The phenotype of an individual may be effected if the modified allele produces
I) No enzyme at all
II) The normal / less efficient enzyme
III) A non-functional enzyme
 

If the modified allele produces normal / less efficient enzyme, it is equivalent to the unmodified allele, i.e., it will produce the same phenotype/trait, i.e., result in the transformation of substrate S. But, if the modified allele produces a non-functional enzyme or no enzyme, the phenotype may be effected.