ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.266G>A (p.Arg89His)

gnomAD frequency: 0.00006  dbSNP: rs200586324
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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel RCV000547185 SCV002032135 uncertain significance Glycogen storage disease, type II 2021-12-02 reviewed by expert panel curation The NM_000152.5(GAA):c.266G>A variant in GAA is a missense variant predicted to cause substitution of arginine by histidine at amino acid 89 (p.Arg89His). This variant has a minor allele frequency in gnomAD is 0.00016 in the South Asian population, which is lower than the ClinGen LSD VCEP threshold (<0.001) for PM2_Supporting, meeting this criterion. REVEL score = 0.819 which is higher than the LSD VCEP threshold for PP3 (>0.7) and therefore meets this criterion. This variant was found in compound heterozygosity (phase unknown) with a unique pathogenic variant in GAA in 1 patient with Pompe disease (PMID: 28196920). Additional cases, both homozygous and compound heterozygous (PMID: 28600779, 25626711, 33202836) have been reported but were not included because it was not clear if they had a second P/LP variant or if they had Pompe disease. At least 4 patients with this variant had documented GAA deficiency with activity in the affected range in muscle, cultured skin fibroblasts, leukocytes, lymphocytes, whole blood or dried blood spot ( PMID: 33202836, 28196920) or were noted to have deficient GAA activity but results were not provided and were reported to be on enzyme replacement therapy for Pompe disease ( PMID: 25626711). (PP4_Moderate). Based on the ClinGen LSD VCEP's specifications, this data meets PP4_Moderate and PM3_Supporting. When expressed in COS cells, this variant was classified as Class E ("presumably nonpathogenic") by Kroos et al, 2012 (PMID:22644586). This includes 43.5% GAA activity in cells and 20% in medium, and is normally synthesized (though less than normal) and processed on Western blot. This meets the ClinGen LSD VCEP specifications for BS3_Supporting. There is a ClinVar entry for this variant (Variation ID: 283219; 1 star review status) with 6 submitters classifying the variant as a variant of uncertain significance and 2 as pathogenic. In summary, this variant meets the criteria to be classified as a Variant of Unknown Significance for Pompe disease. ACMG/AMP criteria met, based on the specification of the ClinGen LSD VCEP: PP4_Moderate, PP3, PM2_Supporting, PM3_Supporting, BS3_Supporting.
Eurofins Ntd Llc (ga) RCV000370905 SCV000335191 uncertain significance not provided 2016-09-13 criteria provided, single submitter clinical testing
Invitae RCV000547185 SCV000626592 pathogenic Glycogen storage disease, type II 2024-01-27 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 89 of the GAA protein (p.Arg89His). This variant is present in population databases (rs200586324, gnomAD 0.1%). This missense change has been observed in individuals with clinical features of Pompe disease (PMID: 22644586, 25626711, 32860008, 34602496; Invitae). ClinVar contains an entry for this variant (Variation ID: 283219). 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 are conflicting or provide insufficient evidence to determine the effect of this variant on GAA function (PMID: 22644586). For these reasons, this variant has been classified as Pathogenic.
Illumina Laboratory Services, Illumina RCV000547185 SCV001287672 uncertain significance Glycogen storage disease, type II 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Broad Institute Rare Disease Group, Broad Institute RCV000547185 SCV001422661 uncertain significance Glycogen storage disease, type II 2020-01-22 criteria provided, single submitter curation The p.Arg89His variant in GAA has been reported in 3 individuals with Glycogen Storage Disease II (PMID: 22644586, 28600779, 25626711), but it is unclear whether this variant causes Glycogen Storage Disease II. This variant has also been reported as a VUS by Invitae and EGL Genetic Diagnostics in ClinVar (Variation ID: 283219), and has been identified in 0.117% (12/10272) of Ashkenazi Jewish chromosomes, 0.016% (5/30550) of South Asian chromosomes, and 0.015% (19/127034) of European (Non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs200586324). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. One individual was homozygous for this variant and another reported pathogenic variant for Glycogen Storage Disease I in G6PC, p.Arg83Cys (PMID: 28600779; Variation ID: 11998). Another individual was homozygous for this variant and another VUS reported in the literature, c.546+45G>C (PMID: 22644586). This variant was also seen in trans with a rare VUS in GAA (PMID: 25626711). In vitro functional studies provide some evidence that the p.Arg89His variant may not impact protein function (PMID: 22644586). 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. In summary, while the clinical significance of the p.Arg89His variant is uncertain, these data suggest that it is more likely to be benign. ACMG/AMP Criteria applied: PP3, BS3_Supporting, BP2 (Richards 2015).
Centogene AG - the Rare Disease Company RCV000547185 SCV001426579 pathogenic Glycogen storage disease, type II criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000370905 SCV001500155 uncertain significance not provided 2021-12-01 criteria provided, single submitter clinical testing
GeneDx RCV000370905 SCV001767424 uncertain significance not provided 2021-12-02 criteria provided, single submitter clinical testing Reported in the homozygous state in the presence of an additional homozygous GAA variant (c.-32-13T>G, a common pathogenic variant in individuals with adult-onset GSDII) in an infant severely affected with GSDII; functional studies indicated only minimally reduced enzyme activity and the R89H variant was classified as presumably non-pathogenic by the authors (Kroos M et al., 2012); Reported in the homozygous state in a patient with a dual diagnosis of GSDII and GSDI who also harbored a homozgyous pathogenic variant in the G6PC gene (Monies D et al., 2017); Reported in additional patients with GSDII with either a variant of uncertain significance in trans or for whom a second variant was not identified (Hahn A et al., 2015; Nair P et al., 2018; Bertoli-Avella AM et al., 2021); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Reported in ClinVar (ClinVar Variant ID# 283219; ClinVar); This variant is associated with the following publications: (PMID: 25626711, 30293248, 31342611, 33202836, 32860008, 22644586, 27927596, 28600779, 34426522, 34602496)
Genome-Nilou Lab RCV000547185 SCV001810207 likely pathogenic Glycogen storage disease, type II 2021-07-22 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002509345 SCV002819388 uncertain significance not specified 2022-12-09 criteria provided, single submitter clinical testing Variant summary: GAA c.266G>A (p.Arg89His) results in a non-conservative amino acid change located in the P-type trefoil domain (IPR000519) of 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 0.00014 in 248182 control chromosomes (gnomAD). It has also been reported at a frequency of 0.0016 in the Turkish population, including one homozygote whose clinical status was not specified (Kars_2021). These frequencies are not significantly higher than expected for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) (0.0042), allowing no conclusion about variant significance. c.266G>A has been reported in the literature in individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease) and also in individuals suspected of the late onset form of the disease, but without a definitive clinical diagnosis (e.g. Hahn_2015, Lin_2017, Nair_2018, Tang_2020, Ficicioglu_2020, Bertoli-Avella_2021). In these reports it has been found in the compound heterozygous state together with pathogenic variants, but also with variants of uncertain significance, and in the heterozygous state where a second allele has not been identified or not specified. Therefore these reports do not provide unequivocal conclusions about association of the variant with Pompe Disease. At least one publication reports experimental evidence evaluating an impact on protein function. It found that the variant results in 43.5% of WT activity in vitro and described the variant as presumably non-pathogenic (Kroos_2012). Nine submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 with conflicting assessments. The majority classified the variant as VUS (n=7) and the other classified the variant as likely pathogenic (n=2). Based on the evidence outlined above, the variant was classified as VUS.
Revvity Omics, Revvity Omics RCV000370905 SCV003816230 uncertain significance not provided 2023-10-26 criteria provided, single submitter clinical testing
Biochemical Genetics Department, Cyprus Institute of Neurology and Genetics RCV000547185 SCV003927052 likely pathogenic Glycogen storage disease, type II 2023-05-05 criteria provided, single submitter clinical testing The classification of the variant was performed according to the recommendations of ClinGen lysosomal storage disorders variant curation expert panel (Guidelines version 2, specific for the GAA gene). The NM_000152.5(GAA):c.266G>A p.(Arg89His) variant is a missense variant that replaces a highly conserved arginine residue (Arg89) by histidine (p.Arg89His). This variant is present at an extremely low frequency in gnomAD databases (ƒExomes = 0.0000141, ƒgenomes = 0.0000657), only in heterozygosity and meets the PM2_Supporting criterion (1pt). The c.266G>A variant confirmed to be in trans with the pathogenic variant NM_000152.5:c.2237G>C p.(Trp746Ser) in our case. Moreover, it has been identified in compound heterozygosity with the c.546+45G>C variant in individuals with clinical features of Pompe disease [PMID: 22644586], thus meets the PM3_strong criterion (2pts). The REVEL score is 0.819 which is higher than the LSD VCEP threshold for PP3 (>0.7) and therefore meets this criterion (1pt). An alternative variant NM_000152.5(GAA):c.265C>A (p.Arg89Ser) is classified as Likely Pathogenic [1 star, ClinVar, PM5_supporting (1pt)]. The four individuals, with the c.[266G>A];[2237G>C] genotype (2-13years), were found to have GAA activity clearly within the patient range (1.1-4.9nmol/h/mg) in leukocytes using 4-methylumbelliferyl-α-D-glucoside as a substrate. Using glycogen as a substrate, the GAA activity was found to be within the range for LOPD patients (3-10nmol/h/mg) for one subject and slightly above the upper limit for the three subjects. The presence of the KM-mutant polymorphism c.271G>A and the pseudodeficiency variant c.[1726G>A (p.Gly576Ser); 2065G>A (p.Glu689Lys)] was excluded. Based on the ClinGen LSD VCEP's specifications, this data meets PP4_Moderate rule (2pts). In summary, this variant meets the criteria to be classified as a likely pathogenic variant (total 7pts) for Pompe disease.
Baylor Genetics RCV000547185 SCV004197883 uncertain significance Glycogen storage disease, type II 2022-11-09 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000370905 SCV004224433 uncertain significance not provided 2022-04-22 criteria provided, single submitter clinical testing PP3, PP4, PM2
Natera, Inc. RCV000547185 SCV001453580 uncertain significance Glycogen storage disease, type II 2020-09-16 no assertion criteria provided clinical testing

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