Against popular belief, Cable and X-Man are not counterparts of each other, as they have different mothers. While it’s true that Cable’s mother, Madelyne Prior, was a clone of Jean Grey and, as such, has the same DNA, the circumstances of Cable’s and Nate’s birth/creation are entirely different. Sure, the two Nates resemble each other a lot and for the most part have similar powers, but that’s not uncommon for siblings, which - genetically speaking - they are.
During his time on Earth 998, ruled by the evil Queen Jean, X-Man not only met one of his counterparts, but he also learned that there had been many Nate Greys in the multiverse. Obviously, he was not as unique as he thought. Apparently, the one thing all Nates had in common was that they had been born/created on a different Earth than the one they later ended up living on. Each Nate Grey being the ultimate telekinetic weapon, Queen Jean hunted them down and lured them to her reality, to make good use of them. She had her scientists come up with a special genetic brand that would prevent the Nates from burning out their powers. However, most of the Nate Greys were dysfunctional and, when the Queen was unsatisfied with their performance, she killed them and moved on to the next. It is unknown how many Nate Greys fell prey to Queen Jean before she was stopped.
In an alternate Age of Apocalypse depicted in What If? X-Men Age of Apocalypse, both Xavier and Magneto were killed when Legion travelled back in time. Nate wasn’t created in a lab but was the natural son of Scott Summers and Jean Grey and grew up in a peaceful haven that mutants created for themselves in the Savage Land. Apocalypse rose to power and attacked this mutant community, declaring them traitors. Nate was the sole survivor and joined a band of heroes led by Captain America to end Apocalypse’s rule. This version of Nate was vengeful and ruthless and when the time came, he deemed that simply keeping Apocalypse wasn’t enough. Betraying his teammates, Nate acquired the power to travel back in time and stop Legion’s initial attack himself. When Captain America attempted to stop him, disaster struck and in addition to Xavier, Magneto, and Legion, thousands of innocent civilians died, resulting in countless new alternate timelines that Apocalypse would also rule.