Fraser syndrome 2 is a rare autosomal recessive inherited disorder caused by mutations in the FREM2 gene that lead to malformations such as cryptophthalmos, syndactyly, and urinary tract and kidney abnormalities. In the described case of a Chinese fetus in the 24th week of pregnancy, the absence of kidneys, absence of a bladder and almost complete lack of amniotic fluid were detected by ultrasound. Trio whole-exome sequencing revealed two novel compound heterozygous variants in the FREM2 gene: the maternal framework variant c.59085909del and the paternal nonsense variant c.7881C>G. These mutations probably lead to the formation of non-functional proteins, which disrupts the function of the FRAS/FREM complex, which is important for the proper development of the skin and internal organs. The case expands the known genotypic spectrum of FREM2 and highlights the importance of Trio-WES in the prenatal diagnosis of recessive genetic disorders. Fraser syndrome 2 is characterized by phenotypic heterogeneity, which complicates clinical diagnosis. The results confirm that mutations in FREM2 lead to severe fetal developmental abnormalities.