SANTA CLARA, Calif. — Scot McCloughan is out as the general manager of the San Francisco 49ers in a “mutual parting,” and director of player personnel Trent Baalke will lead the team into next month’s draft.

Team president Jed York, speaking Monday in a conference call from the owners meetings in Orlando, said it’s in the best interest of both parties and called it a “private personnel matter.” He didn’t elaborate on what went wrong for McCloughan, except to say it had more to do with the GM’s personal issues than anything on the personnel, football side of things.
“Trent is leading us into the draft,” York said. “Trent is the point person in the draft. He is making draft decisions. ... I have full confidence in him. I haven’t decided if we’re going to have a general manager. I’m worried about the draft right now. That’s the only thing that the 49ers are focused on. We’ll address that after the draft.”
York, also the team’s chief executive officer, addressed the situation five days after news broke that McCloughan was on his way out. York said the team “had been prepared for this” but that he told McCloughan he would wait to announce it for five days.
Several reports last Thursday said the Niners were cutting ties with McCloughan because of personal issues, though the GM’s agent said at the time that he had not been informed. A call to Peter Schaffer, McCloughan’s representative, wasn’t immediately returned Monday.
York wouldn’t say whether there is a financial settlement involved — and he believes McCloughan could work in the NFL again one day.
“I wish nothing but the best for Scot,” York said. “I think Scot is a very good personnel guy. I care about Scot from a personal standpoint and I hope Scot gets a job somewhere. I wish nothing but the best for he and his family.”
The team’s draft board is nearly done and Baalke has been “intimately” involved in setting that board, York said. He also plans to be in the draft room April 22.
In January, York assumed the new role of chief executive officer in a reorganization of the team’s front office and business department. In addition, Andy Dolich left the team as chief operating officer but was to remain a senior adviser to York during the transition.
The 49ers hired McCloughan in February 2005 to supervise their personnel department for Mike Nolan, a career assistant coach who was improbably given total control of the club’s football operations by owner John York, Jed’s father and the brother-in-law of former owner Eddie DeBartolo.
McCloughan is a former minor-league baseball player who became a respected young personnel executive during stints with Green Bay and Seattle. He has a mostly solid record during his years with the 49ers, compiling a young talent base that has steadily improved for most of his tenure — yet the 49ers still haven’t reached the playoffs in five seasons since his arrival. Their 8-8 record last season was their best since 2002.
McCloughan was hired as general manager in January 2008 when the 49ers nominally gave him authority over Nolan instead of firing the coach after the 49ers’ third straight losing season. Nolan lasted just seven more games, with Jed York abruptly replacing him with Mike Singletary during the 2008 season.
The 49ers were similarly mysterious about Nolan’s departure, waiting several hours to acknowledge it — well after Nolan already had told reporters he was out.
The 49ers would have several in-house candidates to assume McCloughan’s responsibilities, though York is still undecided on how he will move forward. Baalke, director of pro personnel Tom Gamble, and Paraag Marathe, the 49ers’ executive vice president of football and business operations, are all people the Yorks have depended on for big decisions. Baalke was promoted to his job in February 2008 after a stint as a scout, while Gamble has been with the 49ers since McCloughan arrived.
Jed York has eagerly taken control of the franchise from his much-criticized father over the past two years. The 49ers selected the then-27-year-old York their team president in late December 2008.
McCloughan had the final say on the 49ers’ last two drafts, but Singletary told reporters at the NFL scouting combine last month the club would make its draft-day decisions according to players’ rankings on an overall draft board, not on the gut feelings of any team executives.