SANTA CLARA — The San Francisco 49ers set their initial 53-man roster for the season with one key piece missing.

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All-Pro left tackle Trent Williams remained on the reserve/did not report list Tuesday after the defending NFC champion 49ers made their mandatory roster cuts as he seeks an improved contract.

Among the other notable moves made on cutdown day included San Francisco activating safety Talanoa Hufanga from the physically unable to perform list after he had a season-ending knee injury last November. Hufanga will return to practice Wednesday and can play without sitting out the first four games.

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Key Players on Injury Lists

Linebacker Dre Greenlaw (Achilles tendon) will start the season on the PUP list as expected after getting hurt in the Super Bowl. Defensive tackle Kalia Davis (knee) was placed on IR with the designation to return after missing at least four games and running back Elijah Mitchell was placed on season-ending IR with an undisclosed injury.

Williams has held out of the entire training camp as part of a contract dispute, accruing more than $4 million in fines for missing every practice and three exhibition games. The 36-year-old Williams is owed $20.05 million this season under the six-year, $138.1 million deal he signed in 2021.

Williams’ average annual value of just over $23 million has been surpassed by five offensive linemen since he became the richest player at the position when he signed the deal. Tristan Wirfs, Penei Sewell and Christian Darrisaw all got deals this offseason worth at least $26 million a year.

Williams has been widely considered the top offensive linemen in recent years. He has been the All-Pro left tackle the past three seasons and has been a major reason for San Francisco’s offensive success.

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Contract Disputes and Roster Moves

Williams isn’t the only prominent 49ers player dealing with a contract dispute. Star receiver Brandon Aiyuk has refused to practice all summer as he seeks a new deal to replace the $14.1 million fifth-year option he was supposed to play on this season.

Aiyuk has been with the team all of camp to avoid fines but won’t practice until he gets a new deal or is traded. Aiyuk remains on the 53-man roster that was set Tuesday while contract and trade talks continue.

Among the players cut on Tuesday were two recent third-round picks with receiver Danny Gray (2022) and tight end Cameron Latu (2023) both waived. Gray had one catch in two seasons and Latu missed all of last season with an injury.

The Niners also cut 2023 seventh-round linebacker Jalen Graham and tight end Brayden Willis, 2022 fifth-round cornerback Samuel Womack, and 2024 sixth-round offensive lineman Jarrett Kingston. The other seven members of this year’s draft class made the initial roster.

Among the noteworthy veterans cut were offensive linemen Chris Hubbard and Ben Bartch; receivers Robbie Chosen and Trent Taylor, defensive tackle T.Y. McGill, tight ends Logan Thomas and Eric Saubert; and cornerback Rock Ya-Sin.

Offensive lineman Jon Feliciano (knee) and cornerback Ambry Thomas (hand) made the roster but will likely move to IR on Wednesday to create two open spots.