X-连锁CGD系CYBB基因突变所致，CYBB基因编码NADPH氧化酶的细胞色素b558的gp91phox基因，突变导致吞噬细胞不能产生超氧根、单态氧和H2</sub>O2</sub>，部分病例为Xp21缺失所致。
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