Running back Jerick McKinnon faces an uncertain future with the 49ers after experiencing a setback in practice on Tuesday.

General manager John Lynch, appearing Wednesday morning on the "Murph &Mac" KNBR Morning Show, said McKinnon had difficulty with his surgically repaired right knee during practice.

“It’s a real bummer because he keeps getting to the final step,” Lynch said. “And the final step is actually playing NFL football, especially at his position, where you got to make hard cuts and you have to put your foot in the ground. And we did it a month ago and we got to that step and he kind of regressed, and I would say yesterday we had a similar situation.

“So we’re trying to get, really, what’s the root cause of the problems he’s having. And just because he’s working through this, we’re working through it, I’ll leave it at that. But yesterday was not encouraging from that standpoint with Jet. What that means, we’re not sure, yet. And we’re working hard to find that out.”

McKinnon returned to practice Tuesday after missing 18 days after undergoing a platelet-rich plasma treatment. He sustained discomfort after just two days of practice after being activated from the physically unable to perform list.

McKinnon sustained a torn ACL one week before the start of the regular season last year. He signed a four year, $30 million contract on the first day of free agency in 2018.

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The 49ers must cut their roster to the regular-season limit of 53 players, at which time McKinnon could go on season-ending injured reserve. If the 49ers want to hold out hope of McKinnon playing in 2019, he would have to be carried on the initial 53-man roster before going on injured reserve -- which would make him eligible to play after missing a minimum of eight games.