Outside of his obvious qualities as a CB, I think the most important thing Varane brings to your team is defensive leadership.
You see when he's playing, he's always talking to his teammates, pointing left and right to position them correctly. He makes everyone calm and they know where to focus, and none of your other defensive guys seem to be able to do that so when he's missing it shows.
That's why he is such a good partner to aggressive CBs like Pepe, Ramos, pre-injury Umtiti or Lisandro, because those guys like to go after the opponent and they know with Varane they'll always have cover instead of leaving a hole in the middle of your centre defence. Lisandro, Casemiro, Maguire, or Dalot always seem to play better with Varane around.
I understand why some people think about replacing him because of his injuries (weirldy enough he was never injury prone before joining Man Utd) but if you do that you need to pick a leader, not just a good CB.