SANTA CLARA – San Francisco star receiver Brandon Aiyuk wasn’t at the start of practice on Wednesday despite the team saying he was cleared by doctors to participate, raising the temperature of a contract “hold in” that has been a cloud over the 49ers since the offseason.

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Aiyuk’s Absence Raises Questions

Aiyuk had refused to practice all training camp as he seeks a long-term extension or a possible trade, with coach Kyle Shanahan citing a back injury as the official reason for what is essentially a contract dispute.

Both Shanahan and general manager John Lynch said before practice that Aiyuk had been cleared by team doctors and the expectation was that he would practice. But Aiyuk was not on the field during the portion open to reporters.

Aiyuk had avoided fines in training camp by reporting to the team and attending meetings but could be subject to punishment now that he isn’t practicing after being cleared by doctors.

“At some point, you have to play,” Lynch said.

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Potential Consequences for Aiyuk

According to the collective bargaining agreement, players are subject to fines for missing mandatory practices with those increasing to $16,009 a day by the third offense. Players can also be fined for missing meetings, walkthroughs or other mandatory sessions with the maximum for one day reaching $45,769.

Players can be suspended for up to four weeks without pay for “conduct detrimental to the team” if there is a pattern of misbehavior.

Shanahan said punishment is possible if the situation isn’t resolved soon.

“I’ll deal with that when that happens, if that happens,” he said.

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Contract Negotiations and Market Value

Aiyuk had been set to play on the fifth-year option worth about $14.1 million this season and wanted San Francisco to make him the latest receiver to cash in with a long-term deal or trade him to a team of his choosing that would pay him. Eleven receivers before Aiyuk had signed contracts worth at least $70 million already this offseason with Justin Jefferson’s four-year, $140 million extension with Minnesota setting the top of the market.

Aiyuk had been a key part of San Francisco’s offense last season as he formed a great connection with quarterback Brock Purdy. Aiyuk had 75 catches and a career-high 1,375 yards last season with seven touchdowns as he earned second-team All-Pro honors.

Other 49ers Contract Situations

The Niners are also without All-Pro left tackle Trent Williams, who has been holding out since the start of training camp in search of a new deal. Williams, who is owed about $20 million this year, has accrued more than $4.5 million in mandatory fines.

Lynch said there has been “good communication” with Williams’ camps with both sides proposing ideas but no breakthroughs as of yet.

“I’m optimistic that things will work out with Trent,” Shanahan said. “I’m not sitting here knowing what day it’ll be. We’re getting close to playing a game, so my mind is completely on preparing for the game without those guys. I feel like if two sides want to get a deal done usually it happens.”

Shanahan has said all options remain open with Aiyuk, including a possible trade, an extension or Aiyuk playing out the season on his fifth-year option.

“I’ve seen these things look dire before and they can quickly turn,” Lynch said. “So that gives you hope, that we’ve been in these situations before and those things can quickly be forgotten. We will remain hopeful.”

NOTES: Safety Talanoa Hufanga participated in individual drills in his first practice after a season-ending knee injury last November. … RB Elijah Mitchell re-injured his hamstring on Monday and will undergo season-ending surgery. … Rookie RB Isaac Guerendo tweaked his groin on Monday and won’t practice this week. … LG Aaron Banks (broken pinky) is expected back at practice next week and is on track to play in the opener. … The Niners placed OL Jon Feliciano (knee) and CB Ambry Thomas (forearm) on IR and waived DL Sam Okuayinonu to create room on the roster to bring back OL Ben Bartch, TE Eric Saubert and CB Rock Ya-Sin, who were all cut Tuesday.