How did discovering his real life gender change everything between you? What if he identifies as a girl and that was why he was 'pretending' to be one? It could be that he lied to you because he did not want to be treated with a male gender bias. Had he been up front with you from the start about his gender would you still have allowed him to keep identifying as a girl?
I don't view these things as deceit unless it's a guy pretending to be a girl just to get loot from people then that's quite an issue. I don't exactly know this person or know the full story between you two but there could be more to him than you were willing to understand.