Not so high clouds may threaten so (5)

I believe the answer is:

lower

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'not so high' is the definition.
('low' can be the opposite of 'high' so perhaps 'lower' is reasonable for 'not so high')

I don't understand the rest of the clue.

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(Other definitions for lower that I've seen before include "Take down" , "Let down, being inferior" , "put down" , "Let or haul down" , "Lessen" .)

I've seen this clue in The Globe and Mail.

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