Navigator

Navigators (Homo navigo) are Warp tainted freaks 3-eyed psykers that are responsible for keeping your sorry-ass ship from getting lost in the warp and stop the evil little critters from attacking. Well-known as arrogant cock-suckers who have families richer than Bill Gates and twice as corrupt as any 3rd world country's government.

Also, one of those parts of the Imperium of Man blatantly stolen from Dune.

In the beginning

Navigators were created through genetic engineering during the Dark Age of Technology when humanity realized that a special kind of psyker could find his way through the Warp better than any piece of technology. Navigators, with the third eye in the middle of their forehead, can look directly upon the Warp and perceive its currents, allowing longer and safer journeys through the very heart of the Warp. It's somewhat analogous to a sailing ship cutting right across the sea rather than hugging the coastline (although when you read the fluff on Tau ships it gets more confusing). Since the Astronomican didn't exist at the time, we can only assume the Warp was a much less fucked up place, like a clear sky where you could see the sun and stars and navigate by them. After the Age of Strife, the sky became permanently overcast, and the only beacon of light in all that mess is that fancy lighthouse based on Terra.

The genes that make a Navigator a Navigator are recessive. If a Navigator mates with a regular human, all their kids will be normal. They thus had to form an endogamous caste.

The Imperium

When the Emperor set about uniting Terra and preparing to go to the stars, he was presented with a bit of a problem. Part of the Imperial Truth he was sprouting maintained that humans were destined to rule the stars, and he was still centuries away from getting the Webway project up and running. Simply put, the Emperor needed the Navigators, even if he was fully aware of how "age before beauty" was a horrible lie to the Navigators. Deciding "fuck it, we need space travel", the Big E went to the Paternova (the leader of the Navis Nobilite) and made an agreement: "Keep to yourselves in your part of Terra and your mutant Elders out of sight, and we'll pay you to fly our starships and protect you from some of the more zealous anti-mutant groups". The Paternova agreed, and thus humans can fly through the Warp, using the Astronomican to navigate.

Who knows what the Emperor would have done with them had he completed his secret Webway project. It was pretty clear that he hated any psyker who wasn't absolutely necessary. One time he even told his Space Marines to get rid of their Librarians. That was only to put a leash on Magnus before he or his ilk would befriend some warplings during their magic-research. Too bad it backfired spectacularly.

In the 41st millennium, the Navigators are part of the High Lords of Terra, represented by the Paternoval Envoy. A lot of people in the Administratum, the Ecclesiarchy, and the Inquisition aren't too thrilled with this, but they can't really do anything to the Navigators without irreparably crippling the Imperium. The more extreme ones still try to do something about it. Imperial dogma is frequently contradictory. Pointing this out is heresy.

Being psykers, Navigators are vulnerable to madness and daemonic possession. The Inquisition (about the only people who can really touch them) keeps a close eye on the Navigator Families and has destroyed more than a few who became corrupted. The Navigators try to resolve such problems internally, knowing how overboard the Inquisition likes to go.