Abstract: Objective One case of juvenile neuronal ceroid lipofuscinosis (JNCL) was clinically diagnosed and genetically analyzed, providing clues and directions for classifying the genetic mechanism of JNCL. Methods Diagnosing the clinical feature of the patient and analyzing his pedigree , the DNA of the patient and his parents was extracted and sequenced by whole exome sequencing. Simultaneously, the verification of Sanger sequencing, analysis of the mutation pathogenicity and the homologous comparison of protein sequences were performed on the patient and his parents. Results The patient has carried compound heterozygous mutations of the CLN3, namely c.1001G>A（p.Arg334His）and c.154T>C（p.Tyr52His）, which were inherited from his father and mother, respectively, and analysis of their mutation pathogenicity was deleterious and the homologous comparison of protein sequences was highly conservative . Conclusion The patient has suffered from juvenile neuronal ceroid lipofuscinosis probably caused by compound heterozygous mutations of the CLN3 gene. It's not previously reported that the heterozygous missense mutation, namely c.154T>C（p.Tyr52His）. Whole exome sequencing can be used as a diagnosis method for the discovery of JNCL, and it can provide a basis for the diagnosis of clinical complicated phenotypic diseases.

Key words: Juvenile neuronal ceroid lipofuscinosis, CLN3 gene, Whole exome sequencing, Next generation sequencing