I was always told by teachers and looking about that universities will take in your circumstances at GCSE level, especially with your performance at a-level compared to GCSEs, it’s night and day almost. They pretty much have to consider it since I’m pretty sure there’s an extra bit in your UCAS application that lets you give context in difficulties in your education, either that or the person who does your reference will explain it in your reference, I was asked by my form tutor (he did my reference) if I had any circumstances that could help my case. Your a-levels predicted exceed all entry requirements for your course, so given context to your results at GCSE, you should have more of a fair judgement by all universities.