Colin Kaepernick has played his last snap for the 49ers this season and perhaps for the rest of his career.
The team placed the quarterback on injured reserve Saturday with an injury to his left, non-throwing shoulder that could require surgery early next week. Under NFL rules, players put on injured reserve cannot return to active status the remainder of the season.
Rookie Dylan Thompson, who had been on the 49ers’ practice squad, was elevated to the 53-man roster and will be Blaine Gabbert’s backup for Sunday’s game against the Seahawks in Seattle. Gabbert replaced Kaepernick as the starter earlier this month and led the 49ers to a 17-16 victory over Atlanta in their last game.
On Friday, Kaepernick told The Bee the injury occurred against the Packers in Week 4. The quarterback, however, only appeared on the team’s injury report with a shoulder issue this week.
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According to a league source, Kaepernick had an MRI on the shoulder Monday. Those images were sent to a specialist in Colorado, who said Kaepernick had a “significant” tear in his labrum. The source said Kaepernick offered to be in Seattle for Sunday’s game before traveling to Colorado on Monday, but the team decided to place him on injured reserve. He could have surgery as early as Tuesday.
The source said team doctors initially told the quarterback the injury would heal on its own, and he was not listed on any injury reports with a shoulder issue after Week 4. When the injury continued to bother him following the team’s recent bye week, doctors re-examined the shoulder and he was listed on the weekly practice participation report.
The source said Kaepernick was willing to be on hand for Sunday's game and to fly to Colorado Monday but that the team decided to place him on injured reserve now.
Kaepernick was a full participant in Wednesday through Friday's practices and was listed as probable for Sunday’s game against the Seahawks in Seattle.
Kaepernick said Friday the injury is the result of a hit he absorbed in the team’s 17-3 loss to the Packers in Week 4, during a game in which he was sacked six times. He also absorbed a big hit from Packers linebacker Clay Matthew after handing the ball off on a read-option play.
“To me, not only did I not have the ball, but it was also targeting the head,” Kaepernick said after the game. “But to me, we’re onto the next play. I can’t sit there and complain about it.”
There was no penalty and Matthews was not fined.
Kaepernick never missed a start due to injury since taking over as the starter midway through 2012. He started the 49ers’ first eight games this season before being replaced by Gabbert, who will start his first road game for the 49ers on Sunday. Coach Jim Tomsula had been non-committal on who will quarterback the team for the rest of the season.
Kaepernick’s contract calls for him to earn a significant sum if he suffers a career-ending injury, which this does not appear to be. The contract, however, also allows the 49ers to part ways with him without any significant salary-cap impact if it’s done before April 1. That’s likely to be the case.
The only other time Kaepernick was on an injury report this season was is following a Week 7 loss to Seattle when he suffered a thumb injury.
This season, Kaepernick completed 144 of his 244 passes for 1,615 yards and six touchdowns. His passer rating was 78.5, the lowest of his career.
In five seasons with the 49ers, Kaepernick completed 59.9 percent of his passes for 10,030 yards and 56 touchdowns. He was intercepted 26 times and has an 88.4 passer rating. He also rushed for 1,832 yards on 306 carries.