High homocysteine is one of the most medically recognized consequences of having an MTHFR gene mutation, and learning to lower homocysteine with MTHFR can protect your health long-term. Balancing your methylation and boosting your B vitamins, especially B2, folate or 5-LMTHF, and B12, is the usual first step with MTHFR. But for true health, there are some other things that matter as well.