title: In vitro and in silico analysis reveals an efficient algorithm to predict the splicing consequences of mutations at the 5' splice sites.
abstract: We have found that two previously reported exonic mutations in the PINK1 and PARK7 genes affect pre-mRNA splicing. To develop an algorithm to predict underestimated splicing consequences of exonic mutations at the 5' splice site, we constructed and analyzed 31 minigenes carrying exonic splicing mutations and their derivatives. We also examined 189,249 U2-dependent 5' splice sites of the entire human genome and found that a new variable, the SD-Score, which represents a common logarithm of the frequency of a specific 5' splice site, efficiently predicts the splicing consequences of these minigenes. We also employed the information contents (R(i)) to improve the prediction accuracy. We validated our algorithm by analyzing 32 additional minigenes as well as 179 previously reported splicing mutations. The SD-Score algorithm predicted aberrant splicings in 198 of 204 sites (sensitivity = 97.1%) and normal splicings in 36 of 38 sites (specificity = 94.7%). Simulation of all possible exonic mutations at positions -3, -2 and -1 of the 189 249 sites predicts that 37.8, 88.8 and 96.8% of these mutations would affect pre-mRNA splicing, respectively. We propose that the SD-Score algorithm is a practical tool to predict splicing consequences of mutations affecting the 5' splice site.
authors.affiliation: Division of Neurogenetics and Bioinformatics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
authors.forename: Kentaro
authors.initials: K
authors.lastname: Sahashi
authors.forename: Akio
authors.initials: A
authors.lastname: Masuda
authors.forename: Tohru
authors.initials: T
authors.lastname: Matsuura
authors.forename: Jun
authors.initials: J
authors.lastname: Shinmi
authors.forename: Zhujun
authors.initials: Z
authors.lastname: Zhang
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Takeshima
authors.forename: Masafumi
authors.initials: M
authors.lastname: Matsuo
authors.forename: Gen
authors.initials: G
authors.lastname: Sobue
authors.forename: Kinji
authors.initials: K
authors.lastname: Ohno
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002460:Cell Line; D016384:Consensus Sequence; D030561:Databases, Nucleic Acid; D005091:Exons; D023281:Genomics; D006801:Humans; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D010300:Parkinson Disease / Q000235:genetics; D022821:RNA Splice Sites; D012326:RNA Splicing; D012342:RNA, Small Nuclear / Q000235:genetics
chemical_list: D022821:RNA Splice Sites; D012342:RNA, Small Nuclear; C405483:U1 small nuclear RNA; C405486:U6 small nuclear RNA