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Trainers attend to San Francisco 49ers quarterback Jimmy Garoppolo (10) who was injured after a tackle by Kansas City Chiefs defensive back Steven Nelson during the second half of an NFL football game in Kansas City, Mo., Sunday, Sept. 23, 2018. (AP Photo/Charlie Riedel)
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Trainers attend to San Francisco 49ers quarterback Jimmy Garoppolo (10) who was injured after a tackle by Kansas City Chiefs defensive back Steven Nelson during the second half of an NFL football game in Kansas City, Mo., Sunday, Sept. 23, 2018. (AP Photo/Charlie Riedel)
Cam Inman, 49ers beat and NFL reporter, San Jose Mercury News, for his Wordpress profile. (Michael Malone/Bay Area News Group)
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SANTA CLARA — Jimmy Garoppolo’s season indeed is over, as a MRI exam Monday confirmed he tore the anterior cruciate ligament in his left knee late in the 49ers’ loss Sunday at Kansas City.

“It was hard for him last night, it was hard today and it will be hard over these next few weeks,” coach Kyle Shanahan said. “But Jimmy is a tough person, will bounce back from this and he’ll be ready to go next year.”

Garoppolo’s job now returns to C.J. Beathard, who went 1-4 last season as a rookie starter. The 49ers (1-2) next face the Los Angeles Chargers (1-2) on Sunday in Carson.

Several quarterbacks will audition Tuesday for a potential backup role, and that preliminary list includes former NFL starters Tom Savage, Kellen Clemens, T.J. Yates and Matt Moore.

Asked if the 49ers discussed re-signing Colin Kaepernick, Shanahan said: “No. There was (discussion) last year. I made that decision just because of the style of offense we wanted to go with. That’s what I said last year and it’s kind of the same situation now.

The Raiders’ Miles Burris (56) tries to chase down the 49ers’ Colin Kaepernick (7) on Dec. 7, 2014. (Dan Honda/Bay Area News Group) (Dan Honda/Bay Area News Group)

“I always look into what style of offense I want to do, what style of offense we’ve been doing the last two years,” Shanahan added. “C.J. is our guy and we have Nick Mullens backing him up. When you get to a third and fourth guy, whoever that is, you’d like to bring in guys you felt you don’t have to change your offense for.”

Garoppolo’s knee buckled as he scrambled down the left sideline with 5:27 remaining in the 38-27 defeat. Sacked on the two previous plays, he was flushed from the pocket on third-and-goal and raced 13 yards to the 7-yard line, where, rather than go out of bounds as quarterbacks are coached to do, he endured a helmet-to-helmet hit by cornerback Steven Nelson.

Jimmy Garoppolo #10 of the San ...
Jimmy Garoppolo #10 of the San Francisco 49ers throws a pass during the third quarter of the game against the Kansas City Chiefs at Arrowhead Stadium on Sept. 23rd, 2018 in Kansas City, Missouri. 

So ended Garoppolo’s fifth NFL season. Traded to the 49ers last Oct. 30 after a 3 1/2-season tenure with the New England Patriots, he went 5-0 as their December starter, prompting the 49ers to sign him on Feb. 8 to what then was the richest contract in NFL history (five years, $137.5 million).

“I’m not going to sugarcoat it: it was hard waking up today,” Shanahan said . “We were down, disappointed about it. Because we were looking forward to playing with Jimmy this year and going through the good and the bad, knowing he’d benefit from all of it.

“I know Jimmy’s down about it and so are we.”

Well wishes poured in from across the NFL.

“I saw it on the way to the (Patriots-Lions) game and feel terrible for him,” Tom Brady said Monday on Boston radio’s WEEI. “It’s a tough injury. I feel bad for Jimmy, and it’s football. Things happen like that. I’ve been through an ACL.

“It sucks. You hate to see people go down, and he is someone I really like and have been friends with since the day he got here. It just sucks to have to go through that.”

Raiders coach Jon Gruden opened his Monday press conference by noting: “Just sick to hear about Jimmy Garoppolo. I wish him the best in his recovery. Hate hearing that.”

Garoppolo not only elevated his teammates’ on-field capabilities, he revitalized a frustrated fan base, so much so that the 49ers gave out Garoppolo bobblehead dolls at last week’s home-opening win over the Detroit Lions.

Garoppolo, 26, took a beating through three games, getting sacked 13 times, including six in that win over the Lions. He completed 59.6 percent of his passes (53-of-89) for 718 yards with five touchdowns and three interceptions for a 90.0 passer rating. In last December’s starts, he had a 67.4 completion percentage, a 96.2 passer rating and seven touchdowns vs. five interceptions.

Beathard, a third-round pick from Iowa, served as a go-between starter last season, replacing Brian Hoyer after an 0-6 start and going 1-4 before Garoppolo took over in December. Beathard’s 69.2 passer rating was the 49ers’ lowest since 2004 (Ken Dorsey, 62.4). But he won over teammates with his ability to shake off big hits in the pocket (19 sacks).

Said Shanahan: “We threw him into a tough situation and he got the crap beat out of him a bunch, and never flinched. … I know guys do believe in CJ. I don’t have to convince them of that. That’s a good thing.”

“It’s huge having already played last year in six games,” Beathard said after Sunday’s game. “That helps me going forward.  Second time around, I think it will be a little easier.”

Beathard has yet to play an official down this season. He threw a touchdown pass to George Kittle upon replacing Garoppolo on Sunday but that play got nullified by a pass-interference penalty.

Veteran nose tackle Earl Mitchell added: “He’s a tough guy. He’s been doing well. He’s wise beyond his years, that’s a tribute to Kyle and John Lynch in the type of guys they bring in to our locker room.”

 

QUARTERBACK: San Francisco 49ers C.J. Beathard (3) is all smiles as he waits to be interviewed after defeating the New York Giants during their NFL game at Levi’s Stadium in Santa Clara, Calif., on Sunday, Nov. 12, 2017. San Francisco defeated New York 31-21. (Jose Carlos Fajardo/Bay Area News Group) 

Backing up Beathard will be Nick Mullens, who will be elevated from his second season on the practice squad after going undrafted out of Southern Miss. Mullens completed 72.1 percent of his passes this past exhibition season; Beathard completed 60 percent.

Three weeks ago, the 49ers were reeling from the loss of another offensive stalwart to an ACL tear: running back Jerick McKinnon, who tore his in a non-contact drill at practice Sept. 1. Now McKinnon and Garoppolo will team together in their rehabs.

Said Shanahan: “That was the only good news that Jimmy and I could talk about on the plane: at least he’s got a buddy to go through it with. They’re both in the same boat.”

Sunday’s loss marked only the second in 10 career starts by Garoppolo. He was 20-of-30 for 251 yards with two touchdown passes for a 114.7 passer rating against the Chiefs. He got sacked four times, and he had three carries for 23 yards, including a fourth-and-1 keeper on his final drive.

His third-and-goal run is what resulted in one of the most devastating injuries in 49ers history.

“I think it was his fault,” Chiefs linebacker Justin Houston told ESPN after the game. “I pray he’s not hurt or nothing serious. as a quarterback you should step out of bounds. An inch wouldn’t have made a difference. You’ve got to be smart, think about your team.”

Shanahan agreed, to an extent. He noted that quarterbacks are coached to go out of bounds and avoid contact, although they’re also glorified when they “do a little extra to move the chains.”

“That’s something Jimmy will probably look at differently going forward, because I know he’ll remember this the rest of his life,” Shanahan said. “Nothing against him. It happens with everyone. You see it every Sunday. It’s a reminder for everyone why (going out of bounds) is the obvious coaching point.”

Said left tackle Joe Staley on Sunday: “Jimmy’s just trying to be a ballplayer and trying to make a play. He wasn’t running out of bounds. He was trying to get some extra yards for his team.”

— Cornerback Richard Sherman will miss a few weeks with a strained left calf that Shanahan said is not related to offseason surgery that removed bone spurs from that leg. Sherman also had to rehabilitate a ruptured Achilles in his right leg this offseason. He came out after four series against the Chiefs and left the locker room in an orthopedic boot.

— Running back Matt Breida hyperextended his knee and has calf soreness, so he will be questionable this week. Breida shares the NFL’s rushing lead with Dallas’ Ezekiel Elliott. Alfred Morris, who’s platooned with Breida, briefly went out in the fourth quarter with an ankle and will be rechecked Wednesday.

— Other injuries the 49ers are monitoring: safeties Adrian Colbert (hip) and Jaquiski Tartt (shoulder stinger), and guards Mike Person (sprained foot) and Joshua Garnett (toe).

— The 49ers defense missed 17 tackles Sunday and that raised their NFL-high total to 43 this season, according to Pro Football Focus, which ranked linebacker Fred Warner with the second-best run-stopping percentage this season.