Submissions for variant NM_000152.5(GAA):c.1210G>A (p.Asp404Asn)

gnomAD frequency: 0.00001  dbSNP: rs141533320

Total submissions: 10

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel	RCV000813939	SCV002817441	pathogenic	Glycogen storage disease, type II	2022-09-21	reviewed by expert panel	curation	The NM_000152.5:c.1210G>A variant in GAA is a missense variant predicted to cause substitution of aspartate by asparagine at amino acid 404 (p.Asp404Asn). At least 9 individuals with Pompe disease have been reported with this variant including individuals with documentation of deficient GAA activity and/or combination of clinical features of IOPD and on enzyme replacement therapy (PMID: 16433701, 22538254, 25687635, 26497565, 29205646) (PP4_Moderate). Four patients with Pompe disease are compound heterozygous for the variant, phase unknown, and a variant in GAA that has been classified as pathogenic by the ClinGen LSD VCEP, including c.1064T>C (p.Leu355Pro) (PMIDs 22658377, 23787031, 31193175), c.2481+102_2646+31del (PMID 22538254, 31086307), c.2227C>T (p.Gln743Ter) (PMID 25687635, 29205646), and c.2560C>T (p.Arg854Ter) (PMID 26497565) (0.5 points). In addition, the variant was found in a child in trans with c.2432delT, and his father in trans with c.-32-13T>G (PMID 16433701) (PM3_Strong). The variant has also been reported in compound heterozygosity with c.1445C>T (p.Pro482Leu)(PMID 31086307), c.1979G>A (p.Arg660His) (PMID 31086307), and c.1924G>T (p.Val642Phe) (PMID 29122469). The allelic data from these patients will be used in the assessment of the second variant and is not included here to avoid circular logic. The highest population minor allele frequency in a continental population in gnomAD v2.1.1 is 0.00006 (1/15828 alleles) in the African population, which is lower than the ClinGen LSD VCEP’s threshold for PM2_Supporting (<0.001), meeting this criterion (PM2_Supporting). This variant alters amino acid Asp404, a residue that crystallography studies have shown to be important in the active site of GAA, and therefore has been defined as a critical residue by the ClinGen LSD VCEP (https://www.biorxiv.org/content/10.1101/212837v1.full.pdf, PMID: 29061980) (PM1). When expressed in COS or HEK293 cells, this variant resulted in normal intracellular amounts of 110 kDa precursor, 95 kDa intermediate and 76 kDa mature forms of GAA but <2% wild type activity of GAA indicating that this variant may impact protein function (PMID 19862843, 24384324)(PS3_Supporting). The computational predictor REVEL gives a score of 0.869 which is above the threshold of 0.7, evidence that correlates with impact to GAA function (PP3). Four different missense variants, c.1211A>G (p.Asp404Gly), c.1211A>C (p.Asp404Ala), c.1211A>T (p.Asp404Val), and c.1212C>G (p.Asp404Glu), in the same codon have been reported in patients with Pompe disease (see http://www.pompevariantdatabase.nl/). The data from this variant (c.1210G>A (p.Asp404Asn) will be used to support the classification of the other missense substitutions of Asp404 and is not included here to avoid circular logic. There is a ClinVar entry for this variant (Variation ID: 657348, 2 star review status) with five submitters classifying the variant as pathogenic and two as likely pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease based on the ACMG/AMP criteria applied, as specified by the ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel (Specifications Version 2.0): PM3_Strong, PM1, PP4_Moderate, PP3, PS3_Supporting, PM2_Supporting. (Classification approved by the ClinGen LSD VCEP on Sept 21, 2022).
Labcorp Genetics (formerly Invitae), Labcorp	RCV000813939	SCV000954323	pathogenic	Glycogen storage disease, type II	2024-05-14	criteria provided, single submitter	clinical testing	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 404 of the GAA protein (p.Asp404Asn). This variant is present in population databases (rs141533320, gnomAD 0.006%). This missense change has been observed in individual(s) with Pompe disease (PMID: 16433701, 22658377). 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: 657348). 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: 19862843). This variant disrupts the p.Asp404 amino acid residue in GAA. Other variant(s) that disrupt this residue have been observed in individuals with GAA-related conditions (PMID: 23787031, 24384324), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard	RCV000813939	SCV001422738	pathogenic	Glycogen storage disease, type II	2020-01-22	criteria provided, single submitter	curation	The p.Asp404Asn variant in GAA has been reported in 9 individuals with glycogen storage disease II, segregated with disease in 2 affected relatives from 1 family (PMID: 22538254, 29122469, 29205646, 25687635, 22658377, 23787031, 26497565, 16433701) and has been identified in 0.006% (1/15828) of African chromosomes, 0.005% (1/18308) of East Asian chromosomes, and 0.004% (5/111690) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs141533320). 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 using transfected HEK293T cells provide some evidence that the p.Asp404Asn variant may slightly impact protein function (PMID: 24384324). 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 phenotype of individuals heterozygous for this variant is highly specific for glycogen storage disease II based on GAA enzyme activity in leucocytes, fibroblasts, or lymphocytes being <2% of wild type, consistent with disease (PMID: 26497565, 16433701). Additionally, the presence of this variant in combination with reported pathogenic and likely pathogenic variants (VariationID: 4027, 284093, 370157; PMID: 26497565, 25687635, 29122469, 16433701, 23787031) and in individuals with glycogen storage disease II increases the likelihood that the p.Asp404Asn variant is pathogenic. In summary, this variant meets criteria to be classified as pathogenic for glycogen storage disease II in an autosomal recessive manner based on in vitro functional studies and multiple occurrences with pathogenic variants in affected individuals. ACMG/AMP Criteria applied: PS3, PM3_strong, PM2, PP3, PP4 (Richards 2015).
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000813939	SCV001431893	pathogenic	Glycogen storage disease, type II	2020-08-10	criteria provided, single submitter	clinical testing	Variant summary: GAA c.1210G>A (p.Asp404Asn) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 248242 control chromosomes (gnomAD). c.1210G>A has been reported in the literature in multiple individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) (e.g. Amartino_2006, Desai_2019, Kishnani_2019). These data indicate that the variant is very likely to be associated with disease. Experimental evidence evaluating an impact on protein function demonstrated the variant results in severe reduction of GAA enzyme activity (e.g. Amartino_2006, Flanagan_2009, Nilsson_2014). Two ClinVar submitters (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
GeneDx	RCV001563037	SCV001785909	pathogenic	not provided	2022-12-08	criteria provided, single submitter	clinical testing	Published functional studies demonstrate a significant reduction of GAA activity (Flanagan et al., 2009); Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 16433701, 31254424, 26497565, 29205646, 22538254, 22658377, 25687635, 23787031, 29122469, 31086307, 19862843)
Revvity Omics, Revvity	RCV001563037	SCV002025219	pathogenic	not provided	2023-07-28	criteria provided, single submitter	clinical testing
3billion	RCV000813939	SCV002318505	pathogenic	Glycogen storage disease, type II	2022-03-22	criteria provided, single submitter	clinical testing	Same or different nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000657348, PMID:16433701). The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least one similarly affected unrelated individual(PMID: 16433701). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000959950, PMID:24384324,30155607). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.869>=0.6, 3CNET: 0.975>=0.75). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency:0.0000322). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
AiLife Diagnostics, AiLife Diagnostics	RCV001563037	SCV002502005	pathogenic	not provided	2022-02-17	criteria provided, single submitter	clinical testing
Fulgent Genetics, Fulgent Genetics	RCV000813939	SCV002806290	pathogenic	Glycogen storage disease, type II	2021-11-07	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000813939	SCV004195455	pathogenic	Glycogen storage disease, type II	2024-03-27	criteria provided, single submitter	clinical testing