Mark has two keys, though they're in short supply (6)
I believe the answer is:
scarce
'in short supply' is the definition.
(both can mean rare)
'mark has two keys' is the wordplay.
'two keys' means two replacements for 'key'.
'mark' becomes 'scar' (mark left by an injury).
'has' is a charade indicator (letters next to each other).
'key' becomes 'c' (musical key).
'key' becomes 'e' (musical key).
'scar'+'c'+'e'='SCARCE'
'though they're' is the link.
I am not very happy about this link. Some or all of it may be part of another bit of the clue.
Can you help me to learn more?
(Other definitions for scarce that I've seen before include "Not enough to satisfy demand" , "Like gold dust" , "Rare shock Conservative getting in" , "Common? Definitely not" , "Insufficient to meet demand" .)