Mucopolysaccharidosis type II (MPS II or Hunter Syndrome) is one of lysosomal storage disorder caused by the presence of pathogenic variant in IDS gene. The variant can be found in various exon locations. This research aimed to identify the presence of disease-causing variant that may occurs at exon 2 and 5 of IDS gene on MPS II patient, especially in Indonesia. Based on the previous research that has been conducted in a number of countries, exon 2 and 5 are the exons with the most number of variations. Analysis was conducted on 7 MPS II patient of Indonesian origin and 50 normal individuals as control that consist of 25 male or 25 female individuals. Analysis was done by going through steps of DNA isolation, amplification by polymerase chain reaction (PCR), visualization by electrophoresis, and sequencing. Research result shows that IDS gene from whole samples were successfully analyzed. This study discovered an adenine base deletion c.708+72delA in intron 5 of one healthy individual. The variant is novel and classified as likely benign.