In the novel Freak the Mighty, by Rodman Philbrick, the best friend of Max (the "Mighty") is Kevin ("Freak"). When Max first meets Kevin, he realizes that there is something very different about him- he is very small.
Max recalls being in day-care with Kevin much earlier in their childhood. Kevin, he recalls, was the only child who scared him. Now, Max is intrigued by Kevin and the mechanical bird that he is flying.
When Max sees Kevin trying to get the bird out of the tree he realizes that there is something wrong- Kevin is very small for his (their) age. Max goes over to help.
After their friendship has begun, Max comes to learn that Kevin is more than just small; Kevin's growth condition will eventually take his life. Kevin, in order to accept his condition, has created a fairy-tale for his life where the government is going to conduct an experimental operation and give him a bionic body. Kevin never makes it to the surgery.
Shortly after Christmas and saving Max from his father's abduction, Kevin's condition takes his life. Kevin dies from his growth condition. This is the conversation between Max and Kevin's doctor about his death:
“What happened to him really?” Dr. Spivak answers simply, “His heart just got too big for his body.”
While the name of the condition is never stated in the novel, the film version states that Kevin has Morquio's Syndrome.
You did not answer my question on how did freak actually die?