RNA-sequencing unveils FLT4 splice site variants in variable congenital heart disease

The etiology of congenital heart disease (CHD) is complex, comprising both genetic and environmental factors. Despite documented familial occurrences, the genetic etiology remains largely elusive. Trio exome sequencing identified a heterozygous FLT4 splice site variant in two families with respectively tetralogy of Fallot (TOF), and variable CHD comprising both the TOF spectrum and aortic coarctation. In the first family, Sanger sequencing on cDNA confirmed aberrant splicing for the c.985+1G > A variant. In the second family, transcriptome sequencing uncovered altered splicing for the c.1657+6T > C variant, despite normal targeted Sanger sequencing. In conclusion, our study establishes FLT4 splice site variants as a molecular cause of both left and right-sided isolated CHD, with incomplete penetrance. RNA-sequencing emerges as a valuable technique in unraveling the missing inheritability of CHD.