Khalef has XY chromosomes and testicles. He's got all the genetics and hormones of a man, and went through male puberty.

He's missing a penis. But penises don't actually do very much biologically speaking. You wouldn't tell a man that he's no longer a man just because he lost his penis in a chainsaw accident. What matters is what's inside you. And during puberty what's inside you is a whole lot of hormones.