SANTA CLARA – Alex Boone is making a big mistake.

Boone is the only 49er holding out of training camp. The 27-year-old guard wants a new contract. You can understand why.

He signed his current deal at the end of the 2011 season when he was a backup tackle. The 49ers gave him a four-year contract and $1.7 million guaranteed. Then in 2012, the 49ers made Boone the starting right guard after the previous right guard, Adam Snyder, signed with the Arizona Cardinals during the offseason.

And Boone was great, much better than Snyder had been in 2011. Pro Football Focus ranked Boone the third-best guard in the NFL in 2012, Boone’s first full season starting in the NFL. He was 25 years old, an up-and-comer. But he earned just $540,000 in base salary that season. The guard who Pro Football Focus ranked second-best in 2012 was Marshal Yanda, and he earns an average of $6.4 million annually.

Boone is a terrific run blocker, better than Yanda. Boone plays tackle, too. That’s part of his value. If Joe Staley ever gets injured, Boone takes his place at left tackle, the most important position on the offensive line.

Staley missed most of Week 13 against the Rams last season. Boone played left tackle and faced the Rams’ top pass rusher, Robert Quinn, who finished the year with 19 sacks. Boone didn’t give up any that day.

Boone deserves a raise more than anyone on the 49ers, more than Vernon Davis, who also wants a new contract. Davis is the fourth-highest paid tight end in the NFL. His average base salary is more than $7 million per year. He has earned more than $60 million during his professional career.

But Davis has leverage and Boone doesn’t. The 49ers cannot replace Davis. He’s a key blocker in the running game, and his speed stretches opposing defenses and creates space for Michael Crabtree and Anquan Boldin to get open underneath in the passing game.

Davis is a Pro Bowl player, a franchise player, possibly a future Hall of Famer, and he did not want to try to face down the 49ers in an acrimonious holdout.

Boone is not a bad guy. It would be wonderful if things worked out for him and the 49ers renegotiated his deal. You always pull for the underpaid guy. But he and his agent are reading the 49ers all wrong. If Davis couldn’t face down the 49ers, Boone has no chance.

Boone is not a franchise player, not a star player. He is a guard. Guards are replaceable. As good as Boone is, the 49ers wouldn’t lose much without him. The 49ers did fine without Boone in 2011. Snyder was the right guard, the 49ers won 13 games and the rushing attack ranked eighth in the NFL.

Snyder is back – he re-signed with the 49ers in 2013. And he improved last season, especially as a run blocker. He played 424 snaps and held his own.

Boone regressed last season, especially as a pass protector, and overall was not much better than Snyder. Pro Football Focus ranked Boone as the 39th-best guard in the NFL, and they ranked Snyder No.40.

You can bet the 49ers have plenty of backup plans if Boone continues to holdout. Snyder is one. Joe Looney is another. The 49ers drafted him in the fourth round of the 2012 draft.

And there is Jonathan Martin, whom the 49ers signed this offseason. He’s former second-round pick and he’s a tackle. Boone was a tackle before the 49ers moved him to guard. Martin is talented enough to make the transition, too.

Boone’s situation will get worse every day he holds out. A lineman needs camp. A lineman needs contact. A lineman needs pass protection drills. A lineman needs the weight room and a conditioning program. Why would the 49ers capitulate to a guard who isn’t in football shape?

Maybe the 49ers would trade Boone. Maybe another team would want him long-term and would trade the 49ers a fourth-round pick for him and renegotiate his contract. Maybe.

But the odds of that happening decrease as Boone holds out. Teams can’t count on Boone to play well this season if he doesn’t attend training camp. Boone does not have an extensive track record of success. He has had one dominant season and one decent season and that’s it. He needs all the practice he can get.

He needs to get his butt in camp. That’s his best move. That’s his only move.

Grant Cohn writes sports columns and the “Inside the 49ers” blog for The Press Democrat’s website. You can reach him at grantcohn@gmail.com.