Case Control Study

I am working on a case control study for disease. 50 case and 50 controls subjects. I am looking at about 10 gene mutations to see if any of them are significantly higher in the case subjects. Independently or in combination with one or more of the other 9 mutations. Each person has a possible genotype of AA, AB, or BB for each mutation. I don't know anything about which allele is dominant (A 0r B). I am just testing to see which genotype is present in each subject. I am assuming that a Fisher's exact test would be acceptable when comparing mutation 1 frequencies between cases and controls. For example, the AA genotype of mutation 1 shows up in 20 of 5o cases and in 15 of 50 controls. But what if I think the B allele is important whether it comes in the form of AB or BB genotype? Can I still do a Fisher's test comparing (AB+BB, or 50-AA) in cases with (AB+BB) controls?
What about a combination of mutations? Is a Fisher's test acceptable for comparing the number of case subjects positive for BB in mutations 1,2, and 3 with the same mutations in controls? Mutations 4-10 would be ignored here.
Are there other statistical calculations that would be of interest when looking at combinations of gene mutations?
My statistics experience is pretty limited so any direction on where to go with this would be great.