Quartz from Vatican church missing graduate? (6)
I believe the answer is:
silica
'quartz' is the definition.
(I've seen this in another clue)
'vatican church missing graduate?' is the wordplay.
'vatican church' becomes 'basilica' (St. Peter's Basilica in the Vatican).
'missing' is a deletion indicator.
'graduate?' becomes 'BA' (someone with a Bachelor of Arts degree).
'basilica' with 'ba' removed is 'SILICA'.
'from' acts as a link.
(Other definitions for silica that I've seen before include "Hard colourless compound from rocks" , "Main constituent of sandstone" , "Glassy substance in quartz and sand" , "Main constituent of sand" , "Common base of rock" .)