Tests confirmed that San Francisco 49ers quarterback Jimmy Garoppolo suffered a torn ACL on Sunday against the Kansas City Chiefs. (AP) The worst fears of all San Francisco 49ers fans were confirmed on Monday: quarterback Jimmy Garoppolo has been lost for the remainder of the season after tearing the ACL in his left knee on Sunday. The team confirmed the news on Twitter on Monday afternoon. The 49ers made Garoppolo the highest-paid player in NFL history in February (though the title didn’t remain his for very long) on the strength of his five starts with the team in 2017. And while San Francisco is just 1-2 this year after losing in Kansas City, he’d imbued the franchise and its followers with tremendous hope. All of that is on pause now. What now for the Niners? Without Garoppolo, the Niners will likely turn to second-year backup C.J. Beathard, at least for the short term. A third-round pick out of Iowa in 2017, Beathard already has some experience as a starter, leading the 49ers for five games last season after an injury to veteran Brian Hoyer. San Francisco was 1-4 in his five starts. The win was against the New York Giants on Nov. 12, and Beathard had by far his best game, completing three-quarters of his 25 pass attempts for 288 yards, two touchdowns and one interception. Beathard told reporters on Sunday that he told Garoppolo he was praying for his teammate’s health; Garoppolo told Beathard “to lead these guys.” The 6-foot-2 Beathard is a grandson of Bobby Beathard, the longtime former NFL general manager who was inducted into the Pro Football Hall of Fame in August. What now for Garoppolo? As of this writing, there’s no indication that Garoppolo had any damage beyond his ACL, like to his MCL or LCL. With an MCL tear, the typical plan is to let the MCL heal – it doesn’t require surgery – and about a month later comes the reconstruction for the ACL. Eagles’ quarterback Carson Wentz tore his LCL (lateral collateral ligament) in addition to his ACL last December, which added some time to his recovery. Assuming Garoppolo’s damage is limited to his ACL and he doesn’t have any setbacks like an infection (as former teammate Tom Brady had after his 2008 ACL surgery), he should be good to go for training camp next year. Story continues Though San Francisco is 1-2, Garoppolo has been playing well, particularly the last two weeks. After a bad showing in Week 1 against Minnesota, when he threw three interceptions, he had two passing touchdowns in each of the last two games, with no picks, and his completion percentage went up considerably over that outing against the Vikings. More from Yahoo Sports: • Tiger’s win is the greatest comeback in sports history • White Sox star says what many think about umpire • Charles Robinson: Latest flag on Packers’ Matthews may be worst yet • Rams’ Gurley really isn’t a fan of Thursday games<doc-sep>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. Now Playing: It was the last thing San Francisco 48ers fans wanted to see. With Jimmy Garoppolo out for an extended period of time, former New York Giants running back Tiki Barber discusses where the 49ers go from here. Video: Sports Illustrated “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 See More Collapse 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<doc-sep>AP The injury to 49ers quarterback Jimmy Garoppolo appears to be the worst-case scenario. San Francisco head coach Kyle Shanahan confirmed after today’s loss to the Chiefs that the team fears Garoppolo tore his ACL. That would be a season-ending injury to the quarterback the 49ers traded a second-round draft pick to acquire and gave one of the biggest contracts in NFL history. Although an ACL tear can only be diagnosed definitively with an MRI, experienced athletic trainers can usually tell an ACL is torn by feeling the looseness of the knee. It would be rare for the 49ers’ medical staff to fear a torn ACL and be proven wrong, but the 49ers will cross their fingers. It’s been a rough start to the season for the 1-2 49ers, and the worst may be yet to come, when those MRI results come back.<doc-sep>
Fooch’s update: The 49ers formally announced that Jimmy Garoppolo suffered a torn left ACL. The results from Jimmy Garoppolo’s MRI are in and it’s what we expected; the San Francisco 49ers quarterback has a torn ACL, according to ESPN's Adam Schefter. His season is over and he’ll be moved to injured reserve shortly. With the injury, that means C.J. Beathard is once again the starting quarterback. Beathard took the reigns of the starting job as a rookie last year when Brian Hoyer was ineffective, and relinquished it to the recently acquired Garoppolo after a vicious hit against the Seattle Seahawks. Beathard finished 2017 playing five games and throwing for 1,430 yards. He managed four touchdowns to six interceptions. This also means Nick Mullens will be promoted from the practice squad and serve as Beathard’s backup. With the Mullens promotion, the team will most likely be hunting a quarterback to fill the void on the practice squad. Garoppolo went down Sunday in a strange cut as he was scrambling down the sidelines towards the end of the 49ers contest against the Kansas City Chiefs. At first it appeared to be something shoulder or head related due to the hit he received from Steven Nelson, but his knee buckled before Nelson initiated contact. Garoppolo was carted off and the coaching staff already assumed the worse. Garoppolo has yet to play an entire season in the NFL. In 2016, while with the New England Patriots, he was set to fill in for Tom Brady for four games during the latter’s Deflategate suspension. Garoppolo suffered a shoulder injury in Week 2 that cost him the next two games, after which Brady returned from his suspension. Right now, this is awful, awful news. While the 49ers were nowhere near being a Super Bowl contender, they were thought to be much improved and Garoppolo needed development in Kyle Shanahan’s system. Beathard’s play in 2017 behind a porous offensive line led to him getting hit more than anyone would like, but his toughness earned the respect of the locker room. The 49ers have rallied behind Beathard so it’s on him now. In any case, this team is now Beathard’s team. And don’t count on a midseason trade to get a different starter this year either.