I wouldn't rule out mild SN: I regularly see students who are diagnosed with dyslexia when they start postgraduate studies. How they have managed to keep afloat until then is a mystery as their problems seem pretty obvious to me- and pretty big.
Anyway, it would help to have a few more details: you don't mention any other problems than school refusal/refusing to do school work? Is it all focused on school? Is he violent? Does he refuse to engage in all family activities? Do you think he is into drugs? Also, what kind of support is he getting at school? Is he seeing a school counsellor?
Have you talked to him when he is calm? How does he feel about the whole situation? Does he know why he gets so upset?
I have two children: one has anxiety problems related to disability and goes through regular phases of panic attacks and school refusal- she is seeing the school counsellor and CAHMS (Child & Adolescent Mental Health Service) where she is having therapy and will be taught methods for controlling her anxiety. In the past, her panic attacks took the form of violent tantrums (kicking and biting), now at 14 she is thankfully not violent, but still gets hysterical.
Ds has low self esteem issues and is incredibly negative towards school work, which he struggles with. He does have a disability, though not a learning disability, and obviously feels hard done by. He is convinced that there is no point in trying, and sees any extra intervention as a massive imposition. We are trying to liaise with the school over extra support for him, and have just managed to get him a first CAHMS appointment.
It is not a very easy situation to be in, but I am confident that these problems will get sorted or at least dealt with to a point where dcs can live with them. There is help to be had. But you do need to keep asking. And you absolutely need to keep any negative grandparents out of the equation!