This variant, c.1802C>A (p.Ser601Ter), which results in a premature termination codon, is expected to result in nonsense mediated decay and absence of gene product, meeting PVS1. This is supported by the finding that a patient with this variant has no GAA cross-reactive immunological material in protein isolated from skin fibroblast cultures i.e. CRIM-negative (PMID 21687968). The variant is absent in gnomAD v2.1.1, meeting PM2. This variant was found in compound heterozygosity with c.525del in one patient with Pompe disease meeting the specifications for PP4. The phase is unknown (PMID 26497565). This data meets PM3_Supporting. A patient with the same genotype has been reported (PMID 21687968) and might be the same patient but this could not be verified. There is a ClinVar entry for this variant (Variation ID: 593486, 1 star review status) with one submitter classifying the variant as pathogenic. In summary, this variant meets the criteria to be classified as pathogenic for Pompe disease. GAA-specific ACMG/AMP criteria applied, as specified by the ClinGen LSD VCEP: PVS1, PM3_Suporting, PM2, PP4.