It's very likely that it is a large issue for her. If her body can't get rid of the toxins well enough, then they are in there messing with things!
I only know what to do for the basic MTHFR mutation, and that's slowly titrating up on doses of Methyl B-12 and methyl folate. It would depend on which mutations she has. Have you visited this site yet?
mthfr.net/ It appears to be one of the more informative and accurate sites out there on these issues.