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Although some susceptibility genes have been identified, the genetic basis underlying the majority of CHD cases is still undefined.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>A total of 1320 unrelated CHD patients were enrolled in our study. Exome\u2010wide association analysis between 37 tetralogy of Fallot (TOF) patients and 208 Han Chinese controls from the 1000 Genomes Project was performed to identify the novel candidate gene WD repeat\u2010containing protein 62 (<jats:italic>WDR62<\/jats:italic>). <jats:italic>WDR62<\/jats:italic> variants were searched in another expanded set of 200 TOF patients by Sanger sequencing. Rescue experiments in zebrafish were conducted to observe the effects of <jats:italic>WDR62<\/jats:italic> variants. The roles of WDR62 in heart development were examined in mouse models with <jats:italic>Wdr62<\/jats:italic> deficiency. <jats:italic>WDR62<\/jats:italic> variants were investigated in an additional 1083 CHD patients with similar heart phenotypes to knockout mice by multiplex PCR\u2010targeting sequencing. The cellular phenotypes of <jats:italic>WDR62<\/jats:italic> deficiency and variants were tested in cardiomyocytes, and the molecular mechanisms were preliminarily explored by RNA\u2010seq and co\u2010immunoprecipitation.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Seven <jats:italic>WDR62<\/jats:italic> coding variants were identified in the 237 TOF patients and all were indicated to be loss of function variants. A total of 25 coding and 22 non\u2010coding <jats:italic>WDR62<\/jats:italic> variants were identified in 80 (6%) of the 1320 CHD cases sequenced, with a higher proportion of <jats:italic>WDR62<\/jats:italic> variation (8%) found in the ventricular septal defect (VSD) cohort. <jats:italic>WDR62<\/jats:italic> deficiency resulted in a series of heart defects affecting the outflow tract and right ventricle in mouse models, including VSD as the major abnormality. Cell cycle arrest and an increased number of cells with multipolar spindles that inhibited proliferation were observed in cardiomyocytes with variants or knockdown of <jats:italic>WDR62<\/jats:italic>. <jats:italic>WDR62<\/jats:italic> deficiency weakened the association between WDR62 and the cell cycle\u2010regulated kinase AURKA on spindle poles, reduced the phosphorylation of AURKA, and decreased expression of target genes related to cell cycle and spindle assembly shared by WDR62 and AURKA.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p><jats:italic>WDR62<\/jats:italic> was identified as a novel susceptibility gene for CHD with high variant frequency. 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