Damage caused by mutation originally, mate — one's on top of it (6)
I believe the answer is:
impair
'damage' is the definition.
(impairing is a kind of damaging)
'mutation originally mate one's on top of it' is the wordplay.
'originally' suggests taking the first letters.
'mate one' becomes 'pair' (I can't justify this - if you can you should believe this answer much more).
'on' says to put letters next to each other.
'top of' indicates taking the first letters.
The initial letter of 'mutation' is 'm'.
The first letter of 'it' is 'i'.
'm'+'pair'='mpair'
'mpair' put after 'i' is 'IMPAIR'.
'caused by' is the link.
Can you help me to learn more?
(Other definitions for impair that I've seen before include "Make worse or less effective" , "Damage or injure" , "blunt" , "'Mar, damage (6)'" , "Harm" .)