As of posting, it has never been outright stated in the game that Mizuki is transgender, although the fact can be inferred from several hints in the story, mainly from how their classmates act around them. Outside of the story, there are several visual codes that suggest or even confirm the fact that Mizuki is trans.
A lot of color coding and symbolism is used to suggest that Mizuki is transgender, perhaps the most obvious example being their Fragment SEKAI, which uses the same color palette as the transgender pride flag. You can read more about that in this post.
Both the 2D and 3D MVs for IDSMILE, Mizuki's first commissioned song, switch betwen a pink (typically feminine) and blue (typically masculine) color palette, but are pink for the vast majority of the song. In the 2DMV, the background changes to blue for the first part of the final chorus, before returining to pink before the end of the song.
In the 3DMV, the lighting changes to blue during the instrumental, then shifts between pink and blue during the bridge, and then remains as pink for the final chorus.
A similar use of lighting can be seen in Mizuki's trained The One Who Gave Me Courage 4*. Mizuki's room is lit in blue, with pink light filtering in through the window, which Mizuki is leaning towards.
This point was submitted by @glitter-and-strangle-hugs
And if you look closely at Mizuki's Nightcord icon, you'll notice that it uses the same blue, white & pink color palette as the trans pride flag.
This point was via a reply from @misty-is-a-dragon
All of the symbolism and color-coding aside, the fact that Mizuki is transgender is actually confirmed by their middle school appearance. When they were in middle school, Mizuki had a typically masculine haircut and wore more masculine clothes. They also wore Kamiyama's male uniform, indicated by the tie used, the side of the blazer that the buttons are on, and the fact that they are wearing trousers.
You might also notice that in their middle school bedroom, they have a cloth covering their mirror, but in high school the cloth is folded over and the mirror is visible. This could be linked to their appearance at both points in time, and Mizuki being more comfortable with their feminine presentation.
A final, song-based example of Mizuki’s trans coding is that they (alongside Mafuyu) covered Villain, a song with a transgender narrator. Mizuki also has a solo Another Vocal of the cover, which you can listen to in the video above.
The song IDSMILE also adds to the case, since the lyrics describe Mizuki’s situation of being afraid to tell people their secret [about their gender identity] and distancing themself from their friends by keeping it hidden.
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