Click(2006)

Joonha is a normal, healthy boy of sixteen who has cruised through life without too many problems. Imagine his surprise when a recent trip to the bathroom suddenly reveals that he's not normal at all! With a shriek of "Oh, my God!!!", he finds himself missing, well, something he never thought he could live without. The impact is too much for poor Joonha and he soon passes out. While in his half-conscious state, he overhears the incredible truth: his family is abnormal in the weirdest possible way. After puberty, their chromosomes undergo some kind of mutation, which converts their bodies into the opposite sex! Which means his father is really a woman who has been living as a man since the gene change took place. Now Joonha has to leave behind 16 years of life as a man and live as a woman. What will his childhood friend Jinhoo and the girl he has always liked, Heewon, say when they find out?!

(Source: Netcomics)