ClinVar Miner

Submissions for variant NM_000152.5(GAA):c.569G>A (p.Arg190His) (rs528367092)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169143 SCV000220363 likely pathogenic Glycogen storage disease, type II 2014-05-31 criteria provided, single submitter literature only
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000169143 SCV000919379 pathogenic Glycogen storage disease, type II 2018-04-02 criteria provided, single submitter clinical testing Variant summary: GAA c.569G>A (p.Arg190His) results in a non-conservative amino acid change located in the Galactose mutarotase, N-terminal barrel of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was observed with an allele frequency of 1.6e-05 in 244686 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) (1.6e-05 vs 0.0042), allowing no conclusion about variant significance. The variant, c.569G>A, has been reported in the literature in multiple individuals affected with Glycogen Storage Disease, Type 2 (Pompe Disease). These data indicate that the variant is very likely to be associated with disease. At least one publication reports experimental evidence evaluating an impact on protein function. The most pronounced variant effect results in <10% of normal activity. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as pathogenic.
Invitae RCV000169143 SCV001226092 pathogenic Glycogen storage disease, type II 2020-10-09 criteria provided, single submitter clinical testing This sequence change replaces arginine with histidine at codon 190 of the GAA protein (p.Arg190His). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and histidine. This variant is present in population databases (rs528367092, ExAC 0.01%). This variant has been observed in several individuals affected with Pompe disease (PMID: 23000108, 24444888, 21484825, 29149851, 31076647). ClinVar contains an entry for this variant (Variation ID: 188809). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Tolerated; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). This variant disrupts the p.Arg190 amino acid residue in GAA. Other variant(s) that disrupt this residue have been observed in individuals with GAA-related conditions (PMID: 29046207), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.
Broad Institute Rare Disease Group, Broad Institute RCV000169143 SCV001422620 likely pathogenic Glycogen storage disease, type II 2020-01-22 no assertion criteria provided curation The p.Arg190His variant in GAA has been reported in 2 Dutch and 1 Taiwanese individuals with Glycogen Storage Disease II, segregated with disease in 2 affected siblings from 1 family (PMID: 23000108, 24444888), and has also been reported likely pathogenic by Counsyl and pathogenic by Integrated Genetics in ClinVar (Variation ID: 188809). This variant has been identified in 0.006% (1/16218) of African chromosomes, 0.006% (2/34578) of Latino chromosomes, and 0.001% (1/113436) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs528367092). 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 provide some evidence that the p.Arg190His variant may impact GAA activity and proteolytically activated GAA levels (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. One species (scarlet macaw) carries a Histidine (His) at this position, raising the possibility that this change at this position may be tolerated. However, the presence of this variant in combination with pathogenic and likely pathogenic variants and in individuals with Glycogen Storage Disease II increases the likelihood that the p.Arg190His variant is pathogenic (PMID: 23000108, 24444888). The phenotype of 3 individuals heterozygous for this variant is highly specific for Glycogen Storage Disease II based on abnormally low GAA activity assay results in fibroblasts or a dried blood spot (PMID: 23000108, 24444888). In summary, although additional studies are required to fully establish its clinical significance, this variant is likely pathogenic. ACMG/AMP Criteria applied: PS3, PP3, PM2, PP4, PM3_Supporting (Richards 2015).

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