Highlights: A cohort of 143 compound heterozygous and 10 homozygous IVS1 patients were analyzed in this article. c.510CNT is a genetic modifier in compound heterozygous and homozygous IVS1 patients. This finding is important for neonatal screening programs for Pompe disease.

Background: Neonatal screening for Pompe disease is complicated by difficulties in predicting symptom onset in patients with the common c.-32-13TNG (IVS1) variant/null (i.e. fully deleterious) acid α-glucosidase (GAA) genotype. This splicing variant occurs in 90% of Caucasian late onset patients, and is associated with a broad range of symptom onset.

Methods: A cohort of 143 compound heterozygous and 10 homozygous IVS1 patients were analyzed; and ages at symptom onset and the presence of cis-acting single nucleotide variants (SNVs) were assessed; and splicing analysis and enzyme activity assays were performed.

Findings: In compound heterozygous IVS1 patients, the synonymous variant c.510CNT was uniquely present on the IVS1 allele in 9/33 (27%) patients with childhood onset, but was absent from 110 patients with onset in adulthood. GAA enzyme activity was lower in fibroblasts from patients who contained c.510CNT than it was in patients without c.510CNT. By reducing the extent of leaky wild-type splicing, c.510CNT modulated aberrant splicing caused by the IVS1 variant. The deleterious effect of c.510CNT was also found in muscle cells which are the main target cells in Pompe disease. In homozygous IVS1 patients, the c.510CNT variant was absent in 4/4 (100%) asymptomatic individuals and present in 3/6 (50%) symptomatic patients. In cells from homozygous IVS1 patients, c.510CNT caused reduced leaky wild-type splicing.

Interpretation: c.510CNT is a genetic modifier in compound heterozygous and homozygous IVS1 patients. This finding is important for neonatal screening programs for Pompe disease.

Keywords: Lysosomal storage disease; Modifying factor; Pompe disease; Pre-mRNA splicing; c.510C>T.