To uncover pathogenic deep intronic variants in patients with colorectal 
adenomatous polyposis, in whom no germline mutation in the APC or MUTYH genes 
can be identified by routine diagnostics, we performed a systematic APC 
messenger RNA analysis in 125 unrelated mutation-negative cases. Overall, we 
identified aberrant transcripts in 8% of the patients (familial cases 30%; 
early-onset manifestation 21%). In eight of them, two different out-of-frame 
pseudoexons were found consisting of a 167-bp insertion from intron 4 in five 
families with a shared founder haplotype and a 83-bp insertion from intron 10 in 
three patients. The pseudoexon formation was caused by three different 
heterozygous germline mutations, which are supposed to activate cryptic splice 
sites. In conclusion, a few deep intronic mutations contribute substantially to 
the APC mutation spectrum. Complementary DNA analysis and/or target sequencing 
of intronic regions should be considered as an additional mutation discovery 
approach in polyposis patients.