Jasen Vinlove-USA TODAY Sports

49ers quarterback Colin Kaepernick is back at the team's facility after shoulder surgery

Colin Kaepernick is back at the 49ers facility, despite his uncertain future.

SANTA CLARA, Calif. - 49ers quarterback Colin Kaepernick is back at the team's facility this week following surgery last week to repair a torn labrum on his left throwing shoulder.

"It’s my understanding he’s in today to start his rehab," Jim Tomsula said Monday.

Kaepernick was shut down for the season unexpectedly the day before the game Nov. 22 in Seattle when he was placed on injured reserve. On the practice report leading up to the game, Kaepernick was officially listed as probable to play, despite being demoted from the starting lineup in favor of Blaine Gabbert.

Kaepernick has not spoken publicly since being deactivated, but general manager Trent Baalke said before the loss to the Seahawks the decision for Kaepernick to have season-ending surgery was mutual between the team's medical staff and the second opinion Kaepernick sought in Colorado.

Since taking over the starting job, Gabbert has averaged 255.7 yards passing per game, to Kaepernick's 179.4. Additionally, Gabbert's passer rating is 91.0 while Kaepernick had a 78.5 mark for the season.

Kaepernick's future with the 49ers remains up in the air beyond this season, particularly with Gabbert playing better than Kaepernick since entering the starting lineup. San Francisco could move on from Kaepernick at the start of the next league year, April 1, without significant financial repricussions.

Kaepernick's six-year extension he signed before 2014 provided guarantees run out after the season. His $11.9 million base salary for next season is guaranteed for injury only. His rehab is expected to take four to six months, with April 1 being roughly four months from his initial surgery.

The 49ers will not likely want to pay Kaepernick that much to be Gabbert's back up, making a trade or release a possibility, depending on his medical status.

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