Ovaries from Cct1⁹⁹ mutants contain ovarioles with only one or two egg chambers (rather than the normal six or seven). Mutant germaria sometimes contain few or no germline cells with spectrosomes, indicating a loss of germline stem cells. Mutant females produce egg chambers with mispositioned oocytes and packaging defects. In these ovaries, packaging defects occur with variable frequency and include egg chambers with fewer than 16 germline cysts as well as egg chambers that contain multiple germline cysts. The mis-positioning of the oocyte is seen more consistently - the oocyte is found in the middle or the anterior of the egg chamber. This can be already be seen in the germarium, suggesting a defect in the early positioning of the oocyte. In ovaries from females homozygous for Cct1⁹⁹, ovarioles exhibit a "branched ovariole" phenotype, in which multiple ovarioles are attached to one egg chamber. This phenotype is often seen in ovaries in which some of the ovarioles are separated from each other as in wild-type. Mutant ovaries also contain ovarioles that are curled up within the ovariolar sheath rather than stretched out as in wild-type ovaries. These phenotypes seem to be caused by defects in ovarian morphogenesis. At 20-22.5 hours APF in wild-type, the ovarioles are clearly separated into distinct structures, and basal stalks have started to form. In mutants the apical cells do not appear to have migrated through the cluster of basal cells as expected and basal stalks have not yet started to form. At 39-40 hours APF ovaries from mutant pupae have started to form stalks that are shorter and thicker than wild-type, some of which show incomplete separation.