A Novel STAG2 Frameshift Variant in Mullegama–Klein–Martinez Syndrome with Complex Conotruncal Heart Defect

<b>Background:</b> Mullegama-Klein-Martinez syndrome (MKMS; OMIM #301022) is an X-linked cohesinopathy caused by pathogenic variants in <i>STAG2</i>, which encodes a subunit of the cohesin complex responsible for chromosomal segregation and transcriptional regulation. Individuals typically present with developmental delay, microcephaly, dysmorphic features, and variable congenital anomalies, though complex cardiac malformations are uncommon. <b>Case Presentation:</b> We report a female infant presenting on the first day of life with complex congenital heart disease, including pulmonary atresia, double-outlet right ventricle, large subaortic ventricular septal defect, and patent ductus arteriosus. She exhibited intrauterine growth restriction, mild craniofacial dysmorphism, and left upper-extremity hypotonia. Stepwise genetic evaluation revealed a de novo likely pathogenic <i>STAG2</i> frameshift variant, c.2972_2975dup (p.His992Glnfs*11), identified by rapid trio whole-exome sequencing. This variant truncates the C-terminal domain critical for cohesin binding. A 3D structural model generated by SWISS-MODEL demonstrated disruption of β-strand and loop conformations within this domain, consistent with loss of cohesin complex stability. <b>Conclusions:</b> This case expands the phenotypic spectrum of <i>STAG2</i>-related MKM and highlights the role of <i>STAG2</i> in cardiac development. Recognition of such presentations supports the inclusion of <i>STAG2</i> in the differential diagnosis for complex congenital heart disease and underscores the diagnostic utility of rapid trio exome sequencing in neonatal care. The utility of 3D protein modeling to illustrate structural consequences of truncating variants provides valuable insight into variant pathogenicity and supports precision diagnosis in cohesinopathies.