My experience is 5th-8th grades are very hard socially. Your son in not alone here. Kids who struggle with social cues and are a bit slow on the social development really have a hard time during these grades. Keep in mind that the other kids are also learning their social skills and while they might be better than your son's they don't tend to be the most empathetic.
I know how hard it can be. My son crashed and burned in 6th grade socially. (Still in elementary in his case.) We had high hopes that things would change in junior high but while it did get better, he isolated himself and didn't really try to make friends. At the time he though the other kids immature and didn't think anyone else liked the same things he did.
I did put him in a social skills class for about 6 months starting at the end of 6th grade, and was seeing a therapist for a while then. And for the past year+ in H.S. (There is more than just the social skills, he has anxiety disorder.) I am sure this helped but it didn't show immediately. I don't know exactly what went on in those meetings as I wasn't invited. Mostly I think it was stuff he absorbed but wasn't read to put into practice till he was a bit older. I'm not giving you much specific advice here except I did get professional help. Learning social skills takes time & practice. Even though DS is smart doesn't mean he can pick this type of thing up fast. It takes practice and it can be a bit demoralizing when the other kids have their own agenda's & don't necessarily follow a script.
My DS is a junior in H.S. now. In terms of his social skills you almost can't recognize him. While he's not the most social kid in the school. He has friends, he has joined clubs at school, he just joined an activity by himself recently that has me grinning from ear-to-ear. We went to Thanksgiving at a friends of mine and he conversed politely with the adults and other teens he had never met. I am very proud of how self confident he is these days. The difference is at 6/7th grades he wanted me in his confidence and now he wants me to go away and let him do it HIMSELF. He is in Marching Band and attends a small wilderness camp in the summer. Both have been very good for him emotionally & socially.
