Policies imposed by Morgan Stanley on its wholesale mortgage lending subsidiary discriminate against minorities, a complaint to federal regulators alleges — the first time such charges have been leveled against a Wall Street investment firm over the securitization and sale of mortgage loans on the secondary market.

Morgan Stanley is accused of redlining by establishing high minimum loan amounts in programs offered by its subsidiary, Saxon Mortgage Inc., and not offering those programs for properties on American Indian reservations. Morgan Stanley has allegedly restricted Saxon Mortgage from making some types of loans in rural Alaska and Puerto Rico, Guam and the U.S. Virgin Islands.

The accusations are made in a complaint by the National Community Reinvestment Coalition to the Department of Housing and Urban Development (HUD) and the Securities and Exchange Commission (SEC).

The complaint “recognizes the important role that Wall Street plays in providing liquidity to the housing markets and how that role is often performed in a biased and unfair manner,” NCRC said in a press release.

In a statement, Morgan Stanley said the lending policies of the company and its affiliates “do not discriminate on the basis of race or national origin. We are confident the allegations will prove meritless and would welcome the opportunity to discuss our practices with NCRC.”

NCRC says it wants HUD and the SEC to stop Morgan Stanley from “selling, buying, investing in, serving as a trustee, or otherwise participating in any pooling and servicing agreements involving mortgage loans underwritten from using the discriminatory lending policies identified in the complaint.”

The complaint alleges that Morgan Stanley, which acquired Saxon Mortgage’s parent company, Saxon Capital, in December, has restricted lending to African Americans and Latino neighborhoods by implementing high minimum loan amounts. Saxon Mortgage’s ScorePLUS loan program is not available for loans under $75,000, and the ScorePLUS2 loan program is limited to loans of $100,000 or greater, the complaint alleges.

The policy prevents borrowers whose homes are worth less than the mandatory minimums regardless of their credit worthiness, the complaint alleges, and constitutes redlining under the Fair Housing Act.

The complaint alleges Saxon Mortgages ScorePLUS and ScorePLUS2 loan programs are not available at all on Indian reservations or outside the city limits of Anchorage, Fairbanks and Juneau, Alaska — policies that have a “disproportionate adverse impact on Native Americans.”

Morgan Stanley is accused of prohibiting Saxon Mortgage from making its “Options/Alt-A” and “Premier” programs available to borrowers in Puerto Rico, Guam and the Virgin Islands — policies that impact Latinos, Pacific Islanders and Asians, the complaint alleges.

NCRC claims that all of the allegedly discriminatory practices were implemented after Morgan Stanley acquired Saxon Capital. According to an August 2006 underwriting manual, Saxon Mortgage had previously maintained a $50,000 minimum loan amount for first-lien loans.

NCRC has made similar allegations against NovaStar Financial Inc., claiming the company refused to fund loans backed by row houses in Baltimore, which the company disputes.

A coalition of about 600 nonprofit organizations, NCRC promotes the investment of private capital in underserved communities. The group was awarded $500,000 a year ago after filing a discriminatory lending complaint with HUD against SouthStar Funding LLC. That complaint also alleged redlining involving Baltimore row houses.

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