Interpretation of mRNA splicing mutations in genetic disease: review of the literature and guidelines for information-theoretical analysis

Abstract

The interpretation of genomic variants has become one of the paramount challenges in the post-genome sequencing era. In this review we summarize nearly 20 years of research on the applications of information theory (IT) to interpret coding and non-coding mutations that alter mRNA splicing in rare and common diseases. We compile and summarize the spectrum of published variants analyzed by IT, to provide a broad perspective of the distribution of deleterious natural and cryptic splice site variants detected, as well as those affecting splicing regulatory sequences. Results for natural splice site mutations can be interrogated dynamically with Splicing Mutation Calculator, a companion software program that computes changes in information content for any splice site substitution, linked to corresponding publications containing these mutations. The accuracy of IT-based analysis was assessed in the context of experimentally validated mutations. Because splice site information quantifies binding affinity, IT-based analyses can discern the differences between variants that account for the observed reduced (leaky) versus abolished mRNA splicing. We extend this principle by comparing predicted mutations in natural, cryptic, and regulatory splice sites with observed deleterious phenotypic and benign effects. Our analysis of 1727 variants revealed a number of general principles useful for ensuring portability of these analyses and accurate input and interpretation of mutations. We offer guidelines for optimal use of IT software for interpretation of mRNA splicing mutations.

Activation of cryptic splice sites in three patients with chronic granulomatous disease

“…mRNA, and thus favored the missplicing. Branch site mutations are known to cause missplicing (Caminsky et al, ; Maslen, Babcock, Raghunath, & Steinmann, ). In this case, only Hexplorer indicated increased ESE scores in the new exon (Figure ).…”

“…Other mechanisms are also possible. For instance, we (De Boer et al, ) and others (Caminsky, Mucaki, & Rogan, , in a review) have found mutations that create or activate a “stronger” splice site than the wild‐type (w.t.) splice site, resulting in an incorporation of incomplete or extended exons.…”

“…splice site, resulting in an incorporation of incomplete or extended exons. Caminsky et al () report 28 cases with creation or activation of an exonic or intronic cryptic donor splice site and 11 with activation or creation of an exonic or intronic acceptor splice site. Of these 28 cases, 18 concerned an exonic missense mutation, five an exonic synonymous variation, and five an intronic variation.…”

“…This is a more commonly found cause of cryptic acceptor splice site activation, but less frequently as a cause of cryptic donor splice site activation. Caminsky et al () reported 42 cases of cryptic acceptor splice site activation but only three cases of cryptic donor splice site activation, of which one due to an intronic variation, one to an exonic missense mutation, and one to an exonic synonymous variation.…”

Unexpected ABCC6 mRNA splicing in a Chinese family with pseudoxanthoma elasticum

“…The effect of the splicing mutation c.1177‐2A>G was predicted using the Splicing Mutation Calculator (Caminsky et al. ) (http://splicemc.cytognomix.com/). New splice site prediction was performed using the Berkeley Drosophila Genome Project (BDGP) (Reese et al.…”