McGlinchey suffered the injury in the first half of the Niners' 31-17 loss to the Arizona Cardinals on Sunday at Levi's Stadium. After the game, Niners coach Kyle Shanahan said he was unsure of the severity of McGlinchey's injury, but further testing revealed the tear Monday morning.
The injury will require surgery that will land McGlinchey on injured reserve, cutting short what was shaping up as a bounce-back season for the fourth-year pro.
"I thought Mike was doing a hell of a job coming off his last year," Shanahan said. "We saw some really good things from Mike his first two years. I think he knows -- we all know he had a setback in his third season last year. He struggled at times. He was putting in the work in the offseason and I thought he's had a much better year, getting back to how he was playing in his second year."
Veteran Tom Compton replaced McGlinchey and struggled against an Arizona defense that finished with five sacks. According to Pro Football Focus, McGlinchey had given up two sacks and 13 pressures in 275 pass-blocking snaps. In 35 pass-blocking snaps on Sunday, Compton allowed a sack and four pressures.
Shanahan said postgame that rookie Jaylon Moore did not step in for McGlinchey because he's spent most of his time working at left tackle but acknowledged that if McGlinchey is out for an extended period, Moore would be in consideration to be the long-term replacement, along with Compton.
On Monday, Shanahan mentioned Moore and Compton as potential replacements, and said right guard Daniel Brunskill is also an option, though he's likely to stay at his current spot.
"We've got a number of options in that way so we can see with that but the job will probably go to [Moore or Compton]," Shanahan said.
McGlinchey, the No. 9 overall pick in the 2018 NFL draft, has started all eight games at right tackle this season and missed just four of a possible 56 regular season games in his nearly 3 1/2 seasons in the league.
Even after a disappointing 2020, the 49ers picked up McGlinchey's fifth-year option in April, guaranteeing his $10.88 million salary for the 2022 season.
"I thought he's been getting better each week and having a better year and playing like the right tackle we need him to play like," Shanahan said. "And I think he was going to continue to get better as the year went on. Unfortunately, though, he had that injury and he'll heal up and hopefully this will make him better for next year."
In addition to McGlinchey, the Niners also lost safety Tavon Wilson to a foot injury and receiver Mohamed Sanu to a knee sprain. Those injuries will keep Wilson and Sanu out "for a while," according to Shanahan. Wilson, who started Sunday in place of Jimmie Ward (who is out with a quad injury), is expected to go on injured reserve. Sanu also could, but the Niners were still working through the extent of his injury late Monday afternoon.