B.M.
Hi, I. -
My almost-13-year old son has social issues as well for similar reasons. Without knowing a bit more about your son and his interests, it's hard for me to make suggestions for after school activities. Boy Scouts? A musical group? My son is involved in a theater group and there he is comfortable, respected for his intelligence, and accepted. I wish I could say the same about school but I can't. I try to encourage him to enjoy on the positive situation he has at theater and consider that to be his social group and just focus on getting good grades at school.
Best of luck!