I think you are assuming that a particular "gene" makes us transgender, but that has never been shown (much less proven), although genes can and do make some intersex.
Rather, there is some medical consideration that cross-hormone imbalance or mis-hormone flooding (including the lack of sufficient testosterone for MtFs and too much T for FtMs) sometimes occur during the third trimester of prenatal development (maybe things also go awry during the other developmental periods ...who knows).
I spent quite a lot of time last year looking into the whole question of how "brain sex" and gender identity develop, and the conclusion I reached is that a lot of transgenderism has got to be an unintended consequence of giving hormonal medication to pregnant women. This certainly seems to be the case for a drug called diethylstilbestrol (DES) anyway. I'm sure that many of the people here who were born prior to 1971 would, if they're in a position to ask, find that their mothers were either prescribed DES during the pregnancy or took "pregnancy vitamins" (which often had DES added to them). Just 3mg of DES a day is enough to completely shut down testosterone production in adult men, and doctors were routinely giving pregnant women way more than that.
The default developmental pathway is the female one and it's testosterone that drives male development. Interrupt testosterone production during the time the brain is undergoing it's sexually dimorphic development, and you'll end up with a person who has a male body but a brain that is either intersexed or completely female, depending on how long the hormone interruption lasts. It's mainly the brain that's at risk, because development of the reproductive organs takes place in a relatively short period of time during the early stages of the pregnancy, whereas there is sexually dimorphic brain development taking place throughout the second and third trimester.
Here's some public discussions I found regarding DES and transsexuality:
I don't think the problem is limited to DES either, in fact I'm pretty sure any hormonal medicine given to a pregnant woman in therapeutic doses carries a risk of disrupting the sexual development of her unborn child.
There's a drug called hydroxyprogesterone caproate which is actually one of the hormones recommended in this forum for transitioning mtf transsexuals. If I remember correctly, the dose used as part of the hormone therapy for transitioning is 250mg every 2 weeks. Believe it or not, this exact same drug is also the treatment of choice for pregnant women who are thought to be at risk of premature birth, at a dose of between 250 and 500 mg per week! It's a longlived drug with a plasma half-life of about 10 days, giving it ample time to cross the placenta and interfere with testosterone production in an unborn male child. I've not tried hydroxyprogesterone caproate myself, but I'm fairly sure that if you gave an adult man 250 or 500 mg of it a week their testosterone production would be severely impacted. It's be interesting to know how many people here who were born after DES was discontinued in 1971, had mothers who were thought to be at risk of miscarriage or premature birth and given this treatment.