Hypoplastic Left Heart Syndrome (HLHS) is a complex form of congenital heart disease, characterized by severe underdevelopment of the left ventricle, stenosis or atresia of the mitral and aortic valves, and hypoplasia of the ascending aorta and aortic arch. Despite advances in surgical and palliative strategies leading to improved neonatal survival outcomes, HLHS is still associated with early mortality and long-term morbidity. Elucidation of HLHS etiology is compounded by its complex inheritance mechanism and heterogenous genetic landscape, with studies indicating a multigenic etiology. We performed exome sequencing on a parent-offspring trio in which the proband was affected with HLHS and identified a novel de novo missense variant in the gene, RBFOX2, that was bioinformatically predicted to be pathogenic. RBFOX2 belongs to a family of RNA-binding proteins that is broadly expressed in all tissues and regulates splicing and transcription of many targets, including those involved in heart development. In order to determine the in vivo pathogenicity of the RBFOX2 variant, we generated a knock-in mouse model harboring orthologous missense RBFOX2 variant using CRISPR/Cas9 technology. RBFOX2 KI/KI mice were found to be embryonic lethal. Morphological analysis revealed 100% of homozygous mutants exhibit gross developmental defects. Normal Mendelian ratios are found at E9.5 but homozygous mutants display severe growth retardation from E9.5 to E11.5. Histologic analysis demonstrated underdevelopment of the ventricular chambers starting at E9.5. Overall, these mutant mice, harboring a clinically relevant human HLHS variant in RBFOX2 , display highly penetrant hypoplastic hearts with significant growth retardation. The use of this new murine model will pave the way for better cellular and molecular characterization of the deficits in RBFOX2 function that contribute to HLHS.