The unbeaten chaser, who beat Cue Card in a thrilling Grade One at Ascot in February, has not suffered a career-threatening injury but it is enough to prevent him from heading to Aintree.
Jefferson decided to skip the Cheltenham Festival last month, despite the meeting taking place on his favoured soft ground, as she felt her stable star had not quite recovered from his Ascot exertions.
“Unfortunately, we’ve had a setback and it’s come at the wrong time, with Aintree around the corner,” said the North Yorkshire handler.
“He definitely won’t run again this season and we’re just waiting back for more detail from the vet to see exactly what it is.”
Jefferson could still be represented at Aintree by Cloudy Dream, who finished second in the Arkle and third in the Ryanair at the last two Cheltenham Festivals.
“He’ll have entries at Aintree in the Melling over two-and-a-half miles and the Bowl over three,” she said.
“It’s not certain he’ll go there, though, as there is the race at Sandown that Cue Card is going for (Oaksey Chase) and options at Ayr.”