Function of Genes on Chromosome Y and Diseases Associated with the Y Chromosome

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Facts About the Y Chromosome

The Y chromosome is one of the sex chromosomes found in the cells of males. Males have an X chromosome and a Y chromosome. The XY pair is one of the 23 pairs of chromosomes found in cells. Females have two X chromosomes.

The Y chromosome is unique because it is responsible for sex determination. Its presence or absence in cells determines whether a fetus will develop as a male or female.

Like other chromosomes, the Y chromosome is a bundle of DNA. It contains about 58 million base pairs and a hundred or so genes.1 Each gene contains the base pair sequence required for the cell to produce a specific protein.


SHOX is the acronym for the short stature homeobox gene. It is one of the genes on chromosome Y. A copy of it is also present in the X chromosome. The gene contains the genetic sequence for the SHOX protein. The SHOX protein is involved in the early development of the skeleton. It regulates the activity of other genes and helps in the formation of bones in the arms and legs.2

Disorders of the SHOX Gene

A mutation in the SHOX gene can cause skeletal abnormalities. Leri-Weill dyschondrosteosis is a genetic disorder caused by an improperly functioning SHOX gene. It is characterized by abnormally small forearms and lower legs. A more severe disorder associated with the SHOX gene is Langer mesomelic dysplasia, which is characterized by even shorter bones in the arms and legs, as well as an underdeveloped jaw.2

SRY Gene

SRY stands for the Sex-determining Region Y gene. It is another one of the genes on chromosome Y, and it is responsible for synthesizing the SRY protein. The SRY protein activates other genes and facilitates the development of the fetus as a male.

Disorders of the SRY Gene

A mutation in the SRY Gene inhibits the production of the SRY protein, which leads to Swyer Syndrome. The fetus will develop as a female, even though the cells contain a Y chromosome. A similar disorder occurs when the SRY gene mistakenly translocates to the X chromosome. In this case, SRY proteins are produced, so the fetus will develop as a male, despite the lack of a Y chromosome.3

USP9Y Gene

Another gene on the Y chromosome is the USP9Y gene. It stands for Ubiquitin Specific Peptidase 9, Y-linked gene. It is responsible for producing the ubiquitin-specific protease 9 protein, which is involved in sperm cell development.

Disorders of the USP9Y Gene

A mutation in the USP9Y gene prevents the cell from producing normal ubiquitin-specific protease 9 proteins. This leads to a disorder called Y chromosome infertility, which is characterized by inactive or reduced sperm cell production.4


1. “Y Chromosome.” Genetics Home Reference.

2. “SHOX.” Genetics Home Reference.

3. “SRY.” Genetics Home Reference.

4. “USP9Y.” Genetics Home Reference.