: Spinocerebellar ataxias (SCAs) are a clinically and genetically heterogeneous group accompanied by obvious pontocerebellar limitations. This condition is complex both genetically and phenotypically, making it difficult to describe all the variants simultaneously. Herein, we report a proband from a Chinese mainland family who was admitted to our hospital with paroxysmal limbs jitter and head-shaking. She had experienced broad-based gait, dysarthria, dysmetria, and tremor for about 20 years. Similar clinical symptoms were observed in the daughter, sister and deceased father of this proband. Magnetic resonance imaging showed varying degrees of cerebellar atrophy. The results of whole-exome sequencing (WES) indicated that the three affected members carried the c.590G>A mutation in the CCDC88C gene. Based on the diagnosis of SCA40, this proband was treated with aggressive management. Unfortunately, the proband died of suffocation due to laryngeal oedema. Paroxysmal limbs jitter may be a rare phenotype of SCA40 and may occur as a result of involuntary motion which should be differentiated from chorea and epilepsy. In patients with SCA40, pontocerebellar atrophy occurs to varying degrees. Even in the same family, the multiple patients diagnosed did not all exhibit pontocerebellar atrophy. Furthermore, WES is indispensable for the identification of some atypical phenotypes of SCA40.