To add to the above it depends on the nature of the disease. Is this a complex disease that may have multiple variants associated? If so then n=1 really tells you nothing. It will be virtually impossible to associate which of the private/rare variants are disease related, let alone the more common ones that may be involved. If, on the other hand, you are dealing with a rare, mendelian, recessive disorder the number of homozygous and compound heterozygous variants unique to the individual with low minor allele frequencies may be quite small.
Speaking from personal experience however, this may not always be the case. Keep in mind that you will also not sequence all targeted exons due to capture failure and GC content. Some will have zero coverage, others will have low enough coverage (< 5x) in some regions that no variants will be called.
What species are you working in? If these are human cell lines, there are publicly available control data.
Yes. they are human patient
Do you mean I can use hg19 genomic reference?
Just a comment and not terribly constructive, but an n=1 experiment is likely to be quite challenging to use to define "disease related mutations." Despite any databases of normal variants, there will still likely be many variants that are unaccounted for and having a strategy for following up on those will be important.