Organ stops essentially modulate (5)
I believe the answer is:
ovary
'organ' is the definition.
(ovary is a kind of organ)
'stops essentially modulate' is the wordplay.
'essentially' means to look at the middle letters.
'modulate' becomes 'vary' (I've seen this before).
The centre of 'stops' is 'o'.
'o'+'vary'='OVARY'
(Other definitions for ovary that I've seen before include "Female organ in which eggs are produced" , "Egg-producing organ" , "Female reproductive organ" , "egg supplier" , "Egg producing organ" .)