Dear Igor,
This is my first reply to a post here but my personal experience may help. My father-in-law was a commercial pilot who continued to fly until he had to be stopped following an incident that could have resulted in many fatalities. I did not know him then so cannot say if he was symptomatic at the time of the incident. I suspect, however, that his errors of judgement were an early indication of the onset of HD symptoms.
While I don't feel your pilot should be prevented from flying just because he has the HD gene, I do believe he should be very carefully evaluated for safety to continue flying. It is highly likely that his thinking processes will be impaired at the very early stages of onset of the disease and this needs to be assessed very carefully by someone who understands the disease process in HD.
I feel very strongly that people who have tested positive for the gene should not face discrimination, but I also feel very strongly that the lives of others should not be jeopardised.
I know someone in a management position with a large commercial airline here in England and could ask his advice if you would like me to.
With best wishes,
Sue