The only manga I know of that deals (seriously) with intersexuality is this one: http://www.mangago.zone/read-manga/is_otoko_demo_onna_demo_nai_sei/
It's been quite some time since I read it, so I don't really remember the different stories anymore...
Is it this really offensive manga?
http://www.mangago.zone/read-manga/the_day_of_revolution/
I think this is the manga you are referring to: http://www.mangago.zone/read-manga/click/
a kid who has been living as a boy for sixteen years but after he turned sixteen his sex change, turns out in her family after they experience puberty their sex changes- while she is freaking out her parents are completely relax about it. The manga is basically about her trying to live as a girl while still holding on to the ideals and past relationships while she was a guy but at the same time keeping those lives separate and a secret. its a really fun read. I really liked this manga.
In click, the father was a girl before he turned sixteen. he married his best friend and she was the only one that knew he was once a girl. the manga doesn't really focus on the parents- they tend to be in their own love filled world anyway and leave their daughter to basically take care of herself.
So many years ago I went to an anime convention with friends. One of them bought a manga that I read when I was feeling ill the second day.
Now what I recall the story began with a teenage boy, but it turns out he was born intersex. He was raised as a boy but then when puberty hit the female side of him was dominate and he later became a girl with breasts and long hair naturally. He also had two mom's I think and there was a part when he returns as a girl and is nearly raped by a guy he/she knew before. He wasn't actually going to do it he was playing a horrible prank on him/her, and when it hit him that his friend really was a Female now he stopped.
I have no idea where or what this manga is! HELP ME?!