Unless Im misunderstood Substance Painters role, glass is always done in your DCC application using the Vray Material and has nothing to do with Substance Painter?
As already mentioned You need to set up glass in the Vray material assigned to the geometry that should be glass. No diffuse color, just transparency, and refraction, reflection. Now I don't use Maya, and my version of Vray is in C4D in which I still use the Advance Material but in general its always them combo, Transparency, Reflection, and Refraction. If you do a search on youtube your find tons of glass tutorials for vray on there.
Now as my opening question indicates it could be Im not informed of glass use in Painter but I wouldn't have thought to try to do glass in painter other than for pre viz in painter, but rather make it in Vray applied to the geometry in question.
Dan