WHAT'S A SPLICE MUTATION?
A splice mutation is a mutation impacting the splicing process. Genes are made up by coding region (exons) and non-coding regions (introns). The mRNA produced starting from the DNA sequence is containing exons and introns, but before the translation into protein the non coding parts a cut out to generate a filament including only coding sequence. This process is called the splicing. The splicing is operated by enzymes which recognize specific sequences, to which they bind to in order to cut out the non-coding parts of the messenger (mRNA). There are basically to type so sequences that can be targeted by the splicing enzymatic complex: the highly conserved donor and a acceptor sites and the so called enhancing or silencing sequences. The donor site is invariably constituted by a guanine and a timine (GT) at the first two nucleotide positions of the intron (identified with the cDNA position c.___+1 and c.___+2; the acceptor site is invariably constituted by an adenine-guanine sequence at the last two nucleotide positions of the intron c.___-1 and c.___-2. Any mutation affecting these positions is almost certainly disease-causing. In other words, any nucleotide substitution at cDNA positions +/-1 or +/-2 is very likely damaging. More difficult is to locate splice mutations not affecting the highly conserved donor or acceptor site, but they actually exists! These are difficult to individuate, because the splicing enhancing or silencing sequencing are not phylogenetically conserved and are varying from gene to gene. In general, it is good to evaluate Ba in silico analysis any mutation falling within the first 10 nucleotides from mthe exon/intron boundaries, but these mutations can fall also deeply in an intron or even within an exon. Deep intronic splice mutations are therefore difficult to be screened for because (1) the deep intronic regions, for cost-efficiency reasons, are currently not analyzed in standard genetic diagnosis. Secondly, their interpretation is always difficult because of the very high variability described above. As a very general rule, any deep intronic or exotic mutation creating an
GT or a AG di nucleotide sequence can be suspected to activate a cryptic donor or acceptor splice site, but this is not the rule in every case. In silico analysis with different software is often the best way to predict the effect of such mutations. The are several software available. The output of some of these software can be calculated in parallel with Alamut (Interactive Biosoftware).
