Variation in maths and algebra finally leading to complaint (6)
I believe the answer is:
asthma
'complaint' is the definition.
(asthma is a medical complaint)
'variation in maths and algebra finally' is the wordplay.
'variation in' is an anagram indicator.
'and' means one lot of letters go next to another.
'finally' says to take the final letters.
The last letter of 'algebra' is 'a'.
'maths' is an anagram of 'asthm'.
'asthm'+'a'='ASTHMA'
'leading to' is the link.
(Other definitions for asthma that I've seen before include "Distressing ailment affecting breathing" , "breathing problems" , "Mat has a respiratory disorder" , "Respiratory disorder with wheezing" , "Strange that Mat has difficulty breathing" .)