SEATTLE -- Quarterback Colin Kaepernick’s tumultuous 2015 season with the 49ers has officially come to an end.

And Kaepernick’s future with the organization beyond this season appears to be in serious doubt, too.

The 49ers on Saturday placed Kaepernick on injured reserve with a left shoulder injury just one day after describing him as “probable” -– implying he was all but certain to be available for Sunday’s game against the Seattle Seahawks.

A source close to Kaepernick told CSNBayArea.com that Kaepernick was diagnosed with a torn labrum in his non-throwing shoulder and is likely to undergo surgery early next week in Colorado.

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The possible recovery time of four-to-six months is likely to come into play because Kaepernick’s scheduled $11.9 million salary is fully guaranteed for injury. The salary also becomes fully guaranteed if he remains on the 49ers' roster on April 1.

The 49ers on Saturday promoted undrafted rookie quarterback Dylan Thompson to the 53-man roster to take Kaepernick’s spot on the roster and serve as Blaine Gabbert’s backup.

After returning from the bye week, Kaepernick reported soreness in his left shoulder, according to 49ers spokesman Bob Lange. However, the source close to Kaepernick said the quarterback first reported the discomfort in his shoulder to the 49ers' athletic training staff after the 49ers’ Oct. 4 game against the Green Bay Packers. Kaepernick made the 49ers' next four starts.

 

Kaepernick underwent an MRI examination at Stanford this week after returning from the bye week and experiencing continued soreness, the source said. Kaepernick was told by a team physician that the tear was minor, the source said. Kaepernick sought a second opinion, and Dr. Peter Millet of the Steadman Clinic in Vail, Colorado, determined the injury was a significant tear to his labrum, according to the source.

Kaepernick’s shoulder injury was not noted on the 49ers’ injury reports until this week. The 49ers disclosed the injury in their mandatory filings to the league on Wednesday, Thursday and Friday. Kaepernick was listed as a full participant in each of those workouts, according to the team.

The 49ers on Friday listed Kaepernick as “probable” on the injury report. But after practice, Kaepernick reported his shoulder did not feel any better and asked about his options, the team said. But the source close to Kaepernick said 49ers team doctors agreed with Dr. Millet’s diagnosis of the “extensive tear of the labrum.”

The shocking development of Kaepernick's season-ending injury came just hours before the 49ers were scheduled to fly to Seattle. Kaepernick did not make the trip to Seattle.

The event likely signals a rapid end of a union between the 49ers and the player they considered their franchise quarterback when they signed him in June 2014 to a lucrative contract.

Kaepernick quickly rose to national prominence in 2012 while helping take the 49ers to the Super Bowl with his blend of power and speed – throwing and running.

The club signed him to a $115 million contract extension through the 2020 season. The deal included a relatively low signing bonus of $12.328 million.

The cash value of Kaepernick’s deal through two years is approximately $25 million. He will not collect the remaining $875,000 for the remainder of the season in per-game roster bonuses. Throughout the length of Kaepernick’s contract, he was scheduled to earn a $125,000 bonus for every game he was on the team’s 46-man active roster.

Kaepernick got his initial chance with the 49ers in 2012 when starter Alex Smith, in the midst of his career year, exited the lineup due to a concussion. When Smith received medical clearance, then-coach Jim Harbaugh opted to stick with Kaepernick.

Kaepernick set the NFL single-game record (regular season or playoffs) with 181 yards rushing in a victory over the Green Bay Packers at Candlestick Park in January 2013. He became the fourth quarterback in NFL history to register victories in each of his first three road playoff starts, including a comeback win over the Falcons in the NFC Championship game.

Kaepernick’s 10th NFL start came in Super Bowl XLVII. He threw for 302 yards in the 49ers’ loss to the Baltimore Ravens. Kaepernick has rushed for 1,834 yards and 11 touchdowns in 57 regular-season games, ranking first (641 in 2014) and third (524 in 2013) on the franchise’s list of single-season yards rushing by a quarterback.

His 507 yards rushing ranks second behind only Hall-of-Famer Steve Young for most career rushing yards in the postseason. Kaepernick has played in just six postseason games, while Young had 594 yards rushing in 20 games.

 

Kaepernick’s production as a passer declined every season as the 49ers’ starter. His passer rating in seven 2012 starts was 98.3. In his next two full seasons as the starter, Kaepernick’s rating fell to 91.6 and 86.4.

Kaepernick spent more than two months early in the offseason working with a private quarterbacks coach and getting instruction from former NFL MVP Kurt Warner.

The 49ers’ poor pass protection proved problematic for Kaepernick, who was sacked 28 times through eight games. He was sacked a franchise-most 52 times in 2014.

Gabbert replaced Kaepernick in the starting lineup for the team’s Nov. 8 game against the Atlanta Falcons. The day after the 49ers’ victory, coach Jim Tomsula informed Gabbert and Kaepernick of his plan to stick with Gabbert to face the Seahawks after the bye week.

Kaepernick started the first eight games of the season. He completed 144 of 244 passing attempts (59 percent) for 1,615 yards with six touchdowns and five interceptions. His passer rating is a career-low 78.5.