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San Francisco 49ers quarterback Brock Purdy will not play Sunday and head coach Kyle Shanahan said the lingering discomfort is a concern.

Purdy sat out Friday after he participated in the start of Thursday’s practice with the 49ers, then retreated indoors for what Shanahan said was a treatment session.

Brandon Allen, 32, will start in Purdy’s place, and the 49ers are also without defensive end Nick Bosa (oblique). Shanahan said players believe in Allen, even if he’s an unknown.

“Outside of here people haven’t seen a lot of Brandon. But it’s his second year (with the 49ers),” Shanahan said. “Obviously guys want Brock up, but guys are excited to see Brandon play.”

Shanahan said they are “a little surprised” Purdy experienced tightness and discomfort in his shoulder after an MRI exam on Monday that showed no long-term cause for concern.

“The way it responded this week, it’s really up in the air for next week,” Shanahan said of Purdy.

Allen is familiar to Packers head coach Matt LaFleur, who was an assistant coach with the Rams during Allen’s two-year run in Los Angeles. Allen broke into the NFL in 2016 with the Jaguars and is 2-7 in nine career starts. He went 1-2 with the Broncos in 2019 and 1-5 in six starts over two years with the Bengals in 2020 and ‘21.

Shanahan said Allen’s confidence grew throughout the week and he doesn’t anticipate a major change in how he calls the offense.

Left tackle Trent Williams (ankle) also missed practice for the third consecutive day.

Without disclosing the nature of the ailment to Purdy’s throwing shoulder, general manager John Lynch confirmed Friday an MRI exam took place to determine the severity of any injury.

Allen worked with the first team most of Thursday and Friday with Joshua Dobbs also taking snaps.

Lynch described Purdy’s status for the 49ers (5-5) this week as “tenuous.”

“Hopefully, he makes progress, and we can have a shot at this weekend, but we’ll see,” Lynch said in an interview with KNBR in San Francisco. “I think it’s tenuous.”

When Purdy was on the field this week, he primarily worked on the side in position-specific drills with QB coach Brian Griese.

Williams played through an ankle injury last week after being listed as questionable but exited the stadium with an exaggerated limp on Sunday.

Run game coordinator Chris Foerster said the 49ers aren’t where they want to be at 5-5 because they haven’t won close games, not because of injuries.

“Seven games left is like an eternity,” Foerster said. “So much can happen. Do the math. What was our record last year? It was 12-5. I was on a 13-win team that was nowhere near as good as the team last year.”

With or without Purdy, Foerster said the challenge for the 49ers is not to give up the ball to a defense that has 19 takeaways.

The 49ers have 13 giveaways this season.

–Field Level Media