Prediction and assessment of splicing alterations: implications for clinical testing

Abstract

For the Mutation Pathogenicity Special IssueSequence variants that may result in splicing alterations are a particular class of inherited variants for which consequences can be more readily assessed, using a combination of bioinformatic prediction methods and in vitro assays. There is also a general agreement that a variant would invariably be considered pathogenic on the basis of convincing evidence that it results in transcript(s) carrying a premature stop codon or an in-frame deletion disrupting known functional domain(s). This commentary discusses current practices used to assess the clinical significance of this class of variants, provides suggestions to improve assessment, and highlights the issues involved in routine assessment of potential splicing aberrations. We conclude that classification of sequence variants that may alter splicing is greatly enhanced by supporting in vitro analysis. Additional studies that assess large numbers of variants for induction of splicing aberrations and exon skipping are needed to define the contribution of splicing/exon skipping to cancer and disease. These studies will also provide the impetus for development of algorithms that better predict splicing patterns. To facilitate variant classification and development of more specific bioinformatic tools, we call for the deposition of all laboratory data from splicing analyses into national and international databases. Hum Mutat 29(11), [1304][1305][1306][1307][1308][1309][1310][1311][1312][1313] 2008. r r

Integrated analysis of unclassified variants in mismatch repair genes

“…The probabilities calculated were then classified in five classes, following the guidelines of the Special Issue of Human Mutation. [3][4][5][6][7][8][9][10][11][12] An increasing number of groups are trying to classify UVs using these recommendations, but most of them focus on the BRCA1 and BRCA2 genes, for which a multifactorial likelihood classification has already been developed and refined. Instead, for MMR genes, there are not well-established models or well-characterized features 42 so that, at the time of writing, a very few groups have attempted to classify MMR UVs with the Bayesian likelihood method.…”

Analysis of LDLR mRNA in patients with familial hypercholesterolemia revealed a novel mutation in intron 14, which activates a cryptic splice site

“…15 It is therefore likely that the tissue/developmental variation in splicing factors might also affect the outcome of a mutation and reduce or amplify the degree of aberrant splicing. 14 The relative amount of aberrantly spliced LDLR mRNA was analyzed in blood samples. However, whether leukocytes are representative for hepatic tissue in this context is uncertain.…”

Nasal epithelial cells are a reliable source to study splicing variants in Usher syndrome

“…Identification of abnormal exon skipping, or activation of a new splice site or preexisting pseudo splice site that may result in deletion of exonic bases or retention of intronic bases can provide strong evidence for a pathogenic effect of the variant [Baralle and Baralle, 2005]. Spurdle et al [2008] has reviewed the programs that are currently available to predict splicing effect of UVs, and emphasized that, as they all have both strengths and shortcomings, analysis at the mRNA level remains essential to establish the clinical relevance and the consequences on splice site loss. This mRNA analysis also allows us to assess the presence of ectopic splice sites [Arnold et al, 2009].…”