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Klay Kubiak is in his first season as the 49ers assistant quarterbacks coach. He served as a defensive quality control coach with the team in 2021. Kubiak joined the 49ers after spending the previous three years (2018-20) as the head coach at Strake Jesuit College Preparatory (Houston, TX). He also served as the school's offensive coordinator from 2013-15 and for the 2017 season.

Kubiak and the 49ers defense ranked third in the NFL in 2021, allowing 310.0 total yards per game. San Francisco also was sixth in the NFL, surrendering 206.5 passing yards per game. The Niners forced 22 fumbles on defense in 2021, the most in the NFL and the most in a single season by the 49ers since 1994.