BACKGROUND There are many factors that lead to dwarfism, and the mechanism has not yet been elucidated. Next-generation sequencing may identify candidate-related gene mutations, which may clarify the molecular cause. AIM To analyze genetic variation by using a constructed panel related to dwarfism by utilizing next-generation sequencing platform sequencing analysis to screen candidate-related gene mutations. METHODS Physical and laboratory characteristics, including clinical examination, growth hormone drug challenge test, serum insulin-like growth factor-1 (IGF-1), IGF binding protein 3, other related tests, imaging examination, and chromosome karyotyping, were analyzed. Next-generation sequencing was performed to analyze pathogenicity variability. RESULTS In the 39 dwarfism patients, 10 had pathogenicity variability. Gene variation was found in the OBSL1 , SLC26A2 , PTPN11 , COL27AI , HDAC6 , CUL7 , FGFR3 , DYNC2H1 , GH1 , and ATP7B genes. Of the 10 patients with pathogenicity variability, the related physical characteristics included double breast development and growth hormone deficiency, enuresis and indirect inguinal hernia on the left, two finger distance of 70.2 cm, head circumference of 49.2 cm, ischium/lower body length of 1.8 cm, weak limb muscles, and partial growth hormone deficiency. After 6 mo of growth hormone therapy, the concentrations of IGF-1 and IGF binding protein 3 increased from 215.2 ± 170.3 to 285.0 ± 166.0 and 3.9 ± 1.4 to 4.2 ± 1.1, respectively. CONCLUSION OBSL1 , SLC26A2 , PTPN11 , COL27AI , HDAC6 , CUL7 , FGFR3 , DYNC2H1 , GH1 , and ATP7B genes may be related to the incidence of dwarfism, and more research needs to be performed to elucidate the mechanism.