Nagisa is the son of Hiromi Shiota and her (presumably ex) husband. His mother had hoped for a daughter so she could experience all the things she had missed as a child through her, but got a son instead. As a result, she dictated his life from forcing him to keep his hair long, to being forced to crossdress and verbally abused him whenever he spoke against her. Her personality also caused her husband to leave her and Nagisa.
He was revealed to formally have been in Class D during his first two years of middle school before falling into Class E due to poor grades.
Original Image: Link
Credits to Iraq Lobster for the Image
I just Rendered it