Your doctor should have answered this. The answer is complicated, especially because your son is only 11. Most people with these mutations have no problems, so it's just a minority of people who do. If the problem is severe, then a supplement will be recommended, but people differ on the kind to take and children have different needs and development levels than adults. The high homocysteine level suggests the mutation in your son's case is having an effect. If it can't be resolved through diet and if it isn't caused by a really poor diet, then you should have been given either a good quality homocysteine control supplement, which if of good quality would have the better and better absorbed forms of B12, folic acid (folic acid is always synthetic when taken in supplement form -- the natural form is called folate), and B6. When these are being absorbed properly from food in the appropriate ratio, they control homocysteine levels. When they're out of balance because of excessive supplementation of only one or two of them or from a poor diet or from genetic problems, you need to get them into the person in a form that the person can absorb. Some will advocate the methylated forms. Some will not. If your doctor seems to not be helping, either find a different one or go see a nutritionist or holistic physician of some sort who can help you out with this.
As for the iron deficiency, did the doctor say this is also from a genetic mutation? Iron can be difficult to take in supplement form because often the forms doctors prescribe are not absorbed well by humans. Plant based forms are absorbed best, but those supplements, such as one called Floradix, contain very low levels. Again, you need professional guidance here from a practitioner that really knows both how to treat children and how to diagnose the cause of the problem and the best supplements for best absorption and least negative effects on digestion.
I'm guessing that iron supplement is not well absorbed. I don't understand why you would be supplementing with fish oil, vitamin A or D unless a deficiency was found in them -- Vitamin A, for example, is liver toxic if you consume too much. It's usually given in the form of betacarotene, which converts safely to Vitamin A. As to levels of the nutrients, the body evacuates nutrients, especially water soluble ones, quickly. It's the fat soluble ones such as D and A that accumulate. I can only guess because there are no doctors on this site that some people will show high levels of one of the three and low levels of the other two, or something like that, because they are out of balance. You need a doctor for this, probably a specialist, and probably not the one you're currently seeing. Or at least ask the current doctor what the treatment is for. The homocysteine levels are just high, not super high, and absent those mutations, you would be told, I think, to feed your child less red meat. Absent those mutations, a natural physician might try to get them into balance with a balanced formula. I don't know what a specialist would do, but again, I'd encourage you to see one or see a holistic nutritionist if you can't find a doctor you trust. I wouldn't rest with what you're saying on here, and I don't know that the mutations definitely mean that's the cause. But they could be.
I also don't think the mutations would cause the iron deficiency. What does your son eat? How are his energy levels? Does he show signs of the problems that were found? Were the tests repeated -- sometimes levels can fluctuate quite a bit by the day and even within a day?