In cases where there is a deletion of part of the short arm of chromosome Y, a female phenotype is found because of
the deletion of a gene called SRY that is responsible for testicular development.
This condition is rare. Deletions in the long arm of chromosome Y that do not cause
a loss of the normal male phenotype but that may be associated with the absence
of sperm formation are more common. In most of these cases the deletion is in a
region that does not encode genes and thus has no clinical significance.
If a short Y chromosome is identified, the father should be examined. When the father's
Y chromosome is identical to that found in the fetus, the deletion has no significance,
but when the father does not have an identical Y chromosome structure, and paternity
is not in doubt, the deletion in the fetus may have consequences for the offspring's
final height and sterility (because of a lack of sperm cells), although these conditions
can be treated.
Some men who are sterile have deletions in certain regions of the long arm of the
Y chromosome. These can be detected using molecular methods.