For the record, this is almost certainly a genetic defect of the father, some kind of dominant mutation. Nutrition and other environmental factors most likely didn't play any role in a height difference this big.

There are two copies of each gene. Here, one of the copies got mutated in such a way that it caused the stunted growth of the father. Each sperm contains one randomly selected copy of each gene. Therefore half of the father's sperms contained the mutated gene and the other half the normal version. There was 50% chance the son would be normal height and 50% chance he would be small like his father.

I actually know a family like this. Nothing fishy going on there, the mutation is well described and now new kids with the mutation get growth hormones during their growth to reach normal size.