Glycogen storage disease type II (GSDII) is a recessively inherited disorder due to the deficiency of acid α-glucosidase (GAA) that results in impaired glycogen degradation and its accumulation in the lysosomes. We report here the complete molecular analysis of the GAA gene performed on 40 Italian patients with late onset GSDII. Twelve novel alleles have been identified: missense mutations were functionally characterized by enzyme activity and protein processing in a human GAA-deficient cell line while splicing mutations were studied by RT-PCR and in silico analysis. A complex allele was also identified carrying three different alterations in cis. The c.-32-13T>G was the most frequent mutation, present as compound heterozygote in 85% of the patients (allele frequency 42.3%), as described in other late onset GSDII Caucasian populations. Interestingly, the c.-32-13T>G was associated with the c.2237G>A (p.W746X) in nine of the 40 patients. Genotype–phenotype correlations are discussed with particular emphasis on the subgroup carrying the c.-32-13T>G/c.2237G>A genotype. Hum Mutat 27(10), 999–1006, 2006. © 2006 Wiley-Liss, Inc.
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