Females have two X chromosomes while males have one X-chromosome and one Y-chromosome. Genetic disorders caused by mutations in the Y-chromosome cannot affect females as they do not have a Y-chromosome.
If the father has a genetic disorder that is caused due to a mutation found on the Y-chromosome, irrespective of the genetic profile of the mother, it will certainly be passed on to the male offspring. Also, the disorder cannot be passed on to the female offspring as the female offspring receives only the X-chromosome from the father, not the Y-chromosome.
There are a relatively small list of genetic disorders caused due to mutations on the Y-chromosome as this chromosome is small and contains very few genes as compared to the X-chromosome.