We investigated the contributions ofTyrp1andGpnmbto the iris transillumination defect (TID) in five age cohorts of BXD mice. Using systems genetics, we also evaluated the role of other known pigmentation genes (PGs). Mapping studies indicate thatTyrp1contributes to the phenotype at all ages, yet the TID maps toGpnmbonly in the oldest cohort. Composite interval mapping reveals secondary loci viz.Oca2, Myo5a, Prkcz, and Zbtb20that modulate the phenotype in the age groups up to 10–13 months. The contributions ofTyrp1andGpnmbwere highly significant in all age cohorts. Moreover, in young mice, all six gene candidates had substantial interactions in our model. Our model accounted for 71–88% of the explained variance of the TID phenotype across the age bins. These results demonstrate that along withTyrp1andGpnmb, Oca2, Myo5a, Prkcz, and Zbtb20modulate the TID in an age-dependent manner.