Kaepernick began the week coming off the team's bye with soreness in his non-throwing shoulder and he brought it to the attention of the medical staff Monday.
It apparently happened in the game against Green Bay on October 4, and he has been dealing with the pain ever since. He received treatment throughout the week, even getting a second opinion from a Dr. Peter Millet at the Steadman Clinic in Denver. There, they discovered that he had a significant tear of his labrum in his left shoulder. He could have surgery as early as Tuesday in Denver.
Colin Kaepernick torn labrum in left shoulder. Surgery Tuesday in Denver according to sources.injury could affect future guaranteed money.— Mike Shumann (@MikeShumann) November 21, 2015
He was listed as probable Friday to be available if needed 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.
The team can't waive an injured player, but could work out an injury settlement. He will also lose $875,000 this season in personal game bonuses, missing seven games.
Because of that, many already figured Kaepernick's time with the Niners (3-6) might be done in what so far has been a forgettable season.
Meanwhile, fans, like Darin Robinson, are speaking out.
"We're Kaepernick fans. I wish he got his mojo back this year, but it's a tough go," he said.
But not everyone is so sympathetic.
"Good luck, that's all I can say," said Richard Ivangelho, also a Niners fan. "He hasn't done anything in the first 4-5 games. They should pull him out and replace him>'
Kaepernick He took over the starting job from Alex Smith in November 2012 and immediately showed the dynamic player he could be with his strong arm and quick legs - including that quarterback-record 181 yards rushing in a playoff win against Green Bay on the way to the Super Bowl.
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 this week against the rival Seahawks.
"I'm not into comparing the two guys," Tomsula said this week. "I won't compare the two guys, but Blaine right now is doing a good job for us and did a nice job last week. He's been here for two years, so it's a guy we know and he's busting his tail."
Initially when making the quarterback change, Tomsula said he wanted Kaepernick to "step back and breathe and look at things through a different lens."
To that, Kaepernick said, "I'm not out of breath, so I don't understand that reference."
San Francisco moved quarterback Dylan Thompson from the practice squad to the active roster to back up Gabbert.
Kaepernick's agent didn't immediately return messages Saturday.
The Associated Press contributed to this story.