When the 49ers signed Jimmy Garoppolo to a lucrative, long-term extension in the offseason, it was presumed the team’s top two quarterbacks were set through the 2020 season.

Now, C.J. Beathard’s long-term spot as the 49ers’ backup looks tenuous. Nick Mullens will make his third consecutive start on Sunday when the club returns from the bye week to play at the Tampa Bay Buccaneers.

“Here’s how my thinking’s changed: I think we have three now,” Lynch said on The 49ers Insider Podcast.

Garoppolo’s season came to an abrupt end in Week 3 when he sustained a torn anterior cruciate ligament in his left knee. The 49ers expect Garoppolo to come back strong in 2019 after continuing to learn from coach Kyle Shanahan and quarterbacks coach Rich Scangarello while rehabbing his knee.

“I think we have one special guy in Jimmy Garoppolo,” Lynch said. “I have all the belief in the world in him, as does Kyle. We’re real proud of the way he’s using this as an opportunity, not only to get healthy, which takes a ton of time with an ACL, but he’s also using this as an opportunity to grow his game in the film room.

“We believe, as we did when we committed to him long term, that he’s going to be the guy for years to come at that position.”

Beathard took over for Garoppolo and started the next five games, all 49ers losses. After averaging 297.3 yards passing in his first three starts, Beathard struggled in losses to the Los Angeles Rams and Arizona Cardinals. He was sacked 11 times in those two games.

“I think at some point when you’re struggling, there’s a little regression,” Lynch said. “I think C.J. was going through that. Nick came in and gave us a lift. But I think that was also good for C.J. to get to back off, kind of take things in and really, frankly, learn some things from Nick -- the way he’s getting rid of the football on time.”

Mullens has yet to be sacked while attempting 61 passes in two games. Beathard was sacked 18 times with 169 pass attempts, while Garoppolo was sacked 13 times with 89 pass attempts.

Mullens spent last season and the first three games this year on the practice squad before receiving the promotion to the 49ers’ 53-man roster.

In starts against the Raiders and New York Giants, Mullens has completed 70.5 percent of his passes for 512 yards with four touchdowns, two interceptions and a passer rating of 104.0.

“I’ve told a lot of these players, Nick is a great example of working, such that, when your opportunity presents itself, you’re ready and good things come from that,” Lynch said. “I talked to my own kids about that. Nick Mullens is a great story because of the way he goes about his work each and every day.”