IamDDT

Perhaps this has been asked before, but have you considered epigenetic causes (DNA methylation, histone mods, even alternative splicing defects (which may not "look" interesting by sequencing)?

Unfortunately not, without reading a lot of what has already been done. If you have done NGS exon sequencing, though, it may be that you could look at promoter methylation after bisulfite conversion as well. Just a thought if the top of my head.