ClinVar Genomic variation as it relates to human health

The NM_000152.5:c.925G>A variant in GAA is a missense variant predicted to cause substitution of glycine by arginine at amino acid 309 (p.Gly309Arg). In a cohort of 54 Dutch patients with Pompe disease, the allele frequency of the variant was 5.5%, and evidence suggests that it is a founder variant in that population (PMID 9660056). This variant has been reported in more than 13 individuals diagnosed with Pompe disease; for at least 6 individuals, residual GAA activity is available and is in the deficient range (PMIDs 9660056, 16838077, 23430847, 23601496, 24495340, 27189384), with some patients also reported to be on enzyme replacement therapy and/or to have documentation of symptoms consistent with infantile onset Pompe disease (PMID 23402890, 23430847, 23601496, 24495340) (PP4_Moderate). More data is available in the literature but the maximum strength of evidence for PP4, as specified by the ClinGen LSD VCEP, can already be applied.. Ten of these individuals are compound heterozygous for the variant and a pathogenic variant (PMID: 9660056, 16838077, 16917947, 23402890, 23430847), phase unknown in all cases, and one is homozygous (PMID: 23601496)(PM3_Very strong). The highest continental population minor allele frequency in gnomAD v2.1.1 is 0.00005 (European non-Finnish) which is lower than the ClinGen LSD VCEP threshold (<0.001) for PM2_Supporting. In functional studies, when expressed in COS cells, this variant resulted in no increase in GAA activity and showed evidence of abnormal processing (PMIDs 9660056, 19862843)(PS3_Moderate). The computational predictor REVEL gives a score of 0.963, which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3). There is a ClinVar entry for this variant (Variation ID: 188797; 2 star review status) with 8 submitters all classifying the variant as pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease. ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP (Specifications Version 2.0): PM3_Very Strong, PS3_Moderate, PP4_Moderate, PP3, PM2_Supporting. (Classification approved on August 17, 2021)

Variant summary: GAA c.925G>A (p.Gly309Arg) results in a non-conservative amino acid change located in the Glycoside hydrolase family 31, N-terminal domain of 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 4.6e-05 in 108582 control chromosomes. This frequency is not higher than expected for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) (4.6e-05 vs 0.0042), allowing no conclusion about variant significance. c.925G>A has been reported in the literature in multiple individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The p.Gly309Arg variant in GAA has been reported in the homozygous or compound heterozygous state in >10 individuals with Pompe disease (Kroos 1998, Kroos 2006, Montalvo 2006, Elder 2013, Hansel 2018). It has also been identified in 0.01% (1/9898) of Ashkenazi Jewish and 0.005% (5/110036) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org); however, this frequency is low enough to be consistent with a recessive carrier frequency. This variant has been reported as Pathogenic and Likely Pathogenic in ClinVar (Variation ID 188797). Computational prediction tools and conservation analysis are consistent with pathogenicity. Additionally, an in vitro functional study supports an impact on protein function (Kroos 1998). In summary, the p.Gly309Arg variant meets criteria to be classified as pathogenic for autosomal recessive Pompe disease. ACMG/AMP Criteria applied: PM3_VeryStrong, PM2_Supporting, PP3, PS3_Supporting.

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 309 of the GAA protein (p.Gly309Arg). This variant is present in population databases (rs543300039, gnomAD 0.01%). This missense change has been observed in individual(s) with Pompe disease (PMID: 9660056, 16917947, 17210890, 17616415, 23601496, 24245577, 24495340, 29122469). ClinVar contains an entry for this variant (Variation ID: 188797). 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: 9660056). For these reasons, this variant has been classified as Pathogenic.

Published functional studies demonstrate significantly reduced enzyme activity (Dupe et al., 2022; Goomber et al., 2022); Not observed at 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: 31254424, 33301762, 29653542, 30737479, 31086307, 32959227, 16838077, 9660056, 32071926, 16917947, 23402890, 34530085, 30367637, 24337590, 23601496, 31392188, 35302691, 36246652)

The p.Gly309Arg variant in GAA has been reported in at least 20 individuals (including 8 Dutch, 1 French, 1 Croatian, 1 Hispanic, 1 Greek) with Glycogen Storage Disease II, and segregated with disease in at least 4 affected relatives from 2 families (PMID: 9660056, 23430847, 27189384, 17616415, 23402890, 16917947, 24495340, 23601496, 16838077, 24245577; DOI: 10.21767/2380-7245.100010). This variant has also been reported likely pathogenic by Counsyl and pathogenic by EGL in ClinVar (Variation ID: 188797). This variant has been identified in 0.010% (1/9898) of Ashkenazi Jewish chromosomes, (5/110036) of 0.004% European (non-Finnish) chromosomes, and 0.003% (1/30458) of South Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs543300039). 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 and pulse-chase analysis provide evidence that the p.Gly309Arg variant impacts GAA activity (PMID: 9660056). 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 a pathogenic variant and in homozygosity in individuals with Glycogen Storage Disease II increases the likelihood that the p.Gly309Arg variant is pathogenic (PMID: 24495340, 23601496, 16838077). The phenotype of an individual homozygous or compound heterozygous for this variant is highly specific for Glycogen Storage Disease II with low GAA activity in leukocytes (PMID: 23430847, 23601496, 24495340, 17616415, DOI: 10.21767/2380-7245.100010). In summary, this variant meets criteria to be classified as pathogenic for Glycogen Storage Disease II in an autosomal recessive manner based on occurrences with a reported pathogenic variant in individuals with Glycogen Storage Disease II and other findings from the literature. ACMG/AMP Criteria applied: PM3, PM2, PP3, PP4, PS3 (Richards 2015).