Jewel of Catholicism lies in the Kingdom of God (6)
I believe the answer is:
zircon
'jewel' is the definition.
(I've seen this before)
I cannot understand how the rest of the clue works.
(Other definitions for zircon that I've seen before include "Mineral used as a gemstone in its transparent form" , "Bluish gem cut form translucent mineral" , "jargoon?" , "Mineral of gem quality" , "Crystal-like semi-precious stone" .)