported in 0.0040% of alleles in individuals of African descent in gnomAD. This variant is classified as pathogenic in clinvar by the majority of submitters including the ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel (https://www.ncbi.nlm.nih.gov/clinvar/variation/189065/). This variant is interpreted as pathogenic.