Submarine captain upset by sign (4)
I believe the answer is:
'sign' is the definition.
(I know that omen is a type of sign)
'submarine captain upset' is the wordplay.
'submarine captain' becomes 'nemo' (character from 20,000 Leagues Under the Sea).
'upset' shows that the letters should be reversed in order.
'nemo' in reverse letter order is 'OMEN'.
'by' acts as a link.
(Other definitions for omen that I've seen before include "Harbinger, augury" , "Harbinger, portent" , "Augury, portent" , "premonition" , "Forecast" .)