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SAC Capital Advisors LP, the hedge fund run by billionaire Steven A. Cohen, will pay a record $616 million to settle U.S. regulatory claims that two of its units engaged in insider trading.

Settlement of the civil allegations against the units doesn’t preclude the Securities and Exchange Commission from pursuing Cohen himself in the future, George Canellos, the agency’s acting enforcement director, said on a conference call with reporters today. The investigation by the SEC continues, as does the criminal case against former SAC portfolio manager Mathew Martoma.

“There is no way of predicting what they intend to do,” said Jacob Frenkel, a former SEC enforcement lawyer who is now a partner at Shulman Rogers Gandal Pordy & Ecker PA in Potomac, Maryland. “When the agency is so obviously pursuing someone, and when we do not know what cooperators are saying, there are just too many unknowns.”

Cohen was linked in November to alleged illegal trades done by Martoma in a case that U.S. prosecutors described as the most-lucrative insider-trading scheme they’ve ever uncovered, with profits and averted losses of $276 million. SAC manages $15 billion out of Stamford, Connecticut, 60 percent of which is Cohen’s and his employees’ money. Cohen hasn’t been sued personally by the SEC or charged with a crime.

Boesky, Milken

“Steve Cohen has not been charged with any wrongdoing and has done nothing,” said Jonathan Gasthalter, a spokesman for the company.

SAC is paying almost four times the $156 million Galleon Group LLC founder Raj Rajaratnam, who is serving 11 years in prison for insider trading, paid in civil and criminal fines in 2011. Stock-market arbitrager Ivan Boesky, who pleaded guilty to conspiracy in 1987, paid $100 million and was sentenced to three years in prison.

Michael Milken, the former junk bond financier who pleaded guilty to securities fraud, paid more than $1.1 billion in criminal and civil fines as part of his March 1991 settlement with the Justice Department and SEC. In 1990, Milken was sentenced to 10 years in prison. His sentence was later reduced to two years.

SAC and its affiliates settled the SEC’s claims without admitting or denying wrongdoing. SAC unit CR Intrinsic Investors LLC agreed to pay almost $602 million and Sigma Capital will forfeit about $14 million, the SEC said. They settled for a penalty about equal to the disgorgement amount.

‘Move Forward’

“The historic monetary sanctions against CR Intrinsic and its affiliates are sharp warning that the SEC will hold hedge fund advisory firms and their funds accountable when employees break the law to benefit the firm,” Canellos said in a statement.

“This settlement is a substantial step toward resolving all outstanding regulatory matters and allows the firm to move forward with confidence,” SAC spokesman Gasthalter said. “We are committed to continuing to maintain a first-rate compliance effort woven into the fabric of the firm.”

The SEC’s allegations against CR Intrinsic relate to a November lawsuit against Martoma, who allegedly placed trades ahead of an announcement involving a clinical trial of an Alzheimer’s drug being jointly developed by two pharmaceutical companies. Martoma has pleaded not guilty.

Settlement Cost

The SEC told SAC in November that it was considering pursuing civil claims, citing fraud and control-person liability over its management of CR Intrinsic.

“SAC’s business decision to settle with the SEC in no way changes the fact that Mathew Martoma is an innocent man,” Charles Stillman, a lawyer for Martoma at Stillman & Friedman, said in an e-mail statement. “We will never give up our fight for his vindication.”

SAC will pay the entire settlement expenses, according to a person familiar with the firm who asked not to be named because the information is private. SAC has said it would indemnify clients against disgorgement of illegal profits and legal fees.

The government’s multiyear investigation has linked at least eight current or former SAC employees to allegations of insider trading while working at the hedge fund.

Client Redemptions

The SEC, in an amended complaint today relating to SAC unit Sigma Capital Management, said former analyst Jon Horvath passed inside information to two unidentified fund managers at SAC earning it more than $6.4 million in profits and avoided losses. Previously, the agency had said only one SAC employee received tips from Horvath, who fought insider trading charges filed by the Justice Department until September, when he pleaded guilty a month before trial and agreed to cooperate.

SAC clients last month asked to pull $1.68 billion from the firm, or 27 percent of outside capital, a person with knowledge of the matter said in February. About $660 million is set to leave at the end of this month, the person said.

SAC last month reached a deal with Blackstone Group LP that gives all clients three more months to decide whether to stay in the fund. Blackstone Group LP, one of the biggest investors in SAC, with about $550 million in the fund, will leave most of the money in place for at least another quarter under the new liquidity agreement, it said on Feb. 14 in a statement.

(Corrects to remove erroneous reference why Milken’s sentence was reduced in seventh paragraph.)