As a Pop Warner-playing kid with decent speed, 49ers head coach Kyle Shanahan unwittingly learned an important lesson about quarterbacking: Those who can escape the pocket can struggle to develop as pocket passers.

“I was just trying to think of how to run right away,” Shanahan said of playing quarterback in youth football. “You’re not staying in the pocket looking down the field reading coverages.”

On Saturday, a few decades after Kyle, the kid, was scrambling, Kyle, the coach, was detailing the challenge mobile quarterbacks face in the NFL. That is, many haven’t been forced to master the nuances of the position because their feet have often bailed them out.

Shanahan has been drawn to semi-immobile quarterbacks who can stand and deliver in his complex and traditional offensive scheme.

And his preference was obvious in the offseason. Shanahan overhauled the depth chart he inherited that featured Colin Kaepernick, Blaine Gabbert and Christian Ponder, all highly drafted, mobile quarterbacks who have failed to realize expectations.

The 49ers replaced them by signing Brian Hoyer and Matt Barkley, who have combined for 117 career rushing yards in 62 games — or 64 fewer than Kaepernick had in a single playoff game. They then used a third-round pick on C.J. Beathard, who had minus-14 rushing yards as a senior at Iowa.

So Hoyer, Barkley and Beathard can’t run? Shanahan noted that some of the maestros of the position are lead foots whose physical limitations forced them to focus on mastering the minutiae of the position.

“I would guess Tom Brady and Peyton Manning — I don’t think they were ever mobile when they were seven, when they were 18, when they were 30,” Shanahan said. “I think they’ve always been guys who have to sit in there and look down the field and learn how to get rid of the ball. And if you’ve been doing that since you’re seven years old to the NFL, you’ve had a hell of a lot more reps than this guy who’s been able to run around and make plays all the time.”

Vince Young. Michael Vick. Robert Griffin III. They were top-three picks whose elite running ability helped them dominate in college, but they didn’t replicate that success at the next level.

Why? Shanahan would say it’s partly because they entered the NFL behind the curve as pocket passers and never caught up. And they aren’t alone. Of the top 10 quarterbacks in career rushing yards, only Steve Young and Daunte Culpepper rank among the top 20 in career passer rating.

Shanahan seeks quarterbacks who play in college the way they will need to play in the NFL. It’s why he was attracted to Beathard, one of the few quarterbacks in the draft who played in a pro-style offense, instead of the spread system that proliferates college.

It’s the same principle with college quarterbacks who rely on their legs to make plays, which becomes more difficult against speedy NFL defenders. Shanahan noted the situation has been exacerbated by NFL rules that have limited practice time.

A mobile QB “gets to the NFL and someone’s saying, ‘Hey, do that sometimes, but most of the time you’ve got to sit in there and keep your eyes downfield,’” Shanahan said. “And you’re asking a guy to do that for the first time in his life when you only get so many reps in training camp, so many in OTAs, and now you’re going into Week 1 of the NFL (season) and you’re going to tell a guy to play like that? I mean, they’re going to play what’s made them successful their whole life. So, it’s more about what you’ve worked at your whole life.”

Shanahan’s outlook explains how he viewed the 2012 draft when he was Washington’s offensive coordinator. Washington used the No. 2 pick on Griffin III, the Heisman Trophy winner who displayed his dual-threat ability in a spread offense. But Shanahan coveted Michigan State’s Kirk Cousins, who played in a pro-style system and had minus-127 career rushing yards.

Shanahan’s lobbying landed him Cousins in the fourth round. Five years later, Cousins ranks seventh among active quarterbacks in career passer rating (93.6) and is a candidate to land with the 49ers in 2018.

Of course, the 49ers could look for their franchise quarterback in next year’s draft. And Shanahan’s preferences offer some clues about how they’ll rank the college QBs.

One name that can be safely crossed off the list: Louisville’s Lamar Jackson, who won last year’s Heisman Trophy while completing 56.2 percent of his passes and rushing for 1,571 yards in a spread system.

Shanahan didn’t mention Jackson —or Griffin III — but it’s conceivable he was thinking about them as he discussed dual-threat quarterbackss.

“If I could go win a Heisman running around and just making plays, I think any of us would go do that,” Shanahan said. “Now you get to the NFL and you can’t do that anymore and it just takes time. It’s more about reps. It’s not that (mobile quarterbacks) can’t do it. It’s how long have they been doing it for?”

Eric Branch is a San Francisco Chronicle staff writer. Email: Twitter: @Eric_Branch

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