Some mutations are a mixed bag- a quirk of a gene might mean increased resistance to certain diseases or environmental conditions while increasing susceptibility to others.
For example, Malaria was a true plague of the ancient world...but persons with the sickle cell trait weren't killed by it. Unfortunately, sickle cell anemia (one possible result of having 2 parents with sickle cell trait) is a killer in its own right.
So it would be "realistic" to include mutations that have both benefits and drawbacks.
For example, Polydactyl (multi-fingered) might give bonuses to Perform (Instrument), but give a negative mod to other Charisma based rolls.