Rate missing magistrate - upset by mark of disgrace (6)
I believe the answer is:
stigma
'mark of disgrace' is the definition.
(I've seen this in another clue)
'rate missing magistrate upset' is the wordplay.
'missing' is a deletion indicator.
'upset' indicates anagramming the letters.
'magistrate' with 'rate' taken away is 'magist'.
'magist' is an anagram of 'STIGMA'.
'by' is the link.
(Other definitions for stigma that I've seen before include "part of plant" , "Symbol of disgrace or infamy" , "Disgraceful sign" , "Mark of infamy or disgrace" , "Mark of shame or social disgrace" .)