Brown to miss rest of the season

After missing two of the past three games, 49ers right tackle Trent Brown will miss the final three games of the season.

On Friday, head coach Kyle Shanahan said Brown will be placed on injured reserve due to a shoulder injury that involves his labrum and will require surgery. Shanahan said Brown faces a five- to six-month recovery, which means he could miss the majority of the offseason program.

Brown, who was injured in practice Nov. 23, returned from a one-game absence to start in a win at Chicago on Dec. 3. However, he missed Sunday’s win at Houston after telling the team his injury wouldn’t allow him to play.

“It didn’t get worse,” Shanahan said. “It just didn’t go away. Sometimes the pain goes away with those and it ends up being OK.”

Shanahan was asked if he was disappointed Brown couldn’t play through his injury.

“Not disappointment in him; I’m disappointed that he doesn’t get to play with the team through these last three games,” Shanahan said. “… Trent tried to battle through it. He came back for a game for us versus Chicago and helped us win that game. Trent’s a very important part of this place and our future. When you’re talking about a five- to six-month injury, that’s something we wanted to get going as fast as possible. So, I fully support his decision.”

Brown, a 2015 seventh-round pick, is eligible for a contract extension in the offseason before he enters the final year of his deal.

“I think Trent has a chance to be very dominant at his position,” Shanahan said. “I thought he made huge strides this year. By no means is he fully there. But I thought he had a much better year this year than watching him on tape the previous two years.”

Brown will be replaced by Zane Beadles, 31, for the second straight game when the 49ers host the Titans on Sunday. Hurry up and wait: General manager John Lynch said he has “weekly” dialogue with quarterback Jimmy Garoppolo’s agent, Don Yee, but he isn’t expecting to discuss a potential long-term contract until the offseason. Yee also represents Patriots quarterback Tom Brady.

“It’s kind of refreshing to talk to him because of the way he’s dealt with Tom, a lot of people have learned: He really wants these guys just to go focus on their business,” Lynch said on KNBR. “We’ve agreed that, ‘Hey, there’s going to be a time for that, let’s keep in regular contact.’ But, no, we haven’t started discussions. I’m sure that will come in due time. And we’re looking forward to that time.” Injury report: Rookie cornerbacks Ahkello Witherspoon (knee) and Greg Mabin (calf ) are both questionable for Sunday, and Shanahan termed them game-time decisions.

However, the 49ers will have to determine their availability by 1 p.m. Saturday, which is their deadline for making roster moves. Their only healthy corners are Dontae Johnson and Leon Hall, so they might need to promote at least one player from the practice squad.

Their two cornerbacks on the practice squad are Channing Stribling and Tyvis Powell.