My tree includes a living relative who was born male and is now legally and otherwise female. My only record of the change, at this point, is an alternate name (I use GRAMPS). I have recorded her birth name and gender as male--it's perhaps worth noting that this person did father children, so her original "maleness" needs to be preserved. However, her eventual death record will refer to her as female and I feel that documenting this as a name change only is insufficient.
Your chosen software (GRAMPS) gives you the flexibility to deal with this as suggested by ColeValleyGirl. When you create an event, the types in the list offered are suggestions only. So overwrite with your choice (in this case, Gender Reassignment) and create the event as usual.
The new type will be retained for future use in that tree. So you can enter dates and places (and sources) for each of "began hormone therapy", "adopted new name", "surgery" or whatever you believe is relevant. They will be distinct events but have in common the new category.
When you enter the "alternative name" in the person panel, you could create a name note that explicitly refers to the appropriate event.
Note also that the types of name (birth, aka etc) are also suggestions. You may wish to add your own category (by overtyping what is presented) to make obvious to future readers that this is not some form of typographical error. Perhaps you could use "New Identity".
Unfortunately the "gender" categories are one of the few lists that are fixed in GRAMPS. You will need to decide if it is acceptable to your family to list the person as "unknown".
In the software I use (Family Historian), I have created a custom "Gender Reassignment" event -- can you create a similar event in your software?
I've also recorded the person's gender of choice, but recorded a birth event based on their original birth registration (with an associated note to explain why the individual's gender doesn't match the gender on the birth certificate) and an alternate name (with the same note). The software I use supports recording same-sex couples, so children in his previous incarnation (if there ware any) would be recorded without problems.
All this is not published on the web, just held in my private records.
I have the same situation in my Gramps tree. As far as I know, there is no standard way of doing it. I chose to leave the sex unspecified, to record a custom event for the sex/gender change and to clarify the situation with additional notes. Not very satisfying for me.
The terms gender and sex are sometimes confused.
• Sex is either male or female and so reflects a biological difference. This includes physical, hormonal, and genetic characteristics.
• Gender is either masculine or feminine and so reflects a social or cultural characteristic.
Gender reassignment therefore includes many more aspects than surgery alone, although it is still treated as a synonym of Sex Reassignment Surgery (SRS).
Although cases of indeterminate sex at birth do occur, I would record the birth sex separately from the adopted gender. Unfortunately, I don't know of any commercial software product that makes this differentiation.
Sex and gender are actually not totally binary so the apps that don't allow anything else are outdated.
There is also a privacy concern and respect issue in how you record information about a transitioned individual because the information can be harmful to them. It may not be widely known by an employer, family, government, etc... So you would essentially be outing them by placing all the details in your records.
You should respect what the individual wants.