Following what happens in Logan (2017), almost all the mutants are either killed or captured by the government.
In one scene when Logan is putting Charles Xavier to bed,
Xavier: They do not want me, they want you. Oh, yes. That's how fucking stupid they are.They're waiting for you at the Statue Of Liberty.
Logan: Statue of Liberty was a long time ago, Charles! There are no new mutants. You understand? There was not anyone born in the 25 years. Not anywhere.
Xavier: I've always thought... we were part of God's plan.
Logan: Maybe... May be we're God's mistake.
Logan (2017)
indicating that apart from the captive children at the Transigen research, no other mutants exist (expect Logan, Charles and Caliban of course).
And as Jean Grey puts it in X-Men (2000):
Ladies and gentlemen, we are now seeing the beginnings of another stage of human evolution. These mutations manifest at puberty and are often triggered by periods of heightened emotional stress
X-Men (2000)
indicating that some humans are born with the mutant gene.
So what caused the mutant gene to disappear completely from occurring naturally in humans?