A portal has small stones (6)
I believe the answer is:
agates
'stones' is the definition.
(I've seen this before)
'a portal has small' is the wordplay.
'portal' becomes 'gate' (I've seen this before).
'has' is a charade indicator (letters next to each other).
'small' becomes 's' (abbreviation - e.g. clothes size).
'a'+'gate'+'s'='AGATES'
(Other definitions for agates that I've seen before include "[RING]-fillers required" , "Banded semiprecious stones" , "Ornamental stones" , "Pieces of impure quartz used as gemstones" , "Chalcedonies" .)