Mendokusagari Danshi ga Asa Okitara Onnanoko ni Natteita Hanashi

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This is a list of works focusing on stories where characters experience gender or biological sex shifts as a significant part of the plot.

There is either a supernatural or major psychological component to all of these entries. Pure crossdressing works are excluded.

Comments for each entry are currently a work in progress.

Notable works that are not on MAL (yet; currently in pending approval queue):
Saki to Mika; by Sakujirou
Transgenic Laboratory; by Okano Ahiru/Amoi Jun

manga with things like cross dressing, important characters who are trans/nonbinary and gender bending.

(i havent read every one of these so if i made a mistake with what i wrote about them please tell me)

Gender-bending (sex changing through supernatural methods) characters who turn out to like their new gender and come out as transgender. Some are debatable.

Even more non-binary/x-gender characters in manga.

Part 1: https://myanimelist.net/stacks/28860
Part 2: https://myanimelist.net/stacks/37987

Rules:
-Not a shapeshifter
-Turned into the opposite gender
-Still in the same body (not body swapped)
-Have a physical change
-Not reincarnated as the opposite gender
-Through some phenomenon, power, disease, whatsoever not by surgery (not trans)
-Don't have any power whatsoever by "themselves" to revert their gender (not gender bender)