About half of Hr46^G60S/Df(2R)12 rescued to the third instar by Hr46^hs.PL and heatshock, display defects in their tracheal system. Although formation and branching appear normal, the cuticular structure of the tracheae is defective. The taenidial folds of the tracheal cuticle can be very distorted. In the more severe cases, this can lead to collapse of the tracheal cuticle and obstruction of the lumen, followed by necrosis. Hr46^G60S/Df(2R)12 rescued by Hr46^hs.PL and heat shock, show three distinct lethal phases during metamorphosis. About 25% die during prepupal development. Some of the dead prepupae are slightly bent at the anterior end and fail to fully evert their anterior spiracles. All dead prepupae display defects in gas bubble translocation. About 70% die in the major lethal phase, during early pupal development. This is associated with incomplete eversion of the k adult head and defects in gas bubble translocation, the legs however appear to evert and elongate normally. 5% survive until the pharate adult stage. In contrast to wild-type, salivary glands often survive 24hrs after puparium formation. Generation of Hr46^G60S mutant clones result in a high frequency of adults with wings that are curved or folded and held out from the body, with the position of the clones corresponding to the deformations seen in the wing. Legs appear wild-type in phenotype. No reduction in size of clones is seen. Mutants are also associated with short and rough macrochaetae on the head and thorax, though bristles on the legs are wild-type in appearance. Loss of Hr46 activity is not cell lethal.

Hemizygotes die during the embryonic stage.