ClinVar Genomic variation as it relates to human health

The NM_000152.5:c.1538A>G variant in GAA is a missense variant predicted to cause substitution of aspartic acid by glycine at amino acid 513 (p.Asp513Gly). This variant has been detected in two individuals with clinical features of Pompe disease. One patient with infantile-onset Pompe disease had documented GAA deficiency with 0%, less than 10% of normal mean control level of GAA activity in leukocytes (PMID 31510962). The other patient had documented deficient GAA enzyme activity, muscle weakness, and cardiomyopathy at 11 months old (clinical laboratory data). (PP4_Moderate). These two individuals were homozygous for the variant (PM3 1.0 point, PMID 31510962, clinical laboratory data) (PM3). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). Expression of the variant in COS-7 cells resulted in 0.76% wild type GAA activity in cells and 0% in medium (<5%), and evidence of abnormal GAA synthesis and processing on Western blot, leading the variant to be described as Class B “potentially less severe” (Table 4), indicating that this variant may impact protein function (PMID 31510962) (PS3_Supporting). The computational predictor REVEL gives a score of 0.965 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: 638014). In summary, this variant meets the criteria to be classified as likely pathogenic for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP (specifications version 2.0): PP4_Moderate, PM3, PM2_Supporting, PS3_Supporting, PP3. (Classification approved by the ClinGen Lysosomal Diseases VCEP on July 18, 2023)

This sequence change replaces glutamic acid with glycine at codon 513 of the GAA protein (p.D513G). This variant is absent at least 240 control alleles based on our in-house whole exome database. This variant has not been reported in the literature in individuals with GAA-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, Polyphen-2, PredictSNP2, CADD, DANN, FATHMM, and FunSeq2) all suggest that this variant is damaging/deleterious. The p.D513 residue has been reported to be important for posttranslational modification and intracellular transport of GAA precursor (Hermans et al. 1991). Our in vitro study demonstrated that p.D513G did not interfere with the synthesis of the precursor protein but disturbed protein processing and secretion. This variant displayed enzyme activity equivalent to negative control. Based on 3D structure available (PDB: 5NN8), the p.D513 residue is located at the N-terminus of the fourth beta-stand of the catalytic domain. The interactions of p. D513 which help to position the beta-strand and thus the catalytic acid/base, include salt bridge hydrogen bonds with p.H432 and p.R591 at the C-terminal ends of the second and fourth alpha-helices of the (beta/alpha)8 barrel. Therefore p.D513 has a crucial role in stabilizing the ((beta/alpha)8 structure that is responsible for holding the two catalytic residues and the substrate in the exact position for hydrolysis. Replacing the Aspartic residue with Glycine will result in the loss of this charged H-bonding network, which should significantly destabilize this structure. In summary, due to the available evidence, we interpret this variant has been classified as Pathogenic.