Board Thread:Theories and Speculation/@comment-26107879-20160222005417/@comment-734582-20160223081046

If you look at how the abilities can be defined, then it seems logical to me to conclude that the Rinnegan itself is a mutation.

The Sharingan deals with the barrier between reality and fantasy (Itachi's two favorite words). Base sharingan observes it, Mangekyou weakens this barrier, Rinne Sharingan completely ignores this barrier. Rinne Sharingan after all completely overwrites reality to transport to a new dimension.

Rinnegan's power doesn't really fit this, other than dealing with the barrier between life and death (and those two thing specifically). So Rinnegan is a specialized form of the Sharingan. It seems to be because it requires the Vitality part from the Senju line, specializing it into that eye. Sasuke's eye still has his Mangekyou separately (and has six, not nine tomoe) suggesting that it's somewhere inbetween a Rinnegan, Mangekyou and Rinne Sharingan.

As to Tenseigan, it seems to combine Sage elements with the Byakugan's ability to emit chakra from all tenketsu, forming the cloak. Truthseeking balls are Sage Mode + Six Paths chakra, which is fullfilled with the Tenseigan + the Six Paths chakra it gives. Note that unlike the Rinnegan's Death motif, Tenseigan has a Life motif (Controlling people vs ripping their souls out is a big one).