Nonsense mutation-associated Becker muscular dystrophy: interplay between exon definition and splicing regulatory elements within the DMD gene

Abstract

Nonsense mutations are usually predicted to function as null alleles due to premature termination of protein translation. However, nonsense mutations in the DMD gene, encoding the dystrophin protein, have been associated with both the severe Duchenne Muscular Dystrophy (DMD) and milder Becker Muscular Dystrophy (BMD) phenotypes. In a large survey, we identified 243 unique nonsense mutations in the DMD gene, and for 210 of these we could establish definitive phenotypes. We analyzed the reading frame predicted by exons flanking those in which nonsense mutations were found, and present evidence that nonsense mutations resulting in BMD likely do so by inducing exon skipping, confirming that exonic point mutations affecting exon definition have played a significant role in determining phenotype. We present a new model based on the combination of exon definition and intronic splicing regulatory elements for the selective association of BMD nonsense mutations with a subset of DMD exons prone to mutation-induced exon skipping.

Rapid, comprehensive analysis of the dystrophin transcript by a custom micro-fluidic exome array

“…In addition, a few mutations escape detection by all of these techniques, thereby necessitating the combined use of CGH and RNA analysis, which requires the availability of patients' muscle biopsy. Unfortunately, the issue is further complicated by the fact that duplications or small mutations may have unpredictable effects on the behavior of RNA, influencing splicing events/choices and thereby impacting on the phenotype and genetic prognosis of the disease [Flanigan et al, 2011;Gualandi et al, 2009;Magri et al, 2011]. As described in Flanigan et al, 2011, the prediction of the effect of a mutation could be improved by using bioinformatic tools, but still a few cases remain undisclosed.…”

“…Unfortunately, the issue is further complicated by the fact that duplications or small mutations may have unpredictable effects on the behavior of RNA, influencing splicing events/choices and thereby impacting on the phenotype and genetic prognosis of the disease [Flanigan et al, 2011;Gualandi et al, 2009;Magri et al, 2011]. As described in Flanigan et al, 2011, the prediction of the effect of a mutation could be improved by using bioinformatic tools, but still a few cases remain undisclosed. Hence, definition of the RNA profile is recommended for establishing the genetic prognosis in DMD gene mutations (especially duplications or small mutations of uncertain significance), a fact which is of particular relevance to the forthcoming and ongoing therapeutic trials exploring novel, often mutation-specific approaches.…”

DMD genotypes and loss of ambulation in the CINRG Duchenne natural history study

“…Possible mechanisms include translation reinitiation downstream of N-terminal domain mutations, [15][16][17][18] or low-rate splicing out of specific exons. [19][20][21] Even very small quantities of dystrophin, hardly detectable by immunohistochemistry (IHC) or Western blot (WB), might ameliorate the disease and delay LoA by several years. This is particularly relevant for the development of dystrophin-restoring treatments, such as exon skipping by antisense oligonucleotides (AONs) [22][23][24][25][26][27][28][29][30] and stop codon readthrough, [31][32][33] as variation in baseline levels of dystrophin may confound evaluations of efficacy in clinical trials.…”

Clinical Utility Gene Card for: Becker muscular dystrophy

“…Predicted nonsense variants in exons 23-42 can result in BMD through altering splice definition regions such that the mutated exon is not spliced into the mature mRNA [13,14]. An out-of-frame deletion of exons 3-7, although usually associated with DMD, can result in BMD because of downstream translational reinitiation (exons numbered as per NG_012232.1 and the Leiden Open Variation Database) [15,16].…”

“…Even if a non-private variant is found, large variation in phenotype within families has been reported. However, variants in domain I, responsible for actin binding, usually result in severe BMD, and also intermediate muscular dystrophy (characterised by loss of ambulation between the age of 12 and 15 years) [13]. Domain II (the rod domain) is not essential for protein function and thus variants in this region are often associated with a mild phenotype and occasionally asymptomatic individuals [39,45].…”