What is the Y Chromosome?

By Dr. Ananya Mandal, MDReviewed by Sally Robertson, B.Sc.

There are 23 pairs of chromosomes in the human body which include 22 pairs of autosomal chromosomes that are common to both men and women and one pair of sex chromosomes that determine an individual’s gender (the X chromosome and the Y chromosome).

In a man, both an X and a Y chromosome are present, giving an XY configuration and in a woman there are two X and no Y chromosomes, giving an XX configuration.

Functions of the Y chromosome

In mammals, the Y chromosome contains the SRY gene which is key to the development of the testes in males. Without this gene, the testes would not develop and the fetus would become a female.

The Y chromosome spans approximately 58 million base pairs, contains 86 genes, and represents around 2% of the total DNA in a human male. Traits that are passed from father to son on the Y chromosome are referred to as holandric traits, meaning they only occur in males. Aside from very small regions present at the telomeres, the Y chromosome is unable to recombine with an X chromosome. This majority portion of the Y chromosome is referred to as the non-combining region of the Y chromosome and the single nucleotide polymorphisms in this region are used to determine paternal ancestry.

Genes on the Y chromosome

Genes present on the Y chromosome that correspond to a similar gene on the X chromosome include:

• AMELY/AMELX (amelogenin)
• RPS4Y1/RPS4Y2/RPS4X (ribosomal protein S4)

Genes that are exclusive to the Y chromosome include:

• AZF1 (azoospermia factor 1)
• BPY2 (basic protein on the Y chromosome)
• DAZ1 (deleted in azoospermia 1)
• DAZ2 (deleted in azoospermia 2)
• PRKY (Y-linked protein kinase)
• RBMY1A1 (RNA Binding Motif Protein, Y-linked, family 1, member A1) 
• SRY (sex-determining region Y)
• TSPY (testis-specific protein, Y-linked)
• USP9Y (ubiquitin specific peptidase 9, Y-linked)
• UTY (ubiquitously transcribed tetratricopeptide repeat containing, TPR gene on Y-linked)
• ZFY (zinc finger protein, Y-linked)

Y-linked disease or disorders

Severalc onditions that are specifically linked to the Y chromosome and only transmitted from father to son include:

• Defective or deformed Y chromosome that leads to features of feminization and infertility
• Numerical disorders – These are conditions that arise due to the presence of an abnormal number of chromosomes. In Klinefelter’s syndrome, for example, an additional X chromosome is present, giving an XXY configuration. This condition is characterized by hypogonadism which usually manifests after puberty and refers to incompetence of the gonads in producing androgen, sperm, or both, which can render the male sterile.

Further Reading

• All Chromosome Y Content
• Y Chromosome Evolution
• What is Superman Syndrome?