Niners coaches told McCloughan could be gone for extended period

The San Francisco 49ers have made preparations to move on without general manager Scot McCloughan for an indefinite period -- and perhaps for good.

McCloughan isn't operating in a management position for the team, and he hasn't been in the 49ers' facility in Santa Clara, Calif., as part of the day-to-day operations, NFL Network's Jason La Canfora reported Friday. Director of player personnel Trent Baalke will handle many of the GM duties while McCloughan is gone.

Team management apprised coaches this week that McCloughan's departure from the 49ers could be for an extended period, league sources told La Canfora. The meeting was brief and emotional, according to sources, with owner/team president Jed York, a longtime supporter of McCloughan, explaining the situation.

McCloughan's departure is because of a personal issue, sources told La Canfora, and isn't football related. The 49ers haven't commented on the situation, and McCloughan's agent, Peter Schafer, also has declined comment.

McCloughan hasn't spoken in person about the situation, but he sent text messages to reporters Thursday and Friday.

To SIRIUS NFL Radio's Adam Schein: "Family needs to come first and I lost sight of that with my position at the 49ers. I will be back in league at some point and be very successful."

To the San Jose Mercury News' Tim Kawakami: "It was a great run. Players I brought in will win division for next couple of years."

And to the Sacramento Bee's Matthew Barrows: "I know what I did for the organization and I'm really good with it."

McCloughan remains listed as the 49ers' GM on the team's official Web site.

The timing -- in the middle of free agency and with the NFL draft next month -- has led to much speculation about the reasons for the move.

McCloughan had the final say on the 49ers' last two drafts, but coach Mike Singletary told reporters at the NFL Scouting Combine last month that the team would make its draft-day decisions according to players' rankings on an overall draft board, not on the gut feelings of any team executives.

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The 49ers hired McCloughan in February 2005 to supervise their personnel department for Mike Nolan, a career assistant coach who was given total control of the team's football operations by owner John York.

McCloughan was named GM in January 2008 when the 49ers gave him authority over Nolan instead of firing the coach after the 49ers' third consecutive losing season. Nolan lasted just seven more games, and team president Jed York, the owner's son, abruptly replaced him with Singletary during the 2008 season.

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 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 team still hasn't reached the playoffs in five seasons since his arrival, with an 8-8 record last season that was their best since 2002.

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