On the most basic level, if cells in the lungs mutate, they change function. That means they won't do what they are supposed to do, and will instead do other things…which tells you almost nothing.
The most basic negative kind of change in lung cells is lung cancer, in which some damage to the cell's DNA causes those cells to change form and become tumors. Lung cancer can spread through the body; it can also kill you by itself.
Now, if you're going for a more hypothetical possibility, lung cells might mutate for greater efficiency: they might draw more oxygen from the air, serving the body better.