·The genetic variations of 9 patients with 46,XY CGD were analyzed by combining SRY mutation screening, next generation sequencing (NGS) and chromosome microarray (CMA).

·SRY mutations were identified in 4 of nine 46,XY CGD probands, including 2 patients with novel SRY gene pathogenic/likely pathogenic mutations, namely SRY deletion and c.208T>C (p.Trp70Arg) missense variation, and 2 patients with reported SRY pathogenic mutation, namely c.169C>T(p.Gln57X) and c.264dup(p.Glu89fs*15). One patient was identified with a heterozygous mutation in MAP3K1 gene c.1016G>A (p.Arg339Gln) by NGS, which was likely pathogenic mutation. In addition, CMA analysis and NGS found no pathogenic copy number variations (CNVs) in other 2 sporadic patients. Whole exome sequencing (WES) was performed on the younger of two sisters, whose parents were consanguineous marriage, filtered homozygous variants in the homozygous regions, no specific deleterious variants or likely variants associated with sexual development were found. CNVs analysis found an approximate 14 kb homozygous deletion in intron 2 of DMRT1 gene in both sister cases (Chr9: 866, 388-880, 086, hg19), and PCR sequencing with amplified spanned the junction revealed that healthy parents were heterozygous deletion carriers. Then PhastCons software was used to analyze the conserved fragments of the deletion intron sequences and two conserved non-coding elements (CNEs) were found.

·SRY mutation was the frequent cause accounted for 46,XY CGD, and 2 novel pathogenic mutations in SRY gene were found. The 14 kb homozygous deletion in intron 2 of DMRT1 might be candidate pathogenic mutation for the sister patients. Stepwise analysis of genetic causes of 46,XY CGD patients might help to fully learn about the molecular changes in these patients.