We analyzed two siblings in a Japanese family with delayed onset cone-rod dystrophy (CRD) using whole-exome sequencing. A novel frameshift c.1106dup (p.H370Afs*17) variant and a known missense c.2027 T > A (p.I676N) variant in CDHR1 were identified. Both patients shared the same variants, although they displayed a significant difference in disease severity. A meta-analysis of the relationship between the severity and the variant type was performed using the reported cases in the literature and did not reveal a definitive correlation.