Tony Gutierrez/AP PhotoSan Francisco 49ers defensive lineman Ray McDonald is under investigation for sexual assault.

Tony Gutierrez/AP PhotoSan Francisco 49ers defensive lineman Ray McDonald is under investigation for sexual assault.

49ers release McDonald amid further legal trouble

SANTA CLARA — Citing a pattern of behavior and off-field issues, San Francisco 49ers general manager Trent Baalke informed defensive lineman Ray McDonald that he was released Wednesday amid a sexual assault investigation by San Jose police.

Baalke spoke with McDonald and his agent by phone around 11:30 a.m. PST to let them know the defender is “terminated”

“After the recent allegations concerning Ray McDonald, we as an organization notified him and his agent that he will be terminated, released immediately, effective immediately,” Baalke said. “While this organization has a strong belief in due process and has demonstrated that over time, Ray's demonstrated a pattern of poor decision-making that has led to multiple distractions to this organization and this football team that really can no longer be tolerated.”

Baalke said CEO Jed York and coach Jim Harbaugh also were involved in the decision.

“We expect a lot from our players, hold them accountable for their actions,” Baalke said. “This is a situation that we can all learn from.”

Baalke said the 49ers notified the NFL of the allegations against McDonald, saying: “This is a team decision. This is not a league decision.”

San Jose police Sgt. Heather Randol said Wednesday that the department is investigating McDonald on suspicion of sexual assault and had searched his San Jose home.

Randol said an area hospital notified police late Tuesday night that a woman was seeking treatment.

“The victim alleged she was possibly sexually assaulted a day prior,” Randol said. “Based on preliminary investigation, detectives secured a search warrant and served it at the alleged suspect's residence in San Jose.”

Randol didn't immediately respond to follow up questions seeking to clarify the reference to the alleged victim saying she was “possibly” sexually assaulted.

No arrests have been made nor charges filed. McDonald's agent, Tom Condon, didn't immediately return a call seeking comment.

McDonald's mother, Labrina McDonald, told the San Jose Mercury News the allegation was “laughable” and not true.

She said her son warned her not to talk to the media, but she told the paper that “there's no truth to that stuff.”

NFL spokesman Greg Aiello said the league is “looking into” the case.

York spoke to the 49ers players about two weeks ago about conduct before NFL owners unanimously approved changes last week to the league's personal-conduct policy — and “it was clear” what the expectations are with the 49ers, linebacker Dan Skuta said.

“You just really don't know what to believe, so I'm not getting mad at Ray,” Skuta said. “Obviously you want him here with you and you're a little upset he's not here. I have no business getting upset with him for something that he may or may not have done.”

This is the second time in recent months that McDonald has been the subject of a police investigation.

Last month, the Santa Clara County district attorney's office announced that it declined to file charges against the defensive lineman in a domestic violence investigation. He was arrested Aug. 31 while celebrating his then-upcoming 30th birthday at his home.

Following the arrest, York, Baalke and Harbaugh repeatedly said they have zero tolerance for domestic violence. The 49ers stuck by McDonald throughout the investigation, with Harbaugh regularly saying that “due process” would play out. He played despite outside pressure on Harbaugh and the organization to bench him.

Prosecutors cited conflicting versions of what happened, a lack of verifiable eyewitnesses and a lack of cooperation by the alleged victim, McDonald's fiancee, in explaining their decision not to pursue charges in the domestic violence investigation.

McDonald received a five-year contract in July 2011 and he was one of the top players Baalke had wanted to bring back long term.

“Like you would expect, extremely disappointed,” Baalke said. “We drafted Ray in the third round. He's been an awful good football player and for the most part, has been a tremendous asset to this organization and this community. He has made some poor decisions. He's aware of that. This is a case of being accountable for those decisions.”

McDonald was signed through the 2015 season. He had 26 tackles and three sacks in 14 games this season.

Harbaugh notified the players Wednesday of McDonald's dismissal. An eight-year NFL veteran, McDonald has been a key member of one of the NFL's fiercest front seven units.

“Not a situation you want to hear about, very unfortunate,” quarterback Colin Kaepernick said. “He just brought us together and let us know what the situation was and why he was released. It's tough. He was a good friend to a lot of people on this team. No one around him ever thought bad of him. He was always a good person to everyone around here. Hopefully it's just a misunderstanding.”

49ersNFLRay McDonaldSan Francisco 49ers

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