He is feeling threatened by you because you challenge his ideology which is a very powerful thing in humans...people KILL for ideas, for religion. You can explain that you were born this way just as some XY men develop into women because they are androgen insensitive or some develop with ambiguous genitalia because of genetic mutations. You are no different. You brain is female, the rest of you developed as male. This phenomena is also observed in nature where species have both a female and male apparatus...think of the bonobos where same sex animals sexually interact with each other, etc. God created a world full of diversity, one just needs to take a look at the world of animals. Black and white, man and woman without anything in between is an idea created by man which is in stark contrast to reality.
Your friend is ignorant and the more he becomes aware of reality, of what lies in it, the less likely he is to persevere in his ideas. He has been wrongly conditioned and misinformed.
Accepting and loving someone, even in the face of their disapproval, threats, can be powerfully transformative. Don't lash back. 😉