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Purpose: To identify disease associated mutations in a male infant with congenital heart defects and heterochromia.Methods: A detailed clinical examination and routine laboratory tests were performed on the patient. We applied whole exome sequencing to identify the causal mutation on the proband and other family members.Results: The patient presented with severe congenital heart disease, strabismus, and pigment disturbances of the iris. We identified a deletion of 1.99 megabase [arr[hg19]22q12.3-13.1 (chr22:36656004-38643920) *1], including SOX10and 13 RefSeq genes on this patient, which was associated with atypical Waardenburg syndrome.Conclusion: Our results suggest that a deletion of 1.99 megabase (including SOX10) acts as a dominant pathogenic variant on the clinical presentations of this patient with atypical Waardenburg syndrome.