Colin Kaepernick Injury Update: San Francisco 49ers Place QB on Season-Ending IR

Possibly signaling the end of Colin Kaepernick's tenure in San Francisco, the 49ers surprisingly placed the struggling quarterback on injured reserve, ending his season.

The 49ers announced that QB Dylan Thompson has been promoted from the practice squad to San Francisco's active roster. 

On Wednesday, Cam Inman of the Bay Area News Group reported that Kaepernick was listed on the 49ers' injury report with a left-shoulder injury. Kaepernick told reporters, per Matt Barrows of the Sacramento Bee, on Friday the injury dates back to San Francisco's Week 4 loss against the Green Bay Packers. 

ESPN's Adam Schefter reported that Kaepernick told the 49ers he wanted to have his non-throwing shoulder operated on, leading to the team making this move. Barrows added that a second opinion on Kaepernick's injury found a "significant tear" in his labrum. On Sunday, Ann Killion of the San Francisco Chronicle provided a synopsis of 49ers general manager Trent Baalke discussing the unusual situation:

Kaepernick's brother Kyle praised Colin's effort for continuing to play through the injury:

"

Played 4.5 games with it. Tough kid #proudbrother https://t.co/vXVqFTQtjD

— Kyle Kaepernick (@DarthKaepernick) November 21, 2015"

Looking to the future, NFL Network's Andrew Siciliano noted Kaepernick's salary for 2016 is only guaranteed for injury. He's slated to make $11.9 million next season with a cap hit of $16.8 million, per Spotrac, and his salary becomes fully guaranteed on Apr. 1, 2016.

"By being placed on IR, [Kaepernick] now misses out on $125,000 in per-game roster bonuses—a loss this season of $875,000," noted Schefter.

ESPN's Seth Wickersham noted there is a special clause in Kaepernick's contract that will financially benefit the 49ers:

After starting San Francisco's first eight games this season, Blaine Gabbert replaced Kaepernick in Week 9. The 49ers rank No. 30 in the NFL in passing yards per game this season and last in total offense and scoring. 

Given the nature of Kaepernick's injury, his recovery will likely dictate whether the 49ers do have to pay his salary. The marriage between player and team has been tenuous, to say the least, and his latest setback is another unfortunate obstacle in what once looked like a strong pairing.

Kaepernick has undeniable physical gifts and just turned 28 on Nov. 3, so even if his future isn't in San Francisco, there will be a team that gives him an opportunity in 2016. A fresh start feels like the best thing for the one-time second-round pick at this stage of his career.