Most of a lawsuit that accuses JPMorgan Chase of misleading mortgage investors before the meltdown may advance, a federal judge in Manhattan has decided.

The company must go to trial on allegations by the Federal Housing Finance Agency (FHFA) of wrongdoing in the sale of RMBS, U.S. District Judge Denise Cote ruled Monday.

FHFA filed the lawsuit in December 2011 in its role as conservator for Fannie Mae and Freddie Mac. It has brought 16 actions in district court in Manhattan that charge underwriters of securities backed by residential mortgage loans with misconduct in the offering and sale of securities purchased by Fannie and Freddie over a roughly two-year period beginning in 2005. FHFA alleges that JPMorgan and other defendants represented falsely that the underlying mortgages complied with certain underwriting guidelines and standards, including representations that the borrowers had the ability to repay their loans.

In its motion to dismiss the case, JPMorgan charged FHFA with failing to support its claims that the loans underlying the securitizations departed from the guidelines described in offering documents. The company also contended that downgrades of the securities by rating agencies put Fannie and Freddie on notice of their concerns as early as September 2007 and that FHFA’s claims amounted to what JPMorgan charged was fraud by hindsight.

Judge Cote allowed the case to proceed but winnowed the claims.

While Fannie and Freddie "were certainly aware that they were purchasing securitizations backed by subprime loans," there is nothing in court papers to "establish that they knew that the loans supporting these particular securitizations were so haphazardly originated as to put in jeopardy even the 'AAA'-rated certificates they purchased," the judge wrote in her opinion.

As for the JPMorgan Chase’s argument that Fannie and Freddie waited too long to file their suit, "there is little, if any reason to believe that the downgrade of those tranches should have led the [government-sponsored entities] to discover that the underlying mortgages were not simply risky, but so poorly underwritten as to put at risk even the most senior certificates," Cote added.

A JPMorgan spokesman declined to comment on the ruling, which was first reported by Reuters.

FHFA contends that Fannie and Freddie purchased roughly $33 billion in residential mortgage-backed securities sponsored or underwritten by JPMorgan, Bear Stearns or Washington Mutual over a roughly two-year period beginning in September 2005. JPMorgan acquired Bear Stearns and Washington Mutual following their failures in 2008.

In all, the case concerns 103 securitizations. JPMorgan served as lead underwriter for 30 out of the 103 securitizations at issue in the case. Bear Stearns served as lead underwriter for 38 of the securitizations. Other underwriters included RBS Securities, Citigroup and Goldman Sachs.

The court said it expects depositions in the case to take place next year in anticipation of a trial date set for June 2014.

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