Germline cells are progressively lost in the testes of Nup98-96²²⁸⁸/Df(3R)mbc-R1 males. The gonads of Nup98-96²²⁸⁸/Df(3R)mbc-R1 embryos are similar in size to wild type. However, by the third larval instar, mutant testes are smaller than wild type and do not contain any early stage germ line cells (germline stem cells, gonialblasts or spermatogonia), although spermatocytes are present. Fusomes in the mutant testes consistently have fewer than 16 branches and appear to connect to only two, four or eight spermatocytes, suggesting fewer than the normal 4 rounds of amplification divisions have occurred. The testes of Nup98-96²²⁸⁸/Df(3R)mbc-R1 adults completely lack early germ line cells and rarely contain late stage germline cells. The mutant adult testis is much shorter than normal.

Both spectrosomes and fusomes are absent in most germaria of homozygous and Nup98-96²²⁸⁸/Df(3R)mbc-R1 females. The number of germline cells in the mutant adult females is reduced compared to wild type and does not change significantly between three and ten days after eclosion.