Hi there, I was just looking up information about this condition my son has out of curiosity. He was diagnosed at 3 1/2 with partial sacral agenisis, and is missing his tailbone too. He was diagnosed as a result of gastroenterology treatment for severe constipation. It took 18 months to get the constipation sorted and he is now nearly 11 years old. What problems has the partial sacral agenisis caused? Nothing really. It turns out you don't really need a tailbone & if the spinal cord passes correctly through the deformed sacrum, all is well. He's a good athlete, plays football, runs really fast & is a very fit, healthy active boy. We've always needed to keep his constipation in check which we do. He naturally chooses very good foods, unlike his brother, so this helps.
Good luck with our son. I worried a lot but it was unnecessary in our case. My other son complained of a sore back at one stage. Does anyone else in the family have a sore back? It turned out he was copying his dad. It was very convincing! Hopefully your sons pain resolves itself and his missing tailbone is nothing to concern you.