PHILADELPHIA — As general manager Brodie Van Wagenen continues to insist his manager has full autonomy on game decisions for the Mets, a specific example has surfaced that indicates otherwise.

According to an industry source, it was the rookie GM who instructed Mickey Callaway to remove Jacob deGrom from a game in Arizona earlier this month in which the Mets ace sustained a hip cramp. After deGrom was removed from the game in the seventh inning, the bullpen imploded in a loss that added to the frustration of a 2-5 road trip.

The source said Van Wagenen, who was watching the game at home on TV, communicated with a member of the Mets support staff with an order to remove deGrom from the game. Callaway complied with the order, and deGrom was visibly upset as he departed the field, certain that he could continue pitching. The manager was grilled for the move, but at the time insisted the decision was his.

“Hell, yeah, it’s unusual: sending word to the dugout, telling the manager what to do?” the source said. “I have never heard of that before.”

MLB rules stipulate that players and coaches cannot use cell phones anywhere during a game.

The source added there was grumbling at the time within the clubhouse that Van Wagenen hadn’t come forward and taken responsibility for the decision, as the perception persisted that deGrom was unhappy with a manager fighting to keep his job.

Before the Mets opened a four-game series against the Phillies at Citizens Bank Park on Monday, the GM reiterated that Callaway has full charge of the in-game decisions. Van Wagenen was then asked about the June 1 game in Arizona and the deGrom decision.

“For injury-related situations we can have dialogue if there are situations that are player/health related,” Van Wagenen said. “But as far as player in-game decisions Mickey has control of those decisions for baseball.”

So did Van Wagenen communicate with a member of the support staff with orders to remove deGrom from the game that night?

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“Mickey has control of baseball decisions,” Van Wagenen said.

DeGrom said he’s unsure whose call it was to remove him from the game.

“I wasn’t happy I was coming out, no matter who was taking me out,” deGrom said. He added that he was upset in the heat of the moment that he was removed, but understands the organization’s rationale for wanting to protect him.

A veteran executive from another club indicated that a GM issuing orders to a manager during a game would fall into the category of overstepping boundaries.

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“It really is really crossing the line,” the executive said. “I have never seen that done, personally.”

A source also indicated the decision to limit Edwin Diaz to pitching the ninth inning is not Callaway’s; the front office implemented that plan before the season. Diaz was left in the bullpen Sunday as Seth Lugo was struggling through the eighth inning at Wrigley Field, surrendering a go-ahead homer to Javier Baez.

After getting grilled for the decision by reporters after the game, Callaway became annoyed by Newsday’s Tim Healey in the clubhouse, after the reporter said “see you tomorrow.” An expletive-laced tirade by the manager ensued, and Jason Vargas later had to be restrained from going after Healey.