The Seattle Ethics and Elections Commission on Wednesday approved a settlement of an ethics investigation into Transportation Director Scott Kubly’s involvement with the Pronto bike-share system.

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The Seattle Ethics and Elections Commission on Wednesday approved a settlement resolving a monthslong ethics investigation into Seattle Department of Transportation Director Scott Kubly’s involvement with the city’s Pronto bike-share system.

In the June 21 settlement, made public last week, Kubly agreed to pay the city a fine of up to $10,000 for two violations of Seattle’s Ethics Code.

Before Mayor Ed Murray hired him to run the transportation department in 2014, Kubly was president of Alta Bicycle Share, a company tapped earlier that year to operate Pronto in Seattle.

Because of that connection, which Murray and Kubly made no effort to hide, Kubly was told to either recuse himself or obtain a waiver to work on matters related to Pronto.

He never obtained a waiver, didn’t file a disclosure form until Sept. 1, 2015 and was deeply involved in the launch of Pronto in late 2014.

He also played a leading role last year in negotiations for the city to take over Pronto from its nonprofit owner and expand the system. The City Council approved a takeover this March.

Though the fine is $10,000, the settlement says Kubly will have to pay only $5,000 unless he commits another ethics violation within two years. The settlement is between Kubly and Marilyn Brenneman, a former prosecutor brought on by the commission to conduct the investigation.

Brenneman found no evidence that Kubly sought or received personal financial gain through the dealings with his former employer.

Kubly wasn’t present as the commission took up his settlement during its meeting Wednesday. Eileen Norton, the commission’s chair, said she was “very disappointed” by his absence.

The commissioners initially voted to postpone their decision on the settlement until Kubly could appear; he showed up about 40 minutes after the meeting began and, after hearing from him, the commissioners accepted the settlement.

“I didn’t realize I had to be here today so I wasn’t planning to attend,” Kubly said upon arrival.

“I want to take a moment up front to just apologize for this happening and for the distraction it’s caused. I take full responsibility for my actions,” Kubly said. “I can assure you it’s not going to happen again. I’m actually happy and hopeful we’ll be able to reach closure and allow the public to refocus on the work of the department.”

When asked to explain his lapses, Kubly said: “I don’t know that there’s much explanation I can give.”

He said he thought he had obtained a waiver soon after starting work in Seattle but hadn’t, due to an email snafu. Kubly said he doesn’t remember seeing some reminder emails last year.

“The confusion was my own. I’ve worked in the public sector enough to recognize I should have followed up, and I did not.”

Brenneman recommended the commission approve the settlement in order to avoid a lengthy and expensive hearing.

Commissioner Bruce Carter said Kubly’s fine is the largest ever for violations not involving “self-serving corruption, graft or fraud of some sort.”

Brenneman said Kubly’s initial settlement proposal was that his fine be $500, an amount she regarded as “a no-fly zone.”

Murray last week said he would continue to support Kubly, attributing the transportation chief’s violations to error rather than purposeful deception.

The mayor said the violations highlight “the need for an improved and consistent orientation policy for incoming department directors.”

But Brenneman on Wednesday said it would be wrong to blame Kubly’s violations on inadequate training or outreach by commission staff.

“Any suggestion there was a lapse in training or information is not supported by what I found,” she said.

Brenneman said Kubly received proper information about his responsibilities and “he simply did not fulfill them.”

In a report made public after Wednesday’s meeting, the investigator described Kubly as an intelligent, hands-on manager with prior experience related to government ethics rules.

“It is difficult to credit Kubly’s failure to adhere to the Seattle Ethics and Elections Code to mere carelessness,” Brenneman wrote.

At Wednesday’s meeting, Kubly said he didn’t think his fine needed to be any larger because, “I didn’t seek or receive any financial gain. It was an oversight on my part.”

In an interview afterward, Kubly said the missing waiver was the only thing wrong with him doing business with his former employer.

“I never had any equity in the company, no ongoing financial interest after I left,” he said.