Mark, at church, is seldom seen (6)
I believe the answer is:
scarce
'seldom seen' is the definition.
(I've seen this in another clue)
'mark at church' is the wordplay.
'mark' becomes 'scar' (mark left by an injury).
'at' means one lot of letters go next to another.
'church' becomes 'CE' (abbreviation for Church of England).
'scar'+'ce'='SCARCE'
'is' is the link.
(Other definitions for scarce that I've seen before include "Wanting" , "Deficient in quantity" , "Like gold dust" , "Not plentiful, hard to find" , "Rare shock Conservative getting in" .)