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Nettles said:
Brain doesn't matter.Popping pills won't change the thing that matters most....
Men are born with a Y chromosome, women with another X chromosome.This is what determines gender.
XX = female, XY = male.

That is what determines someone's biological sex not their gender/gender identity which is one of the personal issues many trans people face. A trans person feels detached from their biolgical sex and their gender, so yes the brain does matter and plays an important role in a trans person's psyche and gender identification.