Quality of gem perhaps initially not evident (4)
I believe the answer is:
tone
'quality' is the definition.
(synonyms)
'gem perhaps initially not evident' is the wordplay.
'gem perhaps' becomes 'stone' (gem stone).
'initially not evident' means to remove the first letter (the initial is removed).
'stone' with its first letter removed is 'TONE'.
'of' acts as a link.
(Other definitions for tone that I've seen before include "Pitch (sound)" , "Shade" , "Musical sound of note" , "Musical sound; quality of hue" , "feel" .)