I got curious now, is there any work of art that has something similar to the X-Gene but that makes more sense on a biological level?
To get scientific for a moment since this is a cool question.
There is no biological way for humans to shoot lasers from their eyes or control the weather, most of the mutations we see are impossible or would have drastic physical downsides.
Just accept the handwavey explanation and exist in bliss, the alternative is literal insanity as even healing factors like the one demonstrated by say Wolverine are scientifically improbable at best due to how healing actually works in human beings.
Realistic human mutations do exist, we have several of them in our world such as albinism, Gigantism, Primordial Dwarfism, and if you want something actually hero-esque Myostatin-related muscle hypertrophy which grants increased muscle mass, strength, and reduced fat at the cost of a much higher metabolism which typically means they need to eat more to sustain themselves.
In general though any mutation unless it has no effect will likely have downsides or changes that may not be desirable, people with gigantism often have shorter lifespans primarily from heart issues and may have facial deformities, People with Primordial Dwarfism often die of strokes and aneurysm, and in general have delicate bodies and fragile almost elfin features.
Possible downsides for a person with a healing factor for instance might be at far greater risk of cancer, and an early death by aging if it works through cell division if the mutation does not protect the Telomeres.
This is not just a mutant thing either, human peak in comics is also impossible, unless you believe the authors were under the belief that batman has lifting equipment under his skin and just never brought it up.
