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49ers coach Jim Harbaugh misses practice because of minor medical procedure

San Francisco 49ers coach Jim Harbaugh during first half NFL preseasfootball game against San Diego Chargers Thursday Sept. 1 2011

San Francisco 49ers coach Jim Harbaugh during the first half of a NFL preseason football game against the San Diego Chargers Thursday, Sept. 1, 2011 in San Diego. (AP Photo/Gregory Bull)

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Even San Francisco 49ers coach Jim Harbaugh missed practice Thursday. It’s been that kind of week for the 49ers and the Bears in preparation for their game on Monday Night Football.

Harbaugh, 48, underwent what the 49ers called a ‘‘minor procedure’’ for an irregular heartbeat at Stanford Hospital in Palo Alto, Calif. Special teams coach Brad Seely conducted practice.

‘‘Coach Harbaugh is not at the facility today under doctor’s orders,’’ the 49ers said in a statement. ‘‘We anticipate that he will be back at the facility tomorrow, but do not have any further information to share at this time.’’

Harbaugh’s absence caught his players by surprise.

‘‘We just heard about it actually, a couple of minutes ago ourselves,’’ defensive end Justin Smith said on a conference call with Chicago-­area reporters early Thursday afternoon. ‘‘Prayers are with him and they said it’s no big deal, just a minor procedure and everything should be fine and he’ll be back at work [Friday].’’

Harbaugh’s medical condition is the latest twist in an odd week of preparation for a prime-time game. Neither team knows which quarterback it will face, with the Bears’ Jay Cutler and the 49ers’ Alex Smith recovering from concussions.

While the Bears are likely to be without Cutler, who did not practice Thursday, Smith practiced on a limited basis and could start for the 49ers. He still needs to be cleared by team doctors before he can play in a game.

Smith is third in the NFL in passer rating (104.1) behind the Broncos’ Peyton Manning (108.0) and the Packers’ Aaron Rodgers (107.4). He is 20-5 as a starter.

While both coaches would rather have their No. 1 quarterback starting, the indecision also creates a cat-and-mouse game coaches never mind playing against each other.

“It helps if you know ­exactly who you’re preparing for,’’ coach Lovie Smith said. ‘‘There’s an advantage on our part if they don’t know that Jay’s playing. There’s an advantage on their part that we don’t know if Smith is playing.

Does it really make a difference?

‘‘You look at that a little bit, but eventually you get to trying to defend the quarterback position,’’ Smith said. ‘‘That’s what we’re doing. They’re going to have somebody underneath center that we’ll have to be able to contend with.”

Second-year quarterback Colin Kaepernick will start if Smith cannot play. The 6-4, 230-pound Kaepernick, a second-round draft pick from Nevada in 2011, replaced Smith in the second quarter of a 24-all tie with the Rams last week and was 11-for-17 for 117 yards and no touchdowns. He also rushed for 66 yards on eight carries and scored on a seven-yard run,

“[When] he came out of college, he did a bunch of different things in the running game. But he throws it really well,’’ linebacker Brian Urlacher said. ‘‘He’s got a really good arm. He obviously scrambles well. He’s fast. They do some of that read-option stuff that Carolina did with Cam [Newton]. It’s just a different change-up with them. They do that stuff with Alex Smith as well because they’re both fast guys.’’

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