What does the cryptic crossword clue "Manner lacks latitude, causing a spot of discomfort (4)" mean?

The definition is "spot of discomfort". The wordplay uses a deletion. STYE (deletion) = STYE; definition: "a spot of discomfort" The answer is STYE.

Manner lacks latitude, causing a spot of discomfort (4)

Guardian Cryptic #29085 | 22 Down | 2023-06-01 flower