SANTA CLARA, Calif. -- The San Francisco 49ers have a new man in charge of personnel decisions merely one month before draft day.
Scot McCloughan is out as the 49ers' general manager in what team president Jed York called a "mutual parting," and director of player personnel Trent Baalke will lead the team into next month's draft.
York, speaking Monday in a conference call from the NFL Annual Meeting in Orlando, Fla., said the move is 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 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. ... Trent knows the draft better than anybody else, and I have full confidence in him."
York, who's also the team's chief executive officer, addressed the situation five days after news broke that McCloughan was on his way out of San Francisco. York said the team "had been prepared for this," but that he told McCloughan he would wait to announce it for five days.
"I gave Scot my word I wouldn't comment on this for five days," York said. "My integrity is more important to me than trying to get out a story. I gave Scot five days to think about where we wanted to go, and we decided to have a mutual parting."
When asked why McCloughan wanted to leave the organization, York said, "You'd have to ask Scot."
A call to Peter Schaffer, McCloughan's representative, wasn't immediately returned Monday.
"It's a mutual parting in the interest of both the 49ers and Scot," York said. "We've been prepared. I wanted to make sure Trent was as up to speed as possible. He's taken on more responsibility in the past, and again, I'm confident that he can lead us through this draft and move us forward."
York wouldn't say Monday whether a financial settlement is involved -- and he believes McCloughan could work in the NFL again one day.
 For more on the San Francisco 49ers, check out the latest from our bloggers.
"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 49ers' draft board is nearly done, and Baalke has been "intimately" involved in setting it, York said. He also plans to be in the draft room April 22.
York didn't provide a timeline or definitive answer about whether he would even hire a new GM.
"I haven't decided if we're going to have a general manager," he said. "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."
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 executive vice president of football and business operations Paraag Marathe are all people the 49ers have depended on for big decisions.
York said McCloughan's younger brother, David, is still with the organization in the college scouting department.
"David is a professional," York said. "He has been great through this process and he will continue to be into the draft."
The 49ers hired Scot McCloughan in February 2005 to supervise their personnel department for Mike Nolan, a career assistant coach who was given total control of 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 the Green Bay Packers and Seattle Seahawks. He had a mostly solid record during his years with the 49ers, compiling a young talent base that steadily improved for most of his five-year tenure -- yet the 49ers still didn't reach the playoffs. Their 8-8 record last season was their best since 2002.
McCloughan was hired as GM in January 2008 when the 49ers nominally gave him authority over Nolan instead of firing the coach after the 49ers' third consecutive losing season. Nolan lasted just seven more games, with Jed York abruptly replacing him with Mike Singletary during the 2008 season.
Singletary had the interim tag removed from his title before last season, when the 49ers ended a franchise-worst stretch of six consecutive losing seasons. York gave no indication that Singletary would take on a greater role with McCloughan out.
"Mike is concentrating on coaching," York said.
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 to be their team president in late December 2008.
York assumed the new role of chief executive officer in a January reorganization of the 49ers' front office and business department. Also, Andy Dolich left the team as chief operating officer but was to remain a senior adviser to York during the transition.
Copyright 2010 by The Associated Press