Prenatal molecularly supported diagnosis of a fetus with urinary malformation caused by novel compound heterozygous variants in the FAM149B1 gene

Abstract

Biallelic variants in a family with sequence similarity 149 member B1 gene (FAM149B1, OMIM #618413) causes a range of abnormal phenotypes associated with Joubert syndrome (JS) in humans. However, the phenotypic spectrum and genetic evidence linking FAM149B1 to ciliopathies remain limited, with no prenatal cases previously described. Here, we report the first prenatal case from a non-consanguineous Chinese family presenting with isolated right pelvicalyceal and ureteral dilation at 24 weeks of gestation. Notably, the fetus lacked cerebellar malformations or hallmark neuroimaging features such as molar tooth sign (MTS). Trio-whole-exome sequencing (Trio-WES) identified novel compound heterozygous loss-of-function variants in FAM149B1: paternal c.279T>A (p.Tyr93*) and maternal c.574dup (p.Ser192Phefs*7). Both variants are predicted to trigger nonsense-mediated mRNA decay (NMD), consistent with a loss-of-function mechanism, and parental segregation confirmed asymptomatic heterozygous carrier status, supporting autosomal recessive inheritance. Gene-disease validity assessment assigned a "Strong" classification to FAM149B1-related ciliopathy under ClinGen guidelines, enabling definitive classification of the variants as pathogenic or likely pathogenic. This case expands the phenotypic spectrum of FAM149B1-related disorders to include isolated urinary tract malformations in the prenatal period, where neurological manifestations may be absent or subtle. Our findings highlight the utility of prenatal exome sequencing in atypical cases and contribute to the understanding of the expanding genetic and phenotypic landscape of ciliopathies.