SANTA CLARA, Calif. — San Francisco 49ers defensive end Ray McDonald was cut Wednesday when the team received word that the 30-year-old was named by the San Jose Police Department as a suspect in an alleged sexual assault that occurred at his house.

“While this organization has a strong belief in due process and has demonstrated that over time, Ray has demonstrated a pattern of poor decision-making that has led to multiple distractions for this organization and this football team that really can no longer be tolerated,” 49ers general manager Trent Baalke said.

McDonald was questioned following a domestic-dispute incident on the eve of the season in August. The 49ers opted not to suspend or punish their starter in any way that time, allowing due process to take its course.

Last month, the Santa Clara County District Attorney’s Office determined no charges would be filed.

The alleged victim in the August incident reportedly was McDonald’s fiance. She is not the accuser this time, NBC reported.

According to the report, McDonald’s house was searched late Tuesday night. No charges have been filed.

“Ray and I had multiple conversations since the latest allegations and put together some criteria we felt he needed to do in order to stay in good standing,” Baalke said. “With these latest allegations, it was just one more situation that we just weren’t willing to deal with anymore.”

McDonald had three more non-guaranteed seasons remaining on his contract.

Meanwhile, the 49ers will push through their final two games of the season starting Saturday against the San Diego Chargers, who, unlike the 49ers, are still alive in the playoff chase.

It is the 13th regular-season meeting and the series tied, 6-6.

The Chargers have dominated recent matchups with the 49ers, having won the last three, including 34-7 at San Diego in their most recent head-to-head four seasons ago.

The 49ers haven’t beaten their in-state rival since 2000, but do have a win in their most important meeting with the Chargers — 49-26 in Super Bowl XXIX in Miami in 1995. 49ers coach Jim Harbaugh has lost only one home game to an AFC team in four years.

–Harbaugh has one year remaining on a contract that’s scheduled to pay him $5 million next season.

According to a report by the NFL Network’s Ian Rapoport, the University of Michigan would like to give him a huge pay raise.

The Wolverines have offered Harbaugh a six-year, $48 million contract to be their next football coach, according to the report.

The only way Harbaugh could accept the offer would be if he were fired by the 49ers or if he reached a buyout agreement with the club.

With Harbaugh under contract, the 49ers also retain the right to trade him to another NFL club. If that were to occur, he would take his $5 million contract with him.

Harbaugh earned Big Ten Conference Player of the Year honors as the Michigan quarterback in 1986.

NOTES: Among those not practicing Wednesday were RB Frank Gore (concussion) and RB Carlos Hyde (ankle). RB Alfonso Smith practiced with the first team and RB Phillip Tanner, a fourth-year veteran, was signed. Also not practicing were WR Michael Crabtree (knee) and WR Steve Johnson (knee), OT Anthony Davis (concussion), LB Ahmad Brooks (thumb) and CB Tramains Brock. … TE Garrett Celek (ankle) was placed on injured reserve. … LB Desmond Bishop signed Tuesday and practiced Wednesday and will be listed as the backup to both starting inside linebackers — Michael Wilhoite and Nick Moody. … TE Xavier Grimble and CB Cameron Fuller were added to the practice squad Tuesday.