Kyle’s update, 1:55 PM PT: Kyle Shanahan said 49ers LT Trent Williams started having back spasms today. That’s why he left practice. Williams will be questionable for Sunday:

“I’m not too concerned. Asked Chris (Foerster) if he’s alright and he said it’s big-guy problems. If you have (back spams) on game day, it’s a big deal. Had them today, so he will spend the day resting.”

Shanahan said the team expects to decide on RB Elijah Mitchell going on IR sometime in the next 24 hours. The team has only two designated-to-returns moves left. Shanahan said team is close to opening Javon Kinlaw’s practice window.

Shanahan, on 49ers DT Javon Kinlaw returning: “I do believe it’s getting close. It could be any week now.”

Deebo Samuel (quad) did not do much in practice today, per Kyle Shanahan. The team was expecting him to go full by now, but it didn’t happen. Samuel has a deep thigh bruise. He took a helmet to the quad in the last game against the Saints, and it has not healed as quickly as they had hoped. Samuel’s questionable status is more positive than being listed as doubtful, but he did not do much at practice today, according to Shanahan

Here’s the injury report:

OUT

RB Elijah Mitchell (knee)

QUESTIONABLE

WR Deebo Samuel (quad)

OL Spencer Burford

DL Charles Omenihu

LT Trent Williams

The 49ers told beat reporters that star left tackle Trent Williams left Friday’s practice and headed into the locker room with an apparent back issue. Williams didn’t practice Friday, and we’ll see how that impacts his ability to play Sunday against a Miami Dolphins defense with two quality edge rushers in Jaelan Phillips and Bradley Chubb.

Head coach Kyle Shanahan will speak later Friday afternoon. Colton McKivitz or Jaylon Moore would step in for the All-Pro if Williams cannot play. The 49ers’ roster is deep and can afford to miss a player or two, but Williams isn’t among them. He’s their best player and a big part of what this team does offensively.

Deebo Samuel was in uniform with a helmet on and didn’t practice early during the media portion but came on the field as they walked off. It was an inverse situation of what happened with Williams. Deebo is likely to be listed as limited.

Arik Armstead and Christian McCaffrey both practiced. We’ll update once Shanahan speaks, which is scheduled to be just after 1:30 PM PT Friday.