Waiting for Muni is always a gamble. Even with GPS tracking apps, it’s like Muni suddenly disappears for extended periods of time.

The mystery of vanishing Muni can lately be blamed on the maligned mass transit operator canceling about 35 to 45 bus runs a day without warning. This is to cut down on overtime costs.

Muni no longer pays overtime to replace drivers who call in sick. So when a driver comes down with the flu — or a Giants game — service can be hindered.

Muni relies on an “extra board,” which is a group of drivers who are on call on a given day. When a driver calls in sick, an extra board driver on call takes that person’s place.

Muni routinely schedules 1,200 drivers each weekday, with 100 on call. Previously, if all on-call drivers were working, additional drivers would be called in to replace the remaining open slots. These drivers would be paid overtime.

With a $29 million shortfall, Muni now opts to cancel bus runs instead.

About 150 of 1,200 Muni drivers unexpectedly missed work during the first three months in 2011.

The absentee rate for Muni drivers is higher than the national average, according to the Bureau of Labor Statistics. It is also higher than other who work for the transit system.

The worst transit system for driver absences is AC Transit in the East Bay, with unexpected driver absences running about 12 percent during the last three months of 2011.

Muni drivers attribute absenteeism mostly to stress and health hazards, said Ron Austin, vice president of the union that represents 2,200 Muni drivers:

“We’re dealing with homeless people and sick people and mentally ill people and children and teenagers while we’re trying to keep everything on schedule. All this pressure rests squarely on the operator. You’ve got to be a baby sitter, and you’ve got to drive this 40-foot vehicle through very congested streets.”

In 2010, unplanned absences were at 13.7 percent for Muni. It has since declined to 12.9 percent rate in 2011.

According to Paul Rose, San Francisco Municipal Transit Agency spokesman, the transit system wanted to hire more drivers.

However, Rose said that the job is no longer appealing as Muni drivers are heavily blamed for delays and problems with service.