Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene

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Background: Cystic fibrosis is caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Over 1800 CFTR mutations have been reported, and about 12% of mutations are believed to impair pre-mRNA splicing. Given that several synthetic, non-splice-junction synonymous substitutions have been reported to alter splicing in CFTR, we predicted that naturally occurring synonymous substitutions may be erroneously classified as functionally neutral. Methods: Computational tools were used to predict the effect of synonymous substitutions on CFTR pre-mRNA splicing. The functional consequences of selected substitutions were evaluated using a minigene splicing assay. Results: Two synonymous mutations were shown to have a dramatic effect on CFTR pre-mRNA splicing, and consequently could alter protein integrity and phenotypic outcome. Conclusions: Traditional methods of mutation analysis overlook splicing defects that occur at internal positions in coding exons, especially synonymous substitutions. We show that bioinformatics tools and minigene splicing assays are a potent combination to prioritize and identify mutations that cause aberrant. CFTR pre-mRNA splicing. © 2012.




Scott, A., Petrykowska, H. M., Hefferon, T., Gotea, V., & Elnitski, L. (2012). Functional analysis of synonymous substitutions predicted to affect splicing of the CFTR gene. Journal of Cystic Fibrosis, 11(6), 511–517.

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