Mayor Marion Barry, who was given a cut-rate mortgage that would have saved him $242 in monthly payments, got an additional $1,000 break when his savings and loan firm waived its customary requirement that the borrower pay a "point" at the time of settlement, is was disclosed yesterday.

A "point," which represents one percent of a mortgage, is a service fee charged by lenders to help cover the cost of administering the loan.

At the time Barry got his mortgage from Independence Federal Savings and Loan Association on Oct. 15, most borrowers from that institution were being assessed one point. But Barry paid none, according to William B. Fitzgerald, president of Independence.

Fitzgerald said yesterday that Barry was not charged a service fee because the mayor's wife Effi is a member of the Independence board of directors.

At the time the Barrys received the loan, Independence was charging most other borrowers 12 percent interest plus a one point fee. The Barrys received an 8.75 percent loan. Independence officials said discounts are given all directors and employes of the institution.

Barry said on Wednesday that he would relinquish the 3.25 percent reduction and pay at a 12 percent rate in order to "scrupulously avoid any action that might cast the slightest doubt on the integrity of myself, or my wife or the bank."

Yesterday, Herbert O. Reid, the mayor's legal counsel, said Barry would not say if he would also pay any points to Independence. "The mayor is not making any further comment on that," Reid said.

Hubert R. Merrick, executive vice president of Independence, said he could not immediately say if any point would be assessed to Barry, who is scheduled to make his first $1,028 mortgage payment today.

Barry, facing the first incident in which he may have used his office for personal gain since becoming mayor Jan. 2, had hoped to put the controversy to rest with Wednesday's short press conference.

Yesterday, Jay Janis, chairman of the Federal Home Loan Bank Board, which regulates savings and loan associations, said the 3.25 percentage-point difference between the market rate and the rate of the Barry loan warranted investigation.

"This is something I am looking into right now," Janis said. He declined to comment further, he said, because, "It is under review."

Federal regulations permit financial institutions to give discounts on mortgage loans to their directors and employes. Most area banks and savings and loan associations give discounts but they are usually less than 1 percent.

Fitzgerald said he made the loan at 8.75 percent because that was 1 percent more than the amount Independence was paying at the time to borrow money from large lenders and to attract depositors.

Fitzgerald said that he believed federal regulations would have allowed him to make the loan at an even lower rate, 5.5 percent, the amount being paid to savings depositors. But he chose the higher amount to guarantee a profit of 1 percent, Fitzgerald said.

"From my perspectve, it's normal," Fitzgerald said of the Barry loan. "I could have charged him 5.5 percent, and we charged him 3.25 percent more."

Fitzgerald said yesterday that he had called an investigator from the bank board yesterday "to reasure myself and reassure him of our compliance with the laws and regulations." Fitzgerald said, "I anticipate at some point they will probably want to review the loan and talk to me."

Aides to the mayor described him yesterday as being somewhat "stung" by the controversy surrounding the loan. But he was also confident that his admission on Wednesday that he had received a discount and his announced intention to forfeit it, had begun resolution of the issue.

Mrs. Barry, who was appointed to the Independence board in May, shortly after her husband took office, still has 2 1/2 years remaining on her term. Asked yesterday if he had considered asking her to step down earlier, Fitzgerald responded, "Absolutely not."