A male infant was admitted to the neonatal intensive care unit for respiratory distress 12 minutes after preterm birth. Prenatal fetal echocardiography suggested transposition of the great arteries with an intact ventricular septum. Amniocentesis and family-based whole-exome sequencing identified a heterozygous missense variant in SOX11 (c.152G>C, p.Arg51Pro), leading to a diagnosis of Coffin-Siris syndrome type 9. Postnatal echocardiography and computed tomography angiography confirmed Berry syndrome. Single-stage corrective surgery was performed with good recovery. This report presents the first documented case of Coffin-Siris syndrome type 9 complicated by Berry syndrome and identifies a previously unreported SOX11 variant, expanding the pathogenic phenotypic spectrum associated with this gene and suggesting its potential role in regulating cardiovascular development. These findings provide important evidence for genetic counseling and prenatal diagnosis and indicate that enhanced cardiovascular evaluation is warranted for fetuses carrying SOX11 variants to enable early identification of severe malformations such as Berry syndrome.