"It will be at least a month, probably longer," Shanahan shared.
The injury pushes rookie Malik Mustapha into the spot alongside second-year safety Ji'Ayir Brown. Mustapha has shown promise in his first NFL season, and 49ers coaches are eager to see how the rookie handles the expanded role.
Mustapha started two weeks ago against the New England Patriots, playing every defensive snap and five on special teams. Last Sunday, he played 81 percent of the snaps against the Arizona Cardinals after Hufanga and Brown were both sidelined with injuries, though Brown later returned to the game.
On Tuesday, Shanahan assessed Mustapha's progress and was asked about the rookie's ability to handle the communication responsibilities that come with playing in the NFL.
"I think communication is one of the hardest things, especially for a young guy coming in," Shanahan responded. "I think he's been getting better at that the more he's been out there. I think, just his lack of not hesitating. I think you guys saw that a little in preseason, just with some of the hits he had. Especially, you saw a couple in that Tennessee game, from what I remember.
"And when he's come in, he's done the same stuff. I think he gets faster each week, just recognizing things and not breaking down and trying to run through his tackles."
A fourth-round draft pick out of Wake Forest, Mustapha has already recorded 11 tackles and two passes defensed. His 72.2 run defense grade from Pro Football Focus in Week 4 against the Patriots—where he played all 64 defensive snaps—stands as his best so far. While his grades in other areas haven't been quite as high—including an abysmal 39.7 tackling grade—additional experience may help him round out his performance.
"I feel like I've been more comfortable with the reps these past few weeks, and the game is starting to slow down for me," Mustapha said on Tuesday. "So now, it's about how can I take my game to the next level, about being more consistent. And the guys, even though I'm a rookie, the coaching staff and my teammates have enough faith in me, and I have to have that same faith in myself in order to execute at a high level."
Defensive coordinator Nick Sorensen also highlighted Mustapha's growth as the season progresses.
"I think his strides have come just because he has played a lot," Sorensen remarked. "I mean, we've had a lot of guys play and I think it's good that guys gain knowledge through getting their snaps. And for him, it's just being comfortable being out there.
"I think I've mentioned before, like with safeties, it's that comfort to communicate and the feel of the game and the flow of the game and how it moves and how you have to be a leader back there behind our backers that you can communicate across the board and be tied in. And I think he's done a good job with that."
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