Short stature is clinically defined as a standing height less than two standard deviations below the mean height at the same age, ethnicity, and sex. As a typical complex symptom, height has a high heritability of 80%, which is affected by multiple genes and gene–gene interactions. A genome-wide association study (GWAS) revealed that 23.3% of the heritability of short stature could be explained by 697 independent variants.1 Whole exome sequencing of a large sample size demonstrated that 83 rare and low-frequency variants could explain 1.7% heritability of height, and variants with minor allele frequency <5% have an average effect 10 times greater than that of common variants.2 Here, we analyzed the whole exome sequencing data of 787 short-stature children to find new genes contributing to short stature in Chinese children.