Submissions for variant NM_000152.5(GAA):c.1941C>G (p.Cys647Trp)

gnomAD frequency: 0.00003  dbSNP: rs776948121

Total submissions: 8

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	RCV000665047	SCV002817430	pathogenic	Glycogen storage disease, type II	2022-11-15	reviewed by expert panel	curation	The NM_000152.5:c.1941C>G variant in GAA is a missense variant that is predicted to result in substitution of cysteine by tryptophan at amino acid 647 (p.Cys647Trp). At least 10 patients with this variant have been reported to have Pompe disease including two with documented laboratory values showing deficiency of GAA, one of whom also had reported symptoms consistent with infantile onset Pompe disease (PMID: 7981676, 9535769, 17723315) (meeting PP4_Moderate), three patients with reported symptoms consistent with infantile onset Pompe disease (PMID: 7981676, 19588081, 22658377, 31510962), one patient on enzyme replacement therapy (PMID: 31086307) (all meeting PP4). Four patients are compound heterozygous for the variant and a variant in GAA that has been classified as pathogenic for Pompe disease including c.-32-13T>G (PMID: 25681614, 31931849; 2 patients), c.2481+110_2646+39del (exon 18 deletion, PMID: 7981676), and c.1655T>C (p.Leu552Pro) (PMID: 19588081), all phase unconfirmed. In another patient, the variant is confirmed in trans with an allele containing two pathogenic variants, c.1456_1468del (p.Ala486fsTer30) (confirmed de novo) and c.2238G>C (p.Trp746Cys) (PMID: 7981676), and two patients are homozygous for the variant (PMID: 9535769, 31510962) (PM3_Very Strong). In addition, two patients are compound heterozygous for the variant and either c.1846G>A (p.Asp616Asn) (PMID: 31086307) or c.1781G>C (p.Arg594Pro) (PMID: 19588081). The allelic data from these patients will be used in the classification of the second variant and is not included here to avoid circular logic. In another patient, no second variant was found (PMID: 25681614). When expressed in GAA-deficient SV40 immortalized fibroblasts, the variant resulted in <1% GAA activity compared to the normal control ( PMID: 9535769) (PS3_Supporting).The computational predictor REVEL gives a score of 0.802 which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3). The highest continental population minor allele frequency in gnomAD v2.1.1 is 0.00002 (3/124712 alleles) in the European non-Finnish population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). Of note, the highest population minor allele frequency in gnomAD v2.1.1 is in the "other" population, 0.00014 (1/7006 alleles) which also meets the PM2_Supporting threshold. There is a ClinVar entry for this variant (Variation ID: 550327). In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease. GAA-specific ACMG-AMP criteria met, as specified by the ClinGen Lysosomal Storage Disorders VCEP (Specifications Version 2.0): PM3_Very_Strong, PP4_Moderate, PP3, PS3_Supporting, PM2_Supporting. Classification approved by the ClinGen LSD VCEP on Nov. 15, 2022.
Counsyl	RCV000665047	SCV000789104	likely pathogenic	Glycogen storage disease, type II	2017-01-13	criteria provided, single submitter	clinical testing
Labcorp Genetics (formerly Invitae), Labcorp	RCV000665047	SCV000827584	pathogenic	Glycogen storage disease, type II	2023-11-17	criteria provided, single submitter	clinical testing	This sequence change replaces cysteine, which is neutral and slightly polar, with tryptophan, which is neutral and slightly polar, at codon 647 of the GAA protein (p.Cys647Trp). This variant is present in population databases (rs776948121, gnomAD 0.002%). This missense change has been observed in individual(s) with infantile onset Pompe disease (PMID: 7981676, 9535769, 17723315, 19588081, 22658377, 25681614). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 550327). 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: 7981676). For these reasons, this variant has been classified as Pathogenic.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV000665047	SCV001422988	pathogenic	Glycogen storage disease, type II	2020-01-22	criteria provided, single submitter	curation	The p.Cys647Trp variant in GAA has been reported in at least seven individuals with glycogen storage disease II (PMID: 9535769, 17723315, 19588081, 25681614) and has been Identified in 0.002% (3/124712) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs776948121). 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 Pathogenic by Invitae and as Likely Pathogenic by Counsyl (VariationID: 550327). In vitro functional studies provide some evidence that the p.Cys647Trp variant may impact protein function (PMID: 9535769). However, these types of assays may not accurately represent biological function. The phenotype of an individual homozygous 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: 9535769, 17723315). Computational prediction tools and conservation analyses suggest that this variant may impact the protein, though this information is not predictive enough to determine pathogenicity. Additionally, the presence of this variant in homozygous individuals in individuals with glycogen storage disease II increases the likelihood that the p.Cys647Trp variant is pathogenic (PMID: 9535769, 17723315). In summary, this variant meets criteria to be classified as pathogenic for glycogen storage disease II in an autosomal recessive manner based on its presence in affected individuals in combination with other pathogenic variants or in a homozygous state, in vitro functional studies demonstrating markedly reduced expression, and low frequency in the general population. ACMG/AMP Criteria applied: PS3, PM2, PM3, PP3, PP4 (Richards 2015).
GeneDx	RCV001557095	SCV001778794	pathogenic	not provided	2020-10-08	criteria provided, single submitter	clinical testing	Expression studies found that the variant abolished alpha-glucosidase activity compared to wild-type (Huie et al., 1994); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 31086307, 7981676, 25681614, 19588081, 22658377, 17723315, 9535769)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000665047	SCV001983408	pathogenic	Glycogen storage disease, type II	2021-09-27	criteria provided, single submitter	clinical testing	Variant summary: GAA c.1941C>G (p.Cys647Trp) 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 allele was found at a frequency of 1.2e-05 in 242562 control chromosomes (gnomAD and publication data). c.1941C>G has been reported in the literature in multiple individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) (Huie_1994, Huie_1998, McCready_2007, Kishnani_2019). These data indicate that the variant is very likely to be associated with disease. Functional studies report experimental evidence evaluating an impact on protein function and this variant results in absent enzyme activity from transfected cells and fibroblasts (Huie_1994, Huie_1998, McCready_2007). Four ClinVar submitters (evaluation after 2014) cite the variant as pathogenic (n=3) and likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic.
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein	RCV000665047	SCV003807843	pathogenic	Glycogen storage disease, type II	2022-09-17	criteria provided, single submitter	clinical testing	ACMG classification criteria: PS3 supporting, PS4 strong, PM2 moderated, PM3 moderated, PP3 supporting
Baylor Genetics	RCV000665047	SCV004197785	pathogenic	Glycogen storage disease, type II	2023-11-23	criteria provided, single submitter	clinical testing