Her connections admitted on Friday that preparation had not been "100 percent straightforward", and they then withdrew the favourite from the fillies' Classic on Sunday claiming she wasn't ready.
The unbeaten three-year-old has been top of the market all winter since she concluded her juvenile campaign with a straightforward success in the Fillies' Mile at Newmarket, with Frankie Dettori on board.
She had already won the May Hill at Doncaster prior to that and looked nailed on to carrying on that success in the Guineas.
Chris Richardson, managing director to owners Cheveley Park Stud, said: "John Gosden had an in-depth discussion with the boss, Mrs Thompson, and following that it was decided that sadly she would miss the 1000 Guineas.
"John Gosden feels she wasn't really ready for the race and when you receive that advice from a trainer such as John, you follow it and now we'll look to the Coronation Stakes at Royal Ascot as part of her programme.
"It is disappointing for all concerned but we must heed their advice.
"Royal Ascot is a favoured meeting of the Thompsons and we've had success there previously, it's the start of the year and we've still got lots of opportunities going forward."
Inspiral's absence sees Aidan O'Brien's Tenebrism as the 11-4 market leader with Betfair.