Subtlety is missing from pest (6)
I believe the answer is:
nuance
'subtlety' is the definition.
(synonyms)
'is missing from pest' is the wordplay.
'missing from' suggests deleting specific letters.
'pest' becomes 'nuisance' (I've seen this before).
'nuisance' with 'is' taken out is 'NUANCE'.
(Other definitions for nuance that I've seen before include "Subtle variation, in meaning say" , "Subtle shade of difference" , "Subtle distinction or variation" , "Delicate shade of difference" , "Delicate shade of meaning" .)