Background: Atrial septal defect (ASD) is one of the most common cardiac malformations worldwide. Several genes have been identified so far, which can merely explain small proportion of all the cases, therefore, it is anticipated that there are additional genes causing ASD. The aims of this study were to identify the causal gene of ostium secundum atrial septal defect (ASDII) in a Chinese family. Methods: Whole exome sequencing was performed in three affected members and one control in the ASDII family. We screened mutations of LBX2 in 300 unrelated ASD patients and validated in 400 normal controls by Sanger sequencing. LBX2 knockout zebrafish was generated by CRISPR/Cas9 to detect whether lbx2 deficiency influenced cardiac development. Results: A rare missense mutation in LBX2 (c.A403G:p.K135E) was identified as the pathogenic cause of ASD. Subsequent mutation screening revealed two missense variants in 3 of 300 sporadic patients. We observed expanded size of atrium and ventricle in LBX2 knockout zebrafish through hematoxylin-eosin staining, more incompact distribution of cardiac myocytes was also discovered in homozygote compared with in wildtype. Furthermore, we performed in situ hybridization of crip2 gene to trace the cardiac neural crest cells in the embryo stage and found that the migration of neural crest cells was obviously delayed in the homozygotes. Conclusions: We identified LBX2 for the first time as a pathogenic gene of ASDII. LBX2 deficiency may cause abnormal development of heart through influencing the migration of neural crest cells and affect the process of cardiac septation. (c) 2018 Elsevier B.V. All rights reserved.