Coach Kyle Shanahan has not closed the door on Brandon Aiyuk’s return to the field for the 49ers this season.

The 49ers voided guaranteed money in Aiyuk’s contract months ago, Shanahan confirmed on Saturday afternoon.

And Aiyuk continues physical therapy more than a year after sustaining tears to his ACL, MCL and cartilage in his right knee during a Week 7 game.

When asked about Aiyuk’s current status, Shanahan said Aiyuk remains “week to week.”

He added, “Hoping he can clear all his markers, so he can come back and start his practice window.”

Shanahan declined to get into the specifics of what prompted the 49ers to void the future guarantees.

“There were a number of things that happened in July that to me was more of a business side, dealing with lawyers and stuff and contracts, stuff that is really not my area of expertise,” Shanahan said.

Shanahan said he has not had a lot of recent communication with Aiyuk. He said those conversations were held shortly after the team reported for training camp.

“I talked to him a lot about it back in July,” Shanahan said. “But since July, it’s been all about this season and hoping he would get healthy, and he’s been working to get healthy. And I’ve been waiting for him to come back when he gets healthy.”

Aiyuk chose not to file an official grievance through the players union, The Athletic reported on Friday. In addition to having his future guarantees voided, Aiyuk also incurred multiple team-imposed fines, a source told NBC Sports Bay Area.

What it means is that the 49ers are no longer obligated to pay his formerly guaranteed option bonus of $24.935 million. Aiyuk would have been paid $27 million, including salary and bonuses, for the 2026 NFL season.

Now, the 49ers do not owe him any money beyond this season, and they are expected to part ways with Aiyuk in the offseason. Shanahan expressed a desire to have Aiyuk remain with the team but admitted feeling disappointment with how the situation has turned.

“I’ve been coaching over 20 years, and I’ve never been in a situation where a contract has been voided, so it was extremely unusual to me,” he said.

“Any time you have a good player that has been a part of this team, that guys have really loved and coaches included, and it’s frustrating that it’s not happening right now.”

Aiyuk, 27, would count nearly $30 million based on money already paid but has yet to count against the salary cap. That cap space can be spread out over two seasons.

Aiyuk sustained a severe knee injury in the 49ers’ seventh game last season after he signed a four-year, $120 million contract extension. Now, that contract, it appears, will amount to a two-year, $48.9 million deal.

He remains on the physically-unable-to-perform list. He is eligible to return to play this season, but the 49ers have yet to open his practice window.

“When you have such a big injury like that, you wait until he’s fully comfortable to come up and start practicing,” Shanahan said Monday.

Aiyuk earned the big-money extension — after a contentious few months of negotiations — with back-to-back 1,000-yard seasons.

Aiyuk had 78 receptions for 1,015 yards and eight touchdowns in 2022. He was the team’s top receiver the following year, as he caught 75 passes for 1,342 yards and seven touchdowns.

He entered the NFL as a first-round draft pick (No. 25 overall) from Arizona State. In 69 career games, Aiyuk has 294 receptions for 4,305 yards and 25 touchdowns.

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