Shanahan says quarterback Jimmy Garoppolo, who is still dealing with a right thumb injury, will be limited in practice. However, his starting left tackle, Trent Williams (elbow), will not practice. The coach is still hoping that Williams can play on Sunday against the Cowboys.
"Trent is better today than he was on Sunday," Shanahan said.
The 49ers are opening the practice window for running back Trenton Cannon, who suffered a concussion on December 5 and was placed on injured reserve on December 11.
Others who will not practice on Wednesday are running back Elijah Mitchell (knee) and tight end George Kittle (vet day).
Linebackers Dre Greenlaw (groin), Azeez Al-Shaair (knee) and Marcell Harris (Achilles), safeties Talanoa Hufanga (knee) and Jaquiski Tartt (shoulder), and punter Mitch Wishnowsky (concussion) will be limited.
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