Theoretically, the more dominant genes of the Disciple would overpower the Sufferer’s, causing Karkat to be a normal, albeit probably VERY lowblooded.

However, on this page, http://www.mspaintadventures.com/?s=6&p=004296 

it says: “Especially strong matesprit and kismesis pairings yield more dominant genetic material. The more powerful the complement or potent the rivalry, the more dominant the genes.” Because of the quadrant-defying love/red feelings the Sufferer and Disciple shared, it essentially shocked the system, and their offspring was born with Mutant blood. Following this logic, the Sufferer would have also been the result of a very powerful troll romance.

Ectobiology is the reason for Karkat’s mutant blood. I don’t know how many times I need to say this, but NONE OF THE ANCESTORS ACTUALLY PAILED IN ORDER TO CREATE ANY OF THE TROLL KIDS. It didn’t matter how much love that The Signless and Disciple had, because both ancestors and descendants were made in a god damn lab.

-Pollux