Aligned with Humans:
Carnage: Shriek
Super-
Soldiers: Guvnor
A.R.M.O.R.: Portal
Missing: Snow Leopard (Ilya and Ioakim Koblev), Nuklo, Esme and Eduardo Lobo, Lady Lotus, Sphinx, Lacuna,
Micromax, Melter, Tangerine*, Judas Traveller, Ricochet, Headhunter, Chance, Lighttrakker, Krista Marwan, Nuwa,
Asp**, Tithe, Mister X, Johnny Dee, Gregor Smerdyakov, Adelbert Greywing, Benazir Kaur, Dark Angel***
*Tangerine is confirmed as a mutant in Earth-811, and so presumably Earth-616 as well
**I've seen contradictory information on if Asp is a mutant or if the source of her powers is unknown
***Shevaun registered on Cerebro as a new kind or strain of mutant after gaining her powers, but her actual mutant status is unclear
Mutant Force: Slither, Burner, Shocker, Lifter
Deceased: Jenny and Malcolm Monroe, Snow Leopard (Issa Koblev)