I found this great fic on fanfiction.net where Charlie was born a girl.

‘Baseball Don and Baby-Doll’ By KamalaC
What if 'Charlie' was a diminutive of 'Charlotte', not 'Charles? Don has to deal with his younger sister being a genius - and trying to keep the other male agents from hitting on her while she consults for him, without much luck.
http://www.fanfiction.net/s/5652690/1/Baseball_Don_and_BabyDoll

There's another version Eppescest on the author profile