SEATTLE — The decision for San Francisco quarterback Colin Kaepernick to have season-ending surgery on his left, non-throwing shoulder was a mutual decision between the quarterback and the team, 49ers general manager Trent Baalke said Sunday.
Speaking before the 49ers game in Seattle, Baalke said Kaepernick consulted team doctors and received a second opinion before the decision for surgery was made.
"This was something they felt from a medical standpoint it needed to be taken care of and addressed through surgery," Baalke said. "Which, obviously, if he has surgery, he's not going to be able to play. So moving him to IR is the natural move."
Baalke said he expects Kaepernick to go through offseason recovery with the team and said any belief the former starter's stint with the 49ers was over was unfounded.
"I wouldn't say that at all. I think people are reading into that. For me, where we stand right now, I wouldn't read too much into that right now," Baalke said.
Kaepernick began the week coming off the team's bye with soreness in his shoulder and brought it to the attention of the medical staff Monday. He received treatment throughout the week, and was listed a full participant in practice.
He was listed as probable Friday for Sunday's game at Seattle as the backup to promoted starter Blaine Gabbert.
The 28-year-old Kaepernick's $11.9 million 2016 contract would become fully guaranteed for injury if he's still on the roster on April 1. Because of that, many already figured Kaepernick's time with the Niners (3-6) might be done after what so far has been a forgettable season.
Kaepernick was drafted in the second round out of Nevada in 2011 and took over the starting job from Alex Smith in November 2012, immediately showing the dynamic player he could be with his strong arm and quick legs. He had a quarterback-record 181 yards rushing in a playoff win against Green Bay on the way to the Super Bowl.
Yet that guy never came to life this season, instead making more mistakes than memorable plays. Kaepernick first injured his left shoulder in a Week 4 loss to Green Bay, Baalke said.
"It was an injury that our medical staff looked at, and treated, and he didn't seek any extra treatment," Baalke said. "But it was ongoing. It wasn't something that was all of a sudden it just required surgery."
Gabbert took over for the benched Kaepernick against Atlanta on Nov. 8 and led the team to a 17-16 win. Then coach Jim Tomsula said Gabbert would keep the starting job at least for another game against the rival Seahawks.
But the first-year coach hadn't publicly ruled out Kaepernick returning at some point. With Kaepernick out, the 49ers promoted Dylan Thompson from the practice squad to the active roster to back up Gabbert.
"Right now is not the time to get into the particulars," Baalke said. "Right now he's no different than any other player that's been placed on IR. When that surgery takes place, then the rehab process, getting him ready for the offseason program (that's) the next step."