Mutational mechanisms are not the same for all diseases. There are some diseases in which deletions are more frequent than point mutations.
https://www.nature.com/articles/gim200934
Intragenic deletions (deletions the size of an exon) can be difficult to identify using current sequencing techniques, and may also go undetected by aCGH technology (depending on probe density).
https://www.mrcholland.com/technology/mlpa
Intragenic deletions are of particular importance from a therapeutic standpoint, as in some cases they are candidates for exon-skipping therapy (exon-skipping).
https://www.mdpi.com/2075-4426/8/4/41/htm

For Duchenne disease, there is a online calculator to know if a specific deletion is a candidate for exon-skipping therapy.