Here we show that in the case when double peaked emission lines originate from outer parts of accretion disk, their variability could be caused by perturbations in the disk emissivity. In order to test this hypothesis, we introduced a model of disk perturbing region in the form of a single bright spot (or flare) by a modification of the power law disk emissivity in appropriate way. The disk emission was then analyzed using numerical simulations based on ray-tracing method in Kerr metric and the corresponding simulated line profiles were obtained. We applied this model to the observed H-beta line profiles of 3C 390.3 (observed in the period 1995-1999), and estimated the parameters of both, accretion disk and perturbing region. Our results show that two large amplitude outbursts of the H-beta line observed in 3C 390.3 could be explained by successive occurrences of two bright spots on approaching side of the disk. These bright spots are either moving, originating in the inner regions of the disk and spiralling outwards by crossing small distances during the period of several years, or stationary. In both cases, their widths increase with time, indicating that they most likely decay. Comment: 14 pages, 5 figures, 1 table. Accepted for publication in ApJ