The massive exome sequencing, as the most cost-efficient strategy in the genetic diagnosis of monogenetic Mendelian diseases, has a limitation imposed by its own design: it does not include the sequencing of intronic regions. It is now possible to perform massive sequencing of the entire genome, but nevertheless, the bioinformatics technologies and the scientific accumulation necessary to process the information obtained by this technique have not yet matured enough for it to be used in daily clinical practice. This is why we must be aware of the possibility that some diseases can be explained by deep intronic variants not detected by exome sequencing.
This is of special interest for recessive diseases, and must be taken into account in case a pathogenic variant is detected in one allele, but not in the other, in a case with a phenotype highly suggestive of the disease, given the possibility of compound heterozygosity.
Splicing.
The mechanism by which intronic variants have consequences on the phenotype has mainly to do with splicing.
The presence of introns in the genome is a characteristic biological phenomenon of eukaryotic cells, and the main evolutionary advantage it has is the ability to select different combinations of exons, which increases the diversity of gene expression. The process through which we obtain an mRNA sequence without introns, from a pre-RNA sequence, which is an exact copy of DNA, is known as splicing. The ribonucleoprotein machinery responsible for this function is known as spliceosome.
There are mainly 2, the major spliceosome and the minor spliceosome. It is a machinery modulated by multiple mechanisms, including activators (enhacers) and silencers (silencers). The action of these modulators gives rise to a phenomenon known as alternative splicing, so that the same gene can give rise to different protein products depending on the circumstances. According to current estimates, around 15-50% of disease-causing monogenic point mutations would affect pre-RNA splicing, with the majority of them affecting splice junctions.
Pathogenic mechanisms of intronic mutations.
- Inclusion of pseudo-exons.
- Competition with natural splicing sites.
- Disruption of transcription regulatory elements.
- Inactivation of non-coding RNAs.
- Chromosome rearrangements.
Diseases with pathogenic intronic mutations described in the literature.
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{19955111:KEC49H5E},{19955111:R3BSK2XY}
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