I don't think there's probably any direct translation, at least that I've ever come across, in which case "You're not here and I am lonely" becomes sort of a mix of "loneliness" and "missing".
"Anata ga inakute (or inai to) sabishii desu."
Or perhaps "Anata wo koishii" in a romantic sense (lit. you are dear to me)
While you could also say something like it just hit me that you were gone and I became a little lonely.
Waitekite sukoshi sabishii kimochini narimashita....