Editor’s Note:

This story has been clarified from the original to indicate that A. Scott Keys was an IndyMac employee at the time of his resignation, but no longer held the CFO title.

IndyMac Bancorp Inc. said in a regulatory filing that former Chief Financial Officer A. Scott Keys had officially resigned from the company effective June 30, after going on medical leave two months ago.

The company named S. Blair Abernathy as permanent CFO when Keys began his leave on April 24, company spokesman Evan Wagner said Wednesday, but Keys was still considered an employee without an official title until his June 26 resignation. The company declined to provide details about Keys’ need to take a leave.

Keys’ resignation “was not related to any concerns, issues or disagreements regarding the company’s accounting policies or practices or financial disclosures,” said the Pasadena-based savings institution, whose mortgage loan losses had lead to $900 million in losses over the past three quarters.

The company said in the filing that it had agreed to pay Keys four months of his base salary (around $220,000) and forgive a $50,000 loan as part of his separation agreement.

In other news, mortgage application volume rose 3.6 percent during the week ended June 27, according to the Mortgage Bankers Association’s weekly application survey released Wednesday.

That contributed to 14 percent rise in IndyMac’s share price, closing up 9 cents to 74 cents on the New York Stock Exchange. The company has lost roughly 89 percent of its market value so far this year.