Check with his MD. If your son's cardiologist has cleared him for full activity, make sure he knows that he is normal in gym class. If he has activity restrictions, ask if it's appropriate for him to be in gym, and get a medical exemption if it's not. If he can participate but is limited, ask his gym teacher or school counselor to work out a modified plan for him that lets him do as much as possible.
See below. First check on limitations placed on child by nature of the disease. Then try and include them in what they can participate in. Perhaps use them as assistant coach in parts they can not physically participate in.