My ds1 (17) did his GCSEs last year, got As, Bs and Cs, distinction in IT etc. 7 in Maths. English, he got a 3. This was not a surprise as he is autistic, he hates and doesn't understand English. Subjects like Maths, Science, Computer based ones etc. are his forte.
(When I was at school if you got a lower grade than a 'C' in GCSE English or Maths you couldn't start A Levels, you had to re-sit the appropriate GCSE and do something other than A Levels e.g. BTEC. 2 years earlier my dh did do A Levels and English re-sit at the same time though!)
Now ds is doing A Levels without his English GCSE pass grade - Engineering, Physics, Computing, but has had to re-sit the English GCSE at the same time. Got another 3 this year! (The school were just wanting to get him to a 4 rather than a 5 to not have him redo it again.)
School didn't explain how getting lower than a 5 affected ds. A secondary school teacher at church explained it to us! If he wanted to do an English related subject at A Level, he'd have to have a grade 5 or above in English to do it, (or with a Maths related subject needed a 5 or above in Maths). Because ds is not doing a subject that needs English to pass it, he can do the A Levels he wants to.
If it is the same at your ds's school he can do his A Levels as long as he isn't wanting to do ones that he needs the English for. If he decided to go for English A Level I doubt they would let him, but if he does Chemistry, Physics and Maths then it looks like he might have the ability to pass them going off his GCSE grades in them.
My ds's English GCSE 3 grade is not affecting his A Levels, but it could affect him if he wants to go to university. If ds wants to go to college or university then they will look at his GCSE (particularly English and Maths) grades as well as his A Level grades. Prospective employers will also look at them, so school would like him to improve his English for that reason, but not for his A Levels. Thankfully for ds I have been informed many universities will take into account the fact he is autistic when looking at his English grade if he doesn't manage to get a level 5 next year, school would be happy with a 4 and universities will weigh everything up in accordance with his autism.
Getting a lower English grade than expected does not mean your ds will automatically fail A Level maths/sciences, so don't write them off too soon. It might be worth talking to school to get their opinion on whether or not he should do A Levels or a different course. It might be possible to do a year of A Levels and change to a different course then if it looks like it wasn't the right thing for him (dependent on what the school offers and what is needed to be taught for each course and when.)
My ds thought he had done better in his English re-sit, but wasn't sure about the second paper, turned out he was right to be unsure about that paper! Your ds might have not put in enough work/effort for his English exams, there might have been 'the wrong' questions for him on these papers - different questions and he might have done better, there could be other reasons he got a 3, but don't discount him doing A Levels in other subjects because of this. Get his opinion on what he wants to do, talk to school, talk to other people who know about these things before changing what he will do next year.
Of course, getting him to do the work is another matter altogether!
Also, pity me - ds1 is sitting his final A Levels this coming school year and ds2 is sitting his GCSEs at the same time, this will be fun!
(Sorry for rambling on, I'm not a very concise person and wanted to put as much info in as I could, kudos to you if you got even half way, never mind all the way to the end.)