These variants include those that affect splicing by disrupting or weakening the motifs at intron-exon boundaries, introducing de novo splice acceptor or donor sites, activating cryptic splice sites
, or disrupting enhancer and silencer sequences.
Identification of a nonsense mutation producing a downstream cryptic 3' splice site
Furthermore, our assay demonstrated high sensitivity in detecting different classes of mutations, including nonsense, missense, frameshift, in-frame deletion, splice site
, and large-deletion mutations.
This indicates that small changes in a nucleotide sequence near a splice point can lead to large changes in splice site
choice and proteins produced.
On the other hand, our results obtained with splicing-prediction tools show that 1 of the 30 sequence variants we detected (rs7252245) lies within a predicted splice site
(see Table 1 in the online Data Supplement).
For instance, exon skipping or the activation of a cryptic splice site
(leading to the deletion/insertion of exonic/intronic sequences) provides strong evidence that the variant is pathogenic.
When focusing on the exons and splice sites
, we observed a mean of 26 nonrecurrent Ns (single Ns) per array, which had to be reviewed carefully so as to not overlook missense and splice site
mutations (see below).
In this study researchers at the University of North Carolina (UNC), working in close collaboration with Hybridon, targeted an antisense compound to restore correct splicing at an abnormal splice site
created by a mutation responsible for a genetic blood disorder called beta-thalassemia.
This mutation, which was previously described in individuals of Moroccan origin (7), occurs 23 positions downstream from the 5' splice site
in a tract that, compared with the other junctions, does not contain conserved sequence elements.
Alternatively the mutation at the ultimate nucleotide of exon 9 could affect splicing at the adjacent intron 9 donor splice site
, with various potential splicing outcomes (Fig.
The [alpha] splice site
causes a 36-bp deletion within the conserved reverse transcriptase motif A (16) and was found to be a dominant negative inhibitor of telomerase activity (21).