I'm currently reading Toru: Wayfarer Returns by Stephanie Sorensen. The protagonist of the book, Toru, grew up in Japan, spent 2 years in the US, and has just returned home. It's set during Japan's period of isolation from the rest of the world, so returning comes with a death sentence.
Anyway, in one scene the protagonist shrugged, even though he knew the gesture wouldn't mean anything to the Japanese people around him. It was a gesture that had become ingrained in him during his time in the US, so ingrained that he did it without thinking.
Gestures are integral to communication. So much so, that we often don't realize we're doing them. We pick them up from those around us. I remember bowing when talking on the phone in Japanese. It was so normal to see people doing it that I unconsciously started copying others and did it myself.
In another scene in the book, someone nods 'no'. I like that the author is aware that gestures change from place to place (both within and without countries).
Gestures are often left out of books because while they're so common, they're not things we consciously think about. And yet, it adds a sense of reality, of connection, and of added communication when characters in a book make gestures.