BACKGROUND: Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart disease. However, our current understanding of the genetic etiology for TOF is limited. METHODS: Whole exome sequencing (WES) and Sanger sequencing were applied to a family trio diagnosed with TOF by fetal prenatal ultrasound examination. A minigene assay was performed to confirm the splicing defects. RESULTS: We identified compound heterozygous variants in the cerebral cavernous malformation 2-like (CCM2L) gene, namely the paternally inherited nonsense variant NM_001365692.1:c.741G>A p.(Trp247Ter) and the maternally inherited splice-site variant NM_001365692.1:c.1263+2T>A in a fetus with TOF featuring a ventricular septal defect associated with overriding aorta and pulmonary stenosis. Minigene assay showed that the c.1263+2T>A variant led to skipping of CCM2L exon8 during RNA splicing, which is thought to result in frameshift and premature termination of translation. Both variants were absent from the public population databases (Genome Aggregation Database [gnomAD], 1000 Genomes [1000G], Clinvar) and classified as likely pathogenic according to the ACMG guidelines (PVS1 + PM2 level evidence). CONCLUSION: To our knowledge, this is the first reported case of biallelic loss-of-function variants in human CCM2L. Our findings suggest a potential association of human CCM2L with TOF.