ClinVar Genomic variation as it relates to human health

The NM_000152.5:c.1710C>G (p.Asn570Lys) variant in GAA has a minor allele frequency in gnomAD of 0.0001149 in the African population, which is lower than the ClinGen LSD VCEP threshold (<0.001) for PM2_Supporting, meeting this criterion. At least three individuals have been reported with this variant and documented GAA activity in the affected range and/or were reported to be on enzyme replacement therapy for Pompe disease (PMID: 17151339, 22538254, 29122469, 32248831) (PP4_Moderate). This variant was found in compound heterozygosity with another variant in GAA that has been classified as pathogenic by the ClinGen Lysosomal Diseases VCEP including c.2560C>T (p.Arg854Ter) (ClinVar Variation ID: 4034, SCV001371731.1), phase unconfirmed, in at least one patient with Pompe disease (PMID: 22538254, 22658377, 29122469, 31193175)(0.5 points), and confirmed in trans in a patient with c.953T>C (p.Met318Thr) (ClinVar Variation ID: 4021; SCV002583364.1) (PMID: 36636589) (1 point). Another patient with the variant, along with with c.-32-13T>G and a rare synonymous variant c.1923G>A (p.Leu641=) has been reported (PMID: 32248831). While the allelic data from the latter patient is likely supportive of pathogenicity for c.1710C>G (p.Asn570Lys), it is not included here because the impact of p.Leu641= is unknown (Total 1.5 points) (PM3). Functional assays support a deleterious effect of this variant. When expressed in COS cells, this variant was classified as Class B ("potentially less severe") by Kroos et al, 2012 (PMID:22644586). This includes 0.9% GAA activity in cells and 0.5% in medium, and evidence of abnormal synthesis and processing on Western blot (PS3_Moderate). Computational evidence is inconclusive, REVEL score = 0.662 which is lower than the LD VCEP threshold for PP3 (>0.7) but higher than the LD VCEP threshold for BP4 (<0.5), and therefore does not meet either criterion. There is a ClinVar entry for this variant (Variation ID: 555153). In summary, this variant meets the criteria to be classified as Likely Pathogenic for Pompe disease based on the specifications of the ClinGen Lysosomal Diseases Variant Curation Expert Panel. GAA-specific GAA-specific ACMG/AMP criteria met (Specifications Version 2.0): PS3_Moderate, PM3, PP4_Moderate, PM2_Supporting. (Classification approved by the ClinGen Lysosomal Diseases Variant Curation Expert Panel on November 22, 2024).

Variant summary: GAA c.1710C>G (p.Asn570Lys) 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 was absent in 251344 control chromosomes (gnomAD). c.1710C>G has been reported in combination with another GAA variant in the literature in individuals affected with infantile-onset Pompe disease or late-onset Pompe disease (Banugaria_2011, Kishnani_2019, Vanherpe_2020, De Groot_2021). These data indicate that the variant is likely to be associated with disease. At least one functional paper reports experimental evidence evaluating an impact on protein function and this variant results in reducing alpha-glucosidase activity in transfected cells compared to WT activity. Three ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (n=2) and likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic.

The p.Asn570Lys variant in GAA has been reported in three individuals with glycogen storage disease II (PMID: 29122469, 22658377, 18425781, 22538254) and has been identified in 0.011% (1/8702) of African chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs765362308). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported in ClinVar as a VUS by Counsyl (VariationID: 555153). In vitro functional studies using COS-7 cells transfected with the variant provide some evidence that the p.Asn570Lys variant may impact protein function (PMID: 22644586). However, these types of assays may not accurately represent biological function. The phenotype of an individual heterozygous for this variant is highly specific for glycogen storage disease II based on GAA enzyme activity in fibroblasts being <1% of wild type, consistent with disease (PMID: 17151339). Computational prediction tools do not provide strong support for or against an impact to the protein, but the Asn at position 570 is not conserved in mammals or evolutionary distant species, raising the possibility that a change at this position may be tolerated. However, the presence of this variant in combination with reported pathogenic variant p.Arg584Ter (VariationID: 4034, PMID: 29122469, 22658377, 22538254) and in an individual with glycogen storage disease II increases the likelihood that the p.Asn570Lys variant is pathogenic. In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PS3, PM2, PM3_Supporting PP4 (Richards 2015).

This sequence change replaces asparagine, which is neutral and polar, with lysine, which is basic and polar, at codon 570 of the GAA protein (p.Asn570Lys). This variant is present in population databases (no rsID available, gnomAD 0.01%). This missense change has been observed in individuals with Pompe disease (PMID: 18425781, 22658377, 29122469, 31086307). ClinVar contains an entry for this variant (Variation ID: 555153). 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. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on GAA function (PMID: 22644586). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.