Mostly due no doubt to their already weak grasp of science, Marvel's writers and editors have never gone into much detail over exactly how the 'X-gene' that causes mutantcy is inherited. So I've decided to come up with an explanation myself. Please note that I am not a geneticist or a biologist, just a geek thoroughly obsessed with both Marvel Comics and MAD SCIENCE. Also, my BFF is a biologist and we've discussed this issue, so nyah. She thinks my ideas are sound. The whole reason I got to thinking about this subject is because as she was explaining to me the complicated genetics of horse coloring, I blurted out, "Oh, I bet this is how mutant genes work in the MU!" See, I'm convinced that it's not just the fabled X-gene, there must be at least three genes at work producing mutants, and possibly more.
First of all, let us define the word 'mutant'. In Real Life (RL) a mutant is an organism that has DNA different from that of its parents -- ie, its genes have mutated. Technically, we're ALL mutants. Each and every one of us has some minor genetic differences from our parents, caused when all those base-pairs and chromosomes were being stuck together during our conceptions. So that's a RL mutant.
Clearly, Marvel Comics mutants are not one and the same as RL mutants. For one thing, they're identified as a seperate species (really subspecies, but WTF) homo sapiens superior. For another, they're all said to share an 'X-gene' that makes them mutants. From now on in this essay when I say 'mutant' I refer to a Marvel Comics 616 mutant, not a RL mutant.
Now, I realize that obviously Stan and Jack knew squat about heredity when they first came up with the X-Men, so don't just tell me "oh, it's fictional, don't worry about it." Not only do I know that, I don't care, and that attitude is no fun anyway. If you're gonna be like that, piss off and go write, I dunno, pornographic Pokemon fanfic (hot Skitty on Wailord action!) or something.
Thirdly, you need to know that those nifty little Mendelian genetics diagrams they showed you in fourth grade are completely bunk. Yes, your elementary school science teachers lied to you. Genetics is much more complex than "dominant genes and recessive genes". You can have dominant and recessive traits, incomplete dominance, incomplete penetrance, polygenic traits, etc.
Now, to determine how mutantcy is inherited in Marvel Comics, we have to find a method that works with what is known from canon, which is:
Two humans can produce mutant children: Too many examples to list, but a notable example is the Guthrie family, which has produced both mutant and human children.
Two mutants can produce a human child: Probably the best example is Sabretooth and Mystique's son, Graydon Creed.
A human and a mutant can produce mutant children: Plenty of examples, including Charles Xavier and Gabrielle Haller's son Legion, Magneto and Magda's children Wanda and Pietro, and Banshee and his wife Maeve's daughter Siryn.
Two mutates can produce a mutant child: By mutates, I'm referring to people who gained superhuman powers accidentally, as opposed to naturally. A good example is Reed and Susan Richards of the Fantastic Four, and their very powerful mutant son Franklin.
I can't at present recall a human and a mutant producing a human child, or a mutate/human or mutate/mutant pairing producing either a human or a mutant child, but there may well be examples of both I'm forgetting. There's also a mutant/Inhuman pairing (Quicksilver and Crystal) that produced a human child (Luna), but Inhuman genetics are another thorny issue that's probably too complicated to go into here. But as these examples clearly show, not only can humans, mutants, and mutates (and Inhumans) interbreed, but they can produce viable offspring who may be humans or mutants. Sadly, there aren't many third generation examples to study, and the few there are tend to be too complicated to provide a clear picture of inheritance, such as Speed and Wiccan of the Young Avengers, who's father may be a robot, Mephisto, some combination of the two, or they may have just been generated out of thin air by their mutant mother.
But what does this have to do with horses? Well, horses have two base genes that control coat color, e for the recessive red, and E for the dominant black. In addition, there's also a whole pack of modifying genes that can change the expression of e and E. I think something similar is going on with mutancy, in that there's not one, but several genes controlling whether someone is a mutant or not and how it's inherited.
My theory is that there are AT LEAST two seperate genes that determine if someone is a mutant or not. I think there is one gene that codes for the superpowers themselves -- we'll call it the S-gene for the hell of it. Then I think there's another gene that activates the S-gene, so to speak, and this I believe is the famous X-gene. Many, if not most, humans probably carry an S-gene, but without an X-gene (or radiation or whatever) to activate it, their powers remain dormant their entire lives.
I believe that these genes are probably NOT sex-linked, ie. carried on the X and Y chromosomes. This would mean all humans and mutants would have two alleles of each, resulting in 9 possible combinations:
XX SS *
XX Ss *
Xx SS *
Xx Ss *
The types marked with a * are going to be mutants, as they carry both an S-gene and an X-gene. Furthermore, when it comes to offspring this would result in:
-- The XX SS genotype would be guaranteed to produce mutant offspring regardless of whether it mated with a human or a mutant.
-- XX Ss mated to XX SS or Xx SS would always produce mutant offspring
-- But the other possible pairings, such as a Xx Ss with a xx sS, for example, could produce mutant and/or human offspring
To take this example farther, let's assume that Magneto is Xx Ss (he is unlikely to be XX SS because neither of his parents manifested mutant powers, so he could not have inherited those alleles from them). He and Magda, a baseline human, produced at least two mutant offspring. If Magda were, say, xx SS, then Wanda and Pietro could've inherited an X-gene from their father and an S-gene from their mother, making them both mutants. Their genotype could only be Xx SS. Magneto and Magda's other daughter, Anya, assuming she was human, could've been xx Ss, a carrier for the S-gene but not for the X-gene, rendering her a human.
Of course I have no idea what Magneto or Magda's genotypes might be, but I'm throwing that out there as an example to give you an idea how this might work.
Now, to take it a step further, let's see how an XX SS mutant might arise. Let's assume that Scott Summers is xX SS and that Jean Grey (and by extension, her clone Madelyne Pryor) is Xx Ss. They could produce Nathan Summers, aka Cable/Stryfe/X-Man, who inherit two Xs and two Ss, making them XX SS. Therefore, any offspring any of these Nates produce, no matter the mother, could be nothing other than a mutant. Rachel Grey, from the same parents, inherits Scott's x and Jean's X and Scott's S and Jean's s, making her genotypically xX Ss. She's a mutant, but could produce either mutant or human children unless she mates with a XX SS mutant like her brother(s), in which case all her children would be mutants. Get it?
Aside from the X-gene and the S-gene, I believe there's got to be at least one and possibly at least two more genes influencing mutancy, and maybe even a whole slew of them. This would make mutantcy a polygenic trait like schizophrenia or skin color or eye color. I think there's at least one gene that encodes for what sort of powers a person will manifest (ie. an 'energy-manipulator' gene, a 'telepathy' gene, etc.) as well as another gene that creates the so-called secondary mutations that manifest later in life.