Ya is the twenty-fourth of the thirty consonants and writes a palatal approximant, the y of English yes. It is also one of the four subscripts, where it is called the ya btags and is written beneath a root letter.
Subjoined ya does not add a glide to the letter above it. It changes that letter. In modern Lhasa speech the labials carrying a ya subscript are pronounced as palatals, so a stack of pa with a subjoined ya comes out with an initial closer to ch, and the sequence a learner would expect to hear is simply not produced.
This is the clearest case in the script of the written stack and the spoken syllable parting company, and it is a rule rather than an exception: it applies across the labials consistently, and a reader who knows it can predict the pronunciation of every stack of that shape.
Ya as a plain root letter carries high tone in modern Lhasa speech. As a subscript it takes no tone of its own, since tone belongs to the syllable rather than to any one of its written parts, which is another reason the stack has to be read whole.
As a root letter ya takes superscripts. It is not a prefix, not a suffix and not a superscript, so of the four subscripts it has the narrowest range: ra and la belong to every stacking system there is, while ya works in one position beyond the root and no more.