To no one’s surprise, 49ers head coach Kyle Shanahan confirmed Monday that quarterback Jimmy Garoppolo will miss the rest of the season with a torn ACL in his left knee.

“It’s very unfortunate,” Shanahan said. “I’m not going to sugarcoat it. We’re all down and disappointed about it.”

He quickly moved to put the devastating injury in perspective.

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“It’s part of the NFL, it’s part of life,” he said. “You have to adjust to it. You’ve got to make the best out of it.”

Garoppolo was hailed as the franchise’s shining star last year after he guided the team to five straight wins to finish a 6-10 season. But three games into 2018, he’s done. He’ll have surgery in the next week or two after the swelling subsides, Shanahan said.

The injury “will make him that much more hungry next year,” Shanahan said. “There’s not a doubt in my mind that he’ll come back and be the exact same guy.”

The 1-2 team will have to rally around second-year man C.J. Beathard, who struggled as rookie. He’ll have the starting job beginning with Sunday’s game against the Chargers in Carson (Los Angeles County).

Sunday’s game Who: 49ers (1-2) at L.A. Chargers (1-2) When: 1:25 p.m.TV/Radio:Channel: 5Channel: 13Channel: 46/810, 107.7

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Shanahan called Beathard “as tough and fearless as any quarterback I’ve ever been around.”

There was more bad news for the 49ers. Shanahan also said cornerback Richard Sherman will be out “a couple of weeks” with a strained calf, and tailback Matt Breida will be questionable for Sunday with a hyperextended knee. The 49ers already were without starting tailback Jerick McKinnon, who tore an ACL in a practice a week before the season opener.

The 49ers’ only other quarterback is Nick Mullens, an undrafted free agent who has been on the practice squad since being signed last year. Shanahan said the team will bring in journeymen Kellen Clemens and Tom Savage and possibly T.J. Yates and Matt Moore for workouts.

Clemens was with the Chargers last year. Savage, after three years with the Texans, was one of the final cuts by the Saints this year after Teddy Bridgewater was named the backup. Last year, Yates was with the Texans and Moore with the Dolphins.

There was no discussion of bringing Colin Kaepernick back to the organization, Shanahan said. There was last year, he said, but he decided at that time that Kaepernick wouldn’t fit into his offense. “We’ve got the same situation now,” he said.

The quarterback hasn’t played since opting out of his contract a year and a half ago. He started a protest by many NFL players when he began kneeling during the national anthem in 2016 to highlight racial injustice and police brutality. Kaepernick is suing the NFL for collusion.

Garoppolo was hurt in Sunday’s 38-27 loss in Kansas City. With about 5:35 left to play, his left knee buckled just before he rammed his shoulder into cornerback Steven Nelson at the 7-yard line rather than go out of bounds as he finished a 13-yard run.

Although the knee gave way before the contact, Kansas City linebacker Justin Houston, who had pressured Garappolo before he ran to the sideline, said the quarterback should have stepped out of bounds to avoid the hit.

“That was his fault,” Houston told PFT Live. “I pray he’s not hurt and it’s nothing serious, but as a quarterback, you should step out of bounds. ...You got the yardage you need, you step out of bounds. You’ve got to be smart, think about your team.”

Shanahan basically agreed, without putting it in such stark terms. He said the injury should serve as a reminder why quarterbacks generally should go out of bounds and avoid hits, but he pointed out that quarterbacks are by nature extremely competitive.

“Just turn on the TV Sunday and you’re going to watch 15 plays by quarterbacks jumping over people, not getting out of bounds, doing a little extra to move the chains, where it’s a hell of a play, and everyone’s glad they did it,” he said.

He predicted Garoppolo, 26, probably will choose discretion in similar situations in the future. “He’ll remember this the rest of his life,” he said.

Last year, Beathard started five games as a rookie from Iowa after Brian Hoyer was benched. Beathard had a 1-4 record and a 69.2 passer rating.He eventually was sidelined with knee and hip injuries and was replaced by Garoppolo late in a loss to Seattle.

“I have a lot of confidence in C.J.,” Shanahan said. “He got a lot of experience last year. … He got thrown into as tough a situation as you could imagine putting a rookie quarterback in.

“He’s got the arm talent to make every throw. He’s extremely smart, and I know he’s the type of guy that our team believes in also. ... He’s been waiting for this moment, and that’s why I know he’ll take advantage of it.”

Tom FitzGerald is a San Francisco Chronicle staff writer. Email: tfitzgerald@sfchronicle.com Twitter: @tomgfitzgerald