It would be heterozygous in a very small number of individuals and would get expressed (pop up) in the population in every generation
I don't think that would work in your idea of super gene. Since black is dominate, all the mice be black until the black gene was mutated to junk dna. So in order for there to be light mice to survive on the desert sand, they would have already lost the black gene.
Then there would not have been a black gene for the lava mice to use.