SANTA CLARA — It turns out the 49ers’ defense was decimated more than they let on, as it’s been revealed that safety Malik Mustapha is recovering from his second anterior cruciate ligament repair in three years.

Mustapha’s ACL tear was confirmed in an MRI exam days after he got hurt in the 49ers’ Jan. 6 season finale, although the team did not disclose it publicly then or throughout this offseason. ESPN’s Nick Wagoner reported it first after Saturday’s draft concluded, and a team spokesman confirmed Mustapha’s plight.

Mustapha’s hard-hitting style vaulted him into the starting lineup last season as a rookie, helping cover for the absence of fellow safety Talanoa Hufanga, who was coming off a 2023 ACL tear and also endured a wrist injury.

Mustapha, as ESPN reported, tore the graft from his 2022 ACL repair, from which he returned to play 10 games in 2023 for Wake Forest. This past January’s MRI revealed Mustapha required a second ACL surgery, and his meniscus and cartilage were unscathed.

With Ji’Ayir Brown set to return for his third season as a potential starter, the 49ers signed two veteran safeties last month in free agency — Jason Pinnock (New York Giants) and Richie Grant (Atlanta Falcons). They did not draft a safety until Saturday’s fifth round, when they took Kansas State’s Marques Sigle.

General manager John Lynch made no reference to Mustapha’s health before, during or after the draft, and instead he praised Sigle’s ability to run the 40-yard dash in under 4.4 seconds: “That is a blazing time. He’s got a lot of versatility to his game. He’s a good tackler. He eats up. A term we use is ‘taking the grass’ and this is a guy who takes the grass. He takes the fight to the ball carrier to the receiver. I think he’s going to be a really good fit for us.”

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