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"The preliminary word is that he's had a serious tear of the upper groin area," general manager Terry Donahue said late Friday. "And it will be a substantial amount of time that he's going to miss."
Rattay was injured earlier Friday while rolling out to throw a pass during the opening session of the Niners' first spring mini-camp.
He had an MRI later in the day that revealed the injury.
Rattay is slated to replace Jeff Garcia, who was released this spring in a salary-cap move.
Donahue said team doctors would take a closer look at the injury this weekend and then discuss with Rattay and team officials whether to operate.
Either way, Rattay should be ready for the season's start, Donahue said.
"Tim Rattay is certainly crestfallen, no question about it," Donahue said. "He's just got to come back and come back as quickly as he can, because we need him back."
Rattay is the only quarterback on the 49ers' roster with NFL experience. After appearances in eight games over his first three seasons, the former Louisiana Tech player started three games last season in place of an injured Garcia and went 2-1. He completed 61.9 percent of his passes and had a passer rating of 96.6.
According to San Jose Mercury News staffer Dennis Georgatos, Ken Dorsey, who did not play as a rookie last season, will step in with the first team.
"I'm just going to go out and do my thing. If I'm with the ones, then I've got to perform," he said. "I think my biggest thing is earning my teammates' respect and my coaches' respect. If you do that, that means you're doing your job on the field."
Like Dorsey, Brandon Doman and rookie Cody Pickett are awaiting their first NFL snaps.
Despite the lack of experience, the 49ers had planned to enter the season with their current quarterback corps.
With a league-high $28 million in dead money (for players no longer on the roster), the team was wary of the costs associated with adding another veteran quarterback, along with the potential drag on the development of its young quarterbacks.
But that was before the injury to Rattay. Donahue said he would have to at least revisit the possibility of signing an experienced quarterback.
"We were not pursuing that and did not intend to pursue that," Donahue said. "Whether or not we do now remains to be seen. I don't want to speculate whether we would or wouldn't until we know a little more information."