The real reason why is that the author made that the plot point for the story. However, the name, Runt, is a huge clue: the "runt of the litter" is a puppy, kitten, or similar animal that is MUCH smaller than all the others. Without a lot of help, runts typically die. Sometimes people tease small children by calling them "runt".
The explanation, then, is that for some unknown reason this giant is much smaller than all the others. While this may be rare in the made-up world of the giants, it's not impossible, since this character is like that. I used to tell my children when they balked at story details, "it doesn't happen often, that's why they built a story around it."