Total submissions: 5
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Counsyl | RCV000169390 | SCV000220782 | likely pathogenic | Glycogen storage disease, type II | 2014-10-10 | criteria provided, single submitter | literature only | |
| Revvity Omics, |
RCV001781527 | SCV002025208 | likely pathogenic | not provided | 2021-02-21 | criteria provided, single submitter | clinical testing | |
| Labcorp Genetics |
RCV000169390 | SCV002174547 | pathogenic | Glycogen storage disease, type II | 2025-01-17 | criteria provided, single submitter | clinical testing | This variant, c.2024_2026del, results in the deletion of 1 amino acid(s) of the GAA protein (p.Asn675del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs773958269, gnomAD 0.01%). This variant has been observed in individuals with Pompe disease (PMID: 9554747, 10338092, 29046207). Algorithms developed to predict the effect of variants on gene product structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this variant affects GAA function (PMID: 19862843). For these reasons, this variant has been classified as Pathogenic. |
| Women's Health and Genetics/Laboratory Corporation of America, |
RCV000169390 | SCV004030048 | pathogenic | Glycogen storage disease, type II | 2023-07-31 | criteria provided, single submitter | clinical testing | Variant summary: GAA c.2024_2026delACA (p.Asn675del) results in an in-frame deletion that is predicted to remove one amino acid from the encoded protein. The variant allele was found at a frequency of 8.3e-06 in 241688 control chromosomes (i.e., 2 heterozygotes; gnomAD v2.1 Exomes dataset). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.2024_2026delACA has been reported in the literature in multiple compound heterozygousindividuals affected with infantile-onset Glycogen Storage Disease, Type 2 (Pompe Disease) (e.g., Shieh_1998, Fu_2014, Chen_2017, Ngiwsara_2019). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 28394184, 24269976, 31510962, 9554747). Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. |
| Baylor Genetics | RCV000169390 | SCV004195415 | pathogenic | Glycogen storage disease, type II | 2024-02-21 | criteria provided, single submitter | clinical testing |