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There's a section in the FAQ User Guide under Breeding 101 about lethal genes. You don't have to avoid them completely, just take note of the genes the mare and stallion have that you plan to breed.
In real life, these combos might result in a foal that is born dead or has to be euthanized shortly after birth.
In the game, it just doesn't give you a foal. I had a breeding project that ended up with frame (not intentionally), so my herd sire and most of my mares had it. I lost about 2 out of 10 foals from breeding Frame to Frame. It wasn't my favorite to start with, then an update on the frame gene made them not pretty anymore, so I finally put effort into breeding it out.