Variants related to 46,XY DSD/CHH were found in genes CHD7, FOG2/ZFPM2, and SRA1, variants related to 46,XX DSD/CHH/primary ovarian insufficiency were found in CHD7, DENND1A, FSHR, GLI2, INHA, POR, and SRA1. Other identified gene variants (n = 7) in AKR1C3, DOCK8, NCOR1, FBLN2, NAV1, SMAD6, and GDNF were not previously related to sex development or gonadal function. Here, GLI2 is linked to cartilage-hair hypoplasia.