Submissions for variant NM_000152.5(GAA):c.271G>A (p.Asp91Asn)

gnomAD frequency: 0.02215  dbSNP: rs1800299

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	RCV000531082	SCV003852734	benign	Glycogen storage disease, type II	2023-03-03	reviewed by expert panel	curation	The NM_000152.5:c.271G>A missense variant in GAA (p.Asp91Asn) has a highest population minor allele frequency in gnomAD v2.1.1 of 0.03291 (4183/127102 alleles; 70 homozygotes) in the European non-Finnish population, which is higher than the ClinGen LSD VCEP’s threshold for BA1 (>0.01), and therefore meets this criterion (BA1). The computational predictor REVEL gives a score of 0.396 which is below the threshold of 0.5, evidence that does not predict a damaging effect on GAA function. In addition, the computational splice predictors SpliceAI and varSEAK predict that the variant has no impact on splicing (BP4). This variant is frequently described as a “pseudodeficiency” variant in the literature. It has been identified as the amino acid substitution responsible for the GAA*2 alloenzyme (also known as GAA2) (PMID: 2203258). GAA*2 was identified by its faster migration on starch gel electrophoresis compared to the GAA*1 alloenzyme (PMID: 2688539). In addition, compared to GAA*1, GAA*2 has a 10 fold higher Km for glycogen, but similar Km for maltose and 4-MUG (PMID: 2688539). No differences between the processing of GAA*2 and GAA*1 were noted on Western blot of protein from fibroblasts homozygous for either alloenzyme (PMID: 2688539). Furthermore, comparable amounts of glycogen were found in the lysosomes of the GAA*1 and GAA*2 homozygous cell lines, and there was no evidence of abnormal lysosomal glycogen storage in GAA*2 fibroblasts on electron microscopy (PMID: 2688539). When expressed in SV40-transformed GAA-deficient fibroblasts, c.271G>A (p.Asp91Asn) has similar GAA activity to wild type when 4-MUG is used as the substrate (PMID: 2203258). Studies in cells from patients show a difference in GAA activity depending on the substrate used. In cells from individuals who are homozygous, or compound heterozygous for the variant and a known pathogenic GAA variant, false positives arose when glycogen was used as the substrate in the leukocyte assay, while the expected result was obtained when 4-MUG was used as the substrate in either the leukocyte or fibroblast assays (PMID: 19387865, 33162552). Evidence from the crystal structures of native and recombinant GAA indicate that Asp91 is involved in a sugar binding site, which could explain why this variant binds carbohydrate less effectively (PMID: 29061980; https://www.biorxiv.org/content/10.1101/212837v1 ). In addition, while the computational splice site predictors SpliceAI and varSEAK predict no impact on splicing, a mini-gene assay indicated that the variant results in exon 2 exclusion in about 30% of transcripts (PMID: 31301153). As an explanation for how the biochemical features of this variant result in no clinical features, substrate concentrations are usually far below that required for saturation of the enzyme. A reduction in enzyme activity brought about by decrease in Vmax, or increase in Km, would be compensated for by an increase in substrate concentration, restoring the normal turnover rate and establishing an equilibrium substrate concentration (PMID: 2688539). In patients with Pompe disease, c.271G>A has been found in cis with other variants that have been classified as pathogenic by the ClinGen LSD VCEP, p.Cys103Gly (PMID: 16838077, 33073003) and c.877G>A (p.Gly293Arg) (PMID: 27189384).There is a ClinVar entry for this variant (Variation ID: 4020) with eight submitters classifying the variant as benign, two as likely benign, and two as “other”. In summary, based on the evidence available to date, this variant meets the criteria to be classified as benign for Pompe disease. However, it is important to note that GAA activity may be in the patient range in individuals who are homozygous for the variant, or compound heterozygous for the variant and a pathogenic GAA variant, if glycogen is used as a substrate. Careful evaluation and use of 4-MUG as the substrate is necessary to provide accurate results. Therefore, this variant is classified as “other” to ensure that an explanation for deficient enzyme activity in the context of a clinically benign variant is highlighted. GAA-specific ACMG-AMP criteria applied, as specified by the ClinGen LSD VCEP: BA1.
Eurofins Ntd Llc (ga)	RCV000078177	SCV000110015	other	not provided	2017-12-14	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000117106	SCV000302684	benign	not specified		criteria provided, single submitter	clinical testing
Invitae	RCV000531082	SCV000626594	other	Glycogen storage disease, type II	2019-01-02	criteria provided, single submitter	clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	RCV000531082	SCV001159130	benign	Glycogen storage disease, type II	2023-10-23	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000531082	SCV001287673	likely benign	Glycogen storage disease, type II	2018-01-12	criteria provided, single submitter	clinical testing	This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Genome-Nilou Lab	RCV000531082	SCV001737357	benign	Glycogen storage disease, type II	2021-06-10	criteria provided, single submitter	clinical testing
GeneDx	RCV000078177	SCV001894237	benign	not provided	2018-01-04	criteria provided, single submitter	clinical testing	Associated with pseudodeficiency of alpha-glucosidase enzyme. Homozygosity for D91N or compound heterozygosity for D91N and a pathogenic variant results in low enzyme activity but no clinical symptoms of Pompe disease (Martiniuk et al., 1990; Tajima et al., 2007; Kroos et al., 2008); This variant is associated with the following publications: (PMID: 31301153, 29181627, 25998610, 20080426, 2203258)
Ambry Genetics	RCV002426487	SCV002741448	benign	Cardiovascular phenotype	2015-12-28	criteria provided, single submitter	clinical testing	This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
OMIM	RCV000004235	SCV000024401	benign	Acid alpha-glucosidase, allele 2	2012-10-28	no assertion criteria provided	literature only
Genetic Services Laboratory, University of Chicago	RCV000117106	SCV000151258	likely benign	not specified		no assertion criteria provided	clinical testing	Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Stanford Center for Inherited Cardiovascular Disease, Stanford University	RCV000078177	SCV000925080	benign	not provided	2017-06-02	no assertion criteria provided	provider interpretation	The GAA gene is associated with Pompe disease; however, this variant is not associated with disease. It is known to interfere with assays for GAA enzyme activity and is therefore called a "pseudodeficiency allele". Even individuals with two copies of this variant do not have Pompe disease.
Natera, Inc.	RCV000531082	SCV001463470	benign	Glycogen storage disease, type II	2020-06-03	no assertion criteria provided	clinical testing
GenomeConnect - Invitae Patient Insights Network	RCV000078177	SCV001749821	not provided	not provided		flagged submission	phenotyping only	Variant reported in multiple Invitae PIN participants. Variant interpreted as Benign (Pseudo deficiency allele) most recently on 10/30/2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
GenomeConnect - Invitae Patient Insights Network	RCV000531082	SCV001749872	not provided	Glycogen storage disease, type II		no assertion provided	phenotyping only	Variant interpreted as Benign and reported on 08-27-2020 by Invitae. GenomeConnect-Invitae Patient Insights Network assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. Registry team members make no attempt to reinterpret the clinical significance of the variant. Phenotypic details are available under supporting information.
GenomeConnect, ClinGen	RCV000531082	SCV002074839	not provided	Glycogen storage disease, type II		no assertion provided	phenotyping only	Variant interpreted as Benign, Pseudo-deficiency allele and reported, most recently on 12-16-2020 by Lab or GTR ID 500031. GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.