The rate of Y chromosome loss in the developing wing imaginal disc in homozygous males is not significantly different from that seen in wild type.

Su(var)3-9^ptn is a strong enhancer of position effect variegation (PEV); for example, In(1)w^m4h/Y ; Su(var)3-9^ptn/+ males have a complete w and rst eye mutant phenotype and variegation for vt and In(1)w^m4h females show variegation for N, whereas In(1)w^m4h ; + flies only show variegation of the w gene. Heterozygous females show wild-type fecundity and all of their eggs are fertilised. However, larvae do not hatch from these eggs. When Su(var)3-9^ptn/+ females are mated to wild-type males, two types of embryos are seen. In 50%, development is arrested shortly after initiation of cleavage divisions. Most of these embryos do not initiate cleavage or are arrested around cleavage cycle 1-3 and have a maximum of six small nuclei that appear abnormal in chromatin structure (only 11.5% reach cleavage cycles 4-10). These embryos are zygotically heterozygous for Su(var)3-9^ptn. The other 50% of embryos develop to the larval stage. They have defective cephalopharyngeal head skeletons and do not hatch. These embryos are zygotically wild-type for Su(var)3-9. Three types of embryos develop from Su(var)3-9^ptn/+ females crossed to Su(var)3-9^ptn/+ males. Cleavage divisions do not initiate in 50% of the embryos (these embryos are either zygotically heterozygous for a maternally derived copy of Su(var)3-9^ptn, or are zygotically homozygous for Su(var)3-9^ptn, having received both a paternal and maternal copy), and 25% have abnormal head skeleton development (these are zygotically wild-type for Su(var)3-9). The remaining 25% of embryos contain several hundred small nuclei that are irregularly distributed. The nuclei are strongly condensed and chromatin is frequently fragmented. Cleavage initiates in these embryos, but the nuclei never populate the entire cortex and no blastoderm is formed. These embryos are zygotically heterozygous for a paternally derived copy of Su(var)3-9^ptn. All embryos produced by wild-type females crossed to Su(var)3-9^ptn/+ males develop normally. The egg cell nucleus develops abnormally in homozygous egg chambers. Clumps of condensed chromatin are often seen within nurse cell nuclei and the number of follicle cells is reduced. Chimeric females carrying Su(var)3-9^ptn/+ pole cells in a Su(var)3-9⁺ background produce eggs which show the typical Su(var)3-9^ptn/+ mutant phenotype, indicating that Su(var)3-9^ptn-related female sterility is germ-line dependent. Chimeric females carrying wild-type germ cells in a Su(var)3-9^ptn/+ soma give rise to offspring originating from the transplanted wild-type germ cells (as well as eggs derived from Su(var)3-9^ptn/+ germ cells which fail to hatch).

The suppressor effect of Su(var)3-9 mutations on position effect variegation cannot dominate the enhancer effect of Su(var)3-9^ptn on position effect variegation.

In(1)w^m4h, Su(var)3-9^ptn has partially lethal phenotype

In(1)rst³, Su(var)3-9^ptn has partially lethal phenotype

In(1)sc⁸, Su(var)3-9^ptn has partially lethal phenotype

In(1)sc^S1, Su(var)3-9^ptn has partially lethal phenotype

Df(3L)AC1, Su(var)3-9^ptn has oocyte nucleus phenotype

Df(3L)AC1, Su(var)3-9^ptn has nurse cell & nucleus phenotype

Su(var)3-9^ptn, l(3)S089004^S089302 has follicle cell phenotype

Su(var)3-9^ptn, l(3)S089004^S089302 has oocyte nucleus phenotype

Su(var)3-9^ptn, l(3)S089004^S089302 has nurse cell & nucleus phenotype

Su(var)3-9^ptn, l(3)S089004^S089004 has oocyte nucleus phenotype

Su(var)3-9^ptn, l(3)S089004^S089004 has nurse cell & nucleus phenotype

Df(3L)AC1, Su(var)3-9^ptn has follicle cell phenotype