Splicing mutations in human genetic disorders: examples, detection, and confirmation

Abstract

Precise pre-mRNA splicing, essential for appropriate protein translation, depends on the presence of consensus “cis” sequences that define exon-intron boundaries and regulatory sequences recognized by splicing machinery. Point mutations at these consensus sequences can cause improper exon and intron recognition and may result in the formation of an aberrant transcript of the mutated gene. The splicing mutation may occur in both introns and exons and disrupt existing splice sites or splicing regulatory sequences (intronic and exonic splicing silencers and enhancers), create new ones, or activate the cryptic ones. Usually such mutations result in errors during the splicing process and may lead to improper intron removal and thus cause alterations of the open reading frame. Recent research has underlined the abundance and importance of splicing mutations in the etiology of inherited diseases. The application of modern techniques allowed to identify synonymous and nonsynonymous variants as well as deep intronic mutations that affected pre-mRNA splicing. The bioinformatic algorithms can be applied as a tool to assess the possible effect of the identified changes. However, it should be underlined that the results of such tests are only predictive, and the exact effect of the specific mutation should be verified in functional studies. This article summarizes the current knowledge about the “splicing mutations” and methods that help to identify such changes in clinical diagnosis.

Functional analysis of novel RHD variants: splicing disruption is likely to be a common mechanism of variant D phenotype

“…This dynamic process uses specific sequence recognition signals on the pre‐mRNA, including the critical 5′‐donor and 3′‐acceptor splice sites (SSs), (CAG/GUAAGU and NYAG/G, respectively), to remove non‐coding sequences (i.e., introns) and join coding sequences (i.e., exons) together to generate an open reading frame that will be further translated into a polypeptide by the translation machinery . A single change in either sequence may alter recognition by trans ‐acting factors of the splicing machinery, called the spliceosome (for recent review, see), resulting in improper removal of exon, retention of intron, or activation of a cryptic splice site, and ultimately causing a quantitative and/or qualitative defect in the production of mature mRNA . Importantly, at least 10% of disease‐causing mutations in human genes alter cellular splicing …”

A complete physical mapping of the vitamin D receptor gene for dental implant loss: A pilot study

“…It is interesting to note that these markers are in intronic regions, which initially leads us to believe that they are not functional SNPs. However, there is current evidence that polymorphisms in non‐coding regions are important because they may impact mRNA processing, modifying the action of spliceosome in the removal of introns and union of exons (Anna & Monika, ). This mechanism may bring as a consequence impacts to the protein synthesis.…”

Predicting the change of exon splicing caused by genetic variant using support vector regression

“…The changes of alternative splicing have been widely known to relate to human diseases, and even cancers (Climente‐González, Porta‐Pardo, Godzik, & Eyras, ). For example, variants occurring around splice sites can cause Birt‐Hogg‐Dubé syndrome, cystic fibrosis, Duchenne muscular dystrophy, and others (Anna & Monika, ; Furuya et al, ). Importantly, many synonymous mutations happening in exons that do not change encoded proteins were found to influence gene functions (Goodman, Church, & Kosuri, ; Parmley, Chamary, & Hurst, ), or act as driver mutations in cancers due to their associations with splicing changes (Supek, Miñana, Valcárcel, Gabaldón, & Lehner, ).…”