Klay is one of three sons of former Houston Texans and Denver Broncos head coach Gary Kubiak, who retired last month after spending two seasons with the Minnesota Vikings. 49ers head coach Kyle Shanahan served on the elder Kubiak's staff with the Texans, including two seasons (2008–09) as the team's offensive coordinator.
Klay Kubiak was 24-11 in three seasons with Strake Jesuit and helped the program earn playoff appearances each year.
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