Congenital heart disease (CHD) is the most frequent birth defect. RCAN1 (regulator of calcineurin 1) contributes to CHD in Down syndrome. However, whether RCAN1 is also associated with nonsyndromic CHD remains unclear. This study sequenced the exons and flanking region of RCAN1 in 128 sporadic CHD patients and 150 normal controls. We identified six novel heterozygous mutations in CHD patients. Functional assay showed that the g.482G>T could obviously raise the promoter activity of RCAN1.4 in vitro; However, we failed to detect the expression of RCAN1 in the right auricle, which made it confused to evaluate the pathogenicity of this mutation. In addition, we demonstrated that c.290T>C and g.1056+58C>A had no effect on the alternative splicing of RCAN1. The *196C>T, *790G>A, and *1278C>G did not influence the translation of RCAN1 post transcription. In conclusion, a novel mutation of g.482G>T in RCAN1 may be related to CHD by causing overexpression of RCAN1.4.