Transgender

Among humans at least, a transgender person was someone whose gender did not align with that which they were assigned at birth. The term was used as an adjective, often shortened to simply "trans".

Mickey Smith had a trans friend called Sally Salter, who was part of his Bad Wolf band. (PROSE: Rose) Jack Harkness once had a transgender co-worker, Vanessa, who previously went by the name Vincent. (TV: Greeks Bearing Gifts)

Eleanor Blake, an accomplished mathematician who met the Seventh Doctor and entered a brief romantic relationship with Chris Cwej, was a trans woman who lived through the 1940s. She went on to travel with Alpha Wheeler throughout space. (AUDIO: The Jabari Countdown)

Because gender was commonly assigned at birth, (TV: Day of the Moon, Father's Day) trans people like Sally Salter (PROSE: Rose) and Eleanor Blake came to realise that they had always been a different gender to that which they had been told. Despite others' non-acceptance, Eleanor was fully aware that she had "always been Eleanor". (AUDIO: The Jabari Countdown) In the mid-2000s, Sally had to cut ties with her family in order to begin living life as herself. She found affirmation with her friends and bandmates, together known as Bad Wolf, and a safe space in which to sleep at Mickey's one-bedroom flat. (PROSE: Rose) "Earth takes its time on too many things, and [trans rights] is one of them. Not in this century, I'm afraid. Though the next one is.. a little better."

- Seventh Doctor

Though, according to the Seventh Doctor, circumstances would improve "a little" by the 21st century for trans people, Eleanor had to hide her identity in order to survive in the 1940s. In fact, Eleanor faced violence and discrimination on account of her gender. She was surprised to find Chris Cwej so accepting, noting how he "didn't even blink", but held little hope for changes to come within her lifetime.

Coming as he did from the 30th century, Chris did not understand the fuss about assigned genders. As he explained to Eleanor, on first finding out she was a trans woman, "it seems a bit stupid to care about little stuff like that", considering the breadth of the universe, and all the dangers and variety to be found therein. (AUDIO: The Jabari Countdown)

Cassandra O'Brien.Δ17 also once claimed to Rose Tyler that she had once been "a little boy" on Earth, although she was notoriously prone to misusing words and knowledge from her early Earthly life. (TV: The End of the World)

Behind the scenes
In 2015, Bethany Black became the first openly trans actor to be cast in an episode of Doctor Who, series 9's Sleep No More. She played the role of 474.