A lot of the effects of mutations are simply hardcoded, and there isn’t really a good way to fix it. Over time a lot of them have been able to be JSONized due to their similarity to other mutations (basic stat manipulations, etc.), but since a lot of mutations are just simple one-offs in the code (and sometimes have pretty deep-reaching, rather unique effects) they haven’t really been worth the time it would take to JSONize yet.
Assuming it’s been kept sort of up to date you should be able to find most things that you can currently do with mutations in JSON here.