Kaepernick, according to Schefter, has elected to have surgery on his shoulder, ending any chance of the benched quarterback from being able to return to the starting lineup.
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He is now expected to undergo surgery on his non-throwing shoulder. Kaepernick was told by a team physician that the tear was minor, the source said. The Niners got off to a 2-6 start with Kaepernick under center, with the 28-year-old completing just 59 percent of his passes, good for 26th in the NFL.
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.
What began with an incredible display in 2012 coming off the bench to replace Alex Smith… under Harbaugh… and led to a Super Bowl trip and another NFC championship game appearance…
The source said team doctors originally told the quarterback the injury would heal on its own and he was not listed on any injury reports with a shoulder issue after Week 4.
On October 22, the 49ers managed just 142 total yards in a 20-3 home loss to Seattle, fewer than the 164 they had on Thanksgiving a year ago and their worst total since 133 yards against the Vikings on November 5, 2006.
At least the 49ers’ quarterback controversy can be put to rest: Blaine Gabbert will be the starter from here on out. Gabbert threw two touchdowns and two interceptions in a win over the Falcons 17-16, but he has a big challenge this weekend against the Seattle Seahawks.
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Kaepernick’s 88.4 career passer rating ranks third in franchise history behind Hall of Famers Steve Young (101.4) and Joe Montana (93.5). He has run for 1,832 regular-season yards and 11 touchdowns, including 256 yards and one touchdown this season.
