San Francisco 49ers quarterback Colin Kaepernick (7) walks on the sideline during the second half of an NFL football game against the Atlanta Falcons in Santa Clara, Calif., Sunday, Nov. 8, 2015. (Ben Margot/AP)

Kap placed on IR, 49ers career over

If this was the end of the Colin Kaepernick era, it came not with a bang but under some rather curious circumstances.

On Saturday, the 49ers placed the embattled Kaepernick on the injured reserved list because of what was called a left shoulder injury. The move assured that the one-time Super Bowl quarterback had played his final down of the season and most likely in a 49ers’ uniform.

Quarterback Dylan Thompson was promoted from the practice squad to take Kaepernick’s place on the active roster. He will back up Blaine Gabbert against the Seahawks today in Seattle.

How the decision came about exactly was open to considerable debate, however.

After a bye week, Kaepernick complained of soreness in his left (non-throwing) shoulder last Monday. The injury was brought to the attention of the team medical staff, and he received treatment while he participated in practice the rest of the week.

Kaepernick reportedly sustained the injury in a Week 4 loss against the Green Bay Packers, one in which he was sacked six times. The injury is believed to be a torn labrum, but it hasn’t been serious enough to appear on weekly injury reports since then.

Kaepernick had been listed as probable for the game today and was scheduled to back up Gabbert, who took his place three weeks ago.

But after the team submitted its injury report Friday, Kaepernick returned to the training staff after practice and reported that his shoulder hadn’t made sufficient progress. Several options were reportedly discussed, and according to one report, he could undergo surgery as early as Tuesday in Colorado.

Kaepernick cannot be released as an injured player, but the two sides could work out a settlement. If he sits out the final seven games, he will lose $875,000 in personal bonuses.

In the midst of the worst season of his career, Kaepernick will be paid $11.9 million if the organization doesn’t release him before April 1. That payment might be necessary if Kaepernick isn’t fully recovered from the surgery, which would trigger an injury clause requiring the 49ers to compensate him.

This season, Kaepernick completed 59 percent of his passes for 1,615 yards, six touchdowns and five interceptions. Among NFL qualifiers, his 78.5 passer rating is fifth-lowest in the league.

Gabbert started in place of Kaepernick against the Atlanta Falcons on Nov. 8 and led the team to a 17-16 victory. Coach Jim Tomsula said Gabbert would retain the starter position for at least one more game, but he would not rule out the return of  Kaepernick at some point this season.

“I’m not into comparing the two guys,” Tomsula said earlier 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.”

When the quarterback change was made, Tomsula said he wanted Kaepernick to “step back and breathe and look at things through a different lens.”

But Kaepernick scoffed at the idea on multiple occasions.  “I’m not out of breath, so I don’t understand that reference,” he said.

In Week 7, the 49ers gained only 142 total yards in a 20-3 loss to the Seahawks at home, their lowest total in one game since the 2006 season.

The last-place 49ers have lost four in a row to Seahawks and six of the last seven. They scored in single figures in the last three losses, in which they were outscored by a 56-13
margin.

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