My son (1.5yo) was just diagnosed with a very, very rare genetic disorder (Primary Hyperoxaluria Type III). The specialist who actually described this disease hypothesises that the genetic mutation causes the pathway for the proper breakdown of animal protein to be blocked. Instead, it takes another pathway which causes the excess production of oxalates and has therefore, recommended a vegan diet for my son (milk and butter ok). I am a bit stumped on what to feed him.
Not sure I understand how a vegan diet minimizes oxalates... which is the problem with hyperoxaluria. Oxalates are absent in animal products, and present in many plant foods. I'm guessing it stresses the kidneys so they're just trying to minimize urea production, which seems like treating the symptom more than the underlying disorder.
Get additional doctors' opinion, particularly one who's actually worked with this disorder.
I finally had time to look this up. I'm interested in kidney problems, and apologize if my previous comment was unhelpful to you. Anyhow! Kidney stones sort of run in my family, and I just asked my closest relative which type she deals with (answer: oxalates). So, here's what I found:
Obviously you've learned all this by now, but for others who are looking at this thread, here's some info on the condition: http://www.ohf.org/about_disease.html
This is some information I found about a low-oxalate diet. I'm not sure if it'll help you totally, but it might be a good place to start: http://www.upmc.com/patients-visitors/education/nutrition/Pages/low-oxalate-diet.aspx
As an overview of the above, it looks like the following generally-kid-friendly foods are low-oxalate:
**You mentioned that your son has problems breaking down animal proteins, so I only mention that because it's on the low-oxalate-foods list. I'm not a doctor, so please don't take my word for anything. If he can't digest those proteins, by no means should you just give them to him because they're part of an ideal diet for MOST people. (Your son is not most people.)
At any rate, it looks like a good number of fruits (except a lot of berries) might be okay? I'm a little confused by looking at the condition information whether animal fats might be a problem in addition to proteins, or whether certain starches might be good or bad. If it turns out your son can eat some animal products in small amounts you'll probably have to be pretty choosy as to which ones he eats.
Additionally, dark leafy greens probably aren't the best as they're pretty high in oxalates.
I do think, though, as per my earlier comment, that you may wish to get a second opinion if only to make YOU feel better about making decisions for your son. As a parent, I do not envy your position. Hang in there! You're an awesome parent for trying to figure all this out for your child.
Get a second and third opinion. Do what's best for your family. If you find that all your additional consults advise a vegan diet then do it. It's so different now and you know it's really all first world problems all this diet debate stuff. My mother had a rare disease so be prepared for a lot of ignorance. There's an Internet group for everything. Go find allies :)
Primary hyperoxaluria is more than just avoiding oxalates, though that's important too. Yaacov Firshberg, the specialist your doctor is consulting with, believes (and his evidence is convincing) that people with PH3 have an issue with hydroxyproline due to a mutation of the gene involved with the pathway by which hydroxyproline can be converted into oxalate.
Since animal protein is the really the main significant dietary source of hydroxyproline it makes sense that he would advocate a vegan diet. But I still think it's a bad idea.
I don't have an issue with a diet low in animal protein in this case, but eliminating animal products completely comes with risks of deficiencies. My recommendation is to keep animal protein low except for the occasional nutrient dense animal food, for example oysters, pastured egg yolk, and grass fed beef liver. Beyond that, look for food with low oxalate content, there are lots.
And hey, pastured animal fats are low oxalate and hydroxyproline too!
A friend of mine's kid had a lot of digestive issues for his first 5 years, he was at times diagnosed with various food allergies (dairy, protein, wheat, sugar, etc), later with "leaky gut", and some other things mixed in. She went through at least a half dozen doctors as the kid would get better and then worse again with slightly different symptoms, and it was a long and agonizing road.
After many years, she finally struck on a diagnosis of a fungus overgrowth in his gut, which was found by a homeopathic doctor, and was treated by a high concentration of garlic in his foods for about 6 weeks. It was uncomfortable at first (the theory is that the fungus fights back before dying off) but he was eventually completely cured and has been fine ever since.
I say this not to suggest that your kid has the exact same condition, but just that digestive disorders are tricky to diagnose and doctors don't always get it right, and tend to have strong biases. For example doctors with a genetic background tend to find genetic disorders, homeopathic doctors tend to find problems with diet and well-being, most doctors try to get you out of their office with a prescription. I would get a 2nd or 3rd opinion for your kid.
I am not a doctor but am very skeptical of a vegan diet as a diagnosis, since I think that a vegan diet just simply doesn't nourish a human sufficiently, and have seen many people improve their health significantly by switching FROM a vegan diet. Going vegan might get your kid through a rough patch but I don't think it is a viable long term alternative.
A vegan hunter-gatherer tribe? 7 Answers
Muscle Recovery - Meat vs Plants 2 Answers