Steve Cohen is losing his top lieutenant

Tom Conheeney, the longtime president of SAC Capital and top lieutenant to founder Steve Cohen, is stepping down Monday from the No. 2 spot at the former hedge fund's successor company, Point72, a company insider said.

Conheeney will be replaced as president by Douglas Haynes, a former McKinsey executive, the source said. Haynes joined Point72 in February as managing director of human capital. Point72 manages the assets of Cohen and certain employees and family members.

The surprise exit raises questions about Conheeney's standing at Point72. He joined SAC Capital in a less senior capacity in 1999.

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Through SAC's many brushes with insider trading probes in recent years—federal inquiries culminated in $1.8 billion in regulatory settlements last year—Conheeney has been a staunch advocate of the firm, both with staff internally and in outside gatherings, be they legal or charitable.

Point72, which was officially established in April as a result of the government settlements, manages $9 billion to $10 billion and is up roughly 10 percent through June, according to a person familiar with the matter.

—By CNBC's Kate Kelly