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Y chromosome

Reviewed January 2009

What is the Y chromosome?

The Y chromosome is one of the two sex chromosomes in humans (the other is the X chromosome). The sex chromosomes form one of the 23 pairs of human chromosomes in each cell. The Y chromosome spans about 58 million base pairs (the building blocks of DNA) and represents almost 2 percent of the total DNA in cells.

Each person normally has one pair of sex chromosomes in each cell. The Y chromosome is present in males, who have one X and one Y chromosome, while females have two X chromosomes.

Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. The Y chromosome likely contains between 70 and 200 genes. Because only males have the Y chromosome, the genes on this chromosome tend to be involved in male sex determination and development. Sex is determined by the SRY gene, which is responsible for the development of a fetus into a male. Other genes on the Y chromosome are important for male fertility.

Many genes are unique to the X or Y chromosome, but genes in an area known as the pseudoautosomal region are present on both chromosomes. As a result, men and women each have two functional copies of these genes. Many genes in the pseudoautosomal region are essential for normal development.

Genes on the Y chromosome are among the estimated 20,000 to 25,000 total genes in the human genome.

Genetics Home Reference includes these genes on the Y chromosome:

  • SHOX:short stature homeobox
  • SRY:sex determining region Y
  • USP9Y:ubiquitin specific peptidase 9, Y-linked (fat facets-like, Drosophila)

GeneCards provides a table of genes on the Y chromosome and disorders related to those genes (http://www.genecards.org/cgi-bin/listdiseasecards.pl?type=chrom&search=Y).

There are many genetic conditions related to genes on the Y chromosome.

Genetics Home Reference includes these conditions related to genes on the Y chromosome:

  • Swyer syndrome
  • 46,XX testicular disorder of sex development
  • Y chromosome infertility

GeneCards provides a table of genes on the Y chromosome and disorders related to those genes (http://www.genecards.org/cgi-bin/listdiseasecards.pl?type=chrom&search=Y).

What chromosomal conditions are related to the Y chromosome?

The following conditions are caused by changes in the structure or number of copies of the Y chromosome.

Klinefelter syndrome

Most males with Klinefelter syndrome have one extra copy of the X chromosome in each cell (47,XXY). The additional X chromosome disrupts normal sexual development and causes infertility (an inability to father children).

Variants of Klinefelter syndrome can involve more than one extra sex chromosome. In a small percentage of cases, males with variant Klinefelter syndrome have an extra copy of both the X and Y chromosomes, for a total of two X chromosomes and two Y chromosomes (48,XXYY) in each cell.

46,XX testicular disorder of sex development

In most individuals with 46,XX testicular disorder of sex development, the condition results from an abnormal exchange of genetic material between chromosomes (translocation). This exchange occurs as a random event during the formation of sperm cells in the affected person's father. The translocation affects the gene responsible for development of a fetus into a male (the SRY gene). The SRY gene, which is normally found on the Y chromosome, is misplaced in this disorder, almost always onto an X chromosome. A fetus with an X chromosome that carries the SRY gene will develop as a male despite not having a Y chromosome.

47,XYY syndrome

Males with 47,XYY syndrome have one X chromosome and two Y chromosomes in each cell, for a total of 47 chromosomes. It is unclear why an extra copy of the Y chromosome is associated with tall stature and learning problems in some boys and men.

Some males with 47,XYY syndrome have an extra Y chromosome in only some of their cells. This phenomenon is called 46,XY/47,XYY mosaicism.

Y chromosome infertility

Y chromosome infertility is usually caused by deletions of genetic material in regions of the Y chromosome called azoospermia factor (AZF) A, B, or C. Genes in these regions are believed to provide instructions for making proteins involved in sperm cell development, although the specific functions of these proteins are unknown.

Deletions in the AZF regions may affect several genes. The missing genetic material likely prevents production of a number of proteins needed for normal sperm cell development, resulting in an inability to father children.

other chromosomal conditions

Chromosomal conditions involving the sex chromosomes often affect sex determination (whether a person has the sexual characteristics of a male or a female), sexual development, and the ability to have children (fertility). The signs and symptoms of these conditions vary widely and range from mild to severe. They can be caused by missing or extra copies of the sex chromosomes or by structural changes in these chromosomes.

Rarely, males may have more than one extra copy of the Y chromosome in every cell (polysomy Y). For example, the presence of two extra Y chromosomes is written as 48,XYYY. The extra genetic material in these cases can lead to skeletal abnormalities, decreased IQ, and delayed development, but the features of these conditions are variable.

Is there a standard way to diagram the Y chromosome?

Geneticists use diagrams called ideograms as a standard representation for chromosomes. Ideograms show a chromosome's relative size and its banding pattern. A banding pattern is the characteristic pattern of dark and light bands that appears when a chromosome is stained with a chemical solution and then viewed under a microscope. These bands are used to describe the location of genes on each chromosome.

Ideogram of the Y chromosome
See How do geneticists indicate the location of a gene? (http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation) in the Handbook.

Where can I find additional information about the Y chromosome?

You may find the following resources about the Y chromosome helpful. These materials are written for the general public.

  • Additional NIH Resources - National Institutes of Health
    • National Human Genome Research Institute: Chromosome Abnormalities (http://www.genome.gov/11508982)
    • National Human Genome Research Institute: Researchers Discover Use of Novel Mechanism Preserves Y Chromosome Genes (June 18, 2003) (http://www.genome.gov/11007628)
  • Educational resources - Information pages
    • Genome News Network: Sex and "The Y" (June 27, 2003) (http://www.genomenewsnetwork.org/articles/06_03/y_chrom.shtml)
    • Pacific Northwest Regional Genetics Group: 47,XYY Syndrome (http://mchneighborhood.ichp.edu/pacnorgg/media/Sex_Chrom/xyy_eng.pdf)
    • The Wellcome Trust: Y Chromosome Quick Facts (http://genome.wellcome.ac.uk/doc%5Fwtd020746.html)
    • The Wellcome Trust: Y Chromosome Sequence Unveiled (http://genome.wellcome.ac.uk/doc%5Fwtd020714.html)
    • University of British Columbia: Trisomy X or Y Mosaicism (http://www.medgen.ubc.ca/wrobinson/mosaic/specific/chrom_xy.htm)
  • MedlinePlus - Health information
    Encyclopedia: Chromosome (http://www.nlm.nih.gov/medlineplus/ency/article/002327.htm)

You may also be interested in these resources, which are designed for genetics professionals and researchers.

  • Gene Reviews - Clinical summary (http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=gene&part=yci)
  • Gene Tests - DNA tests ordered by healthcare professionals
    • DNA Test: Y Chromosome Detection (http://www.genetests.org/query?testid=2559)
    • DNA Test: Y Chromosome Infertility (http://www.genetests.org/query?testid=193552)
  • Research Resources - Tools for researchers
    • Cancer Genetics Web (http://www.cancerindex.org/geneweb/clinkc24.htm)
    • Database of Genomic Variants (http://projects.tcag.ca/variation/cgi-bin/tbrowse/tbrowse?source=hg17&table=Locus&show=table&keyword=&flop=AND&fcol=_C19&fcomp==&fkwd=chrY&cols=)
    • Ensembl Human Map View (http://www.ensembl.org/Homo_sapiens/mapview?chr=Y)
    • Oak Ridge National Laboratory: Chromosome Y Overview (http://genome.ornl.gov/cgi-bin/GCat/GetChrom.cgi?org=human&chr=Y)
    • The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003 Jun 19;423(6942):825-37. (http://www.nature.com/nature/journal/v423/n6942/full/nature01722.html)
    • U.S. Department of Energy: Human Chromosome Launchpad (http://www.ornl.gov/sci/techresources/Human_Genome/launchpad/chromY.shtml)
    • Y Chromosome Haplotype Reference Database (YHRD) (http://www.yhrd.org/)
  • PubMed - Recent literature (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=PubMed&term=(Chromosomes,+Human,+Y[MAJR])+AND+(Y+Chromosome[TI])+AND+english[la]+AND+human[mh]&orig_db=PubMed&filters=ON&pmfilter_EDatLimit=360+Days)
  • Map Viewer - Genetic maps (http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?org=human&maps=ideogr,morbid,pheno&zoom=100&chr=Y)

What glossary definitions help with understanding the Y chromosome?

azoospermia ; base pair ; cell ; chromosome ; deletion ; DNA ; fertility ; fetus ; gene ; infertility ; IQ ; mosaicism ; protein ; pseudoautosomal region ; sex chromosomes ; sex determination ; sign ; sperm ; spermatogenesis ; stature ; symptom ; syndrome ; translocation

You may find definitions for these and many other terms in the Genetics Home Reference Glossary (http://ghr.nlm.nih.gov/glossary).

References
  • Ensembl Human Map View (http://www.ensembl.org/Homo_sapiens/mapview?chr=Y)
  • Ginalski K, Rychlewski L, Baker D, Grishin NV. Protein structure prediction for the male-specific region of the human Y chromosome. Proc Natl Acad Sci U S A. 2004 Feb 24;101(8):2305-10. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=14983005)
  • Krausz C, Quintana-Murci L, Forti G. Y chromosome polymorphisms in medicine. Ann Med. 2004;36(8):573-83. Review. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=15768829)
  • Li Z, Haines CJ, Han Y. "Micro-deletions" of the human Y chromosome and their relationship with male infertility. J Genet Genomics. 2008 Apr;35(4):193-9. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=18439975)
  • Map Viewer: Genes on Sequence (http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=human&MAPS=ideogr,ugHs,genes&CHR=Y)
  • Noordam MJ, Repping S. The human Y chromosome: a masculine chromosome. Curr Opin Genet Dev. 2006 Jun;16(3):225-32. Epub 2006 May 2. Review. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=16650761)
  • Nussbaum, Robert L; McInnes, Roderick R; Willard, Huntington F; Thompson, Margaret W((Margaret Wilson),); Thompson & Thompson genetics in medicine.; 6th ed., rev. reprint / Robert L. Nussbaum, Roderi; Philadelphia : Saunders, c2004.
  • Rizvi AA. 46, XX man with SRY gene translocation: cytogenetic characteristics, clinical features and management. Am J Med Sci. 2008 Apr;335(4):307-9. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=18414071)
  • Russo P, Siani A, Miller MA, Karanam S, Esposito T, Gianfrancesco F, Barba G, Lauria F, Strazzullo P, Cappuccio FP. Genetic variants of Y chromosome are associated with a protective lipid profile in black men. Arterioscler Thromb Vasc Biol. 2008 Aug;28(8):1569-74. Epub 2008 May 29. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=18511697)
  • Skaletsky H, Kuroda-Kawaguchi T, Minx PJ, Cordum HS, Hillier L, Brown LG, Repping S, Pyntikova T, Ali J, Bieri T, Chinwalla A, Delehaunty A, Delehaunty K, Du H, Fewell G, Fulton L, Fulton R, Graves T, Hou SF, Latrielle P, Leonard S, Mardis E, Maupin R, McPherson J, Miner T, Nash W, Nguyen C, Ozersky P, Pepin K, Rock S, Rohlfing T, Scott K, Schultz B, Strong C, Tin-Wollam A, Yang SP, Waterston RH, Wilson RK, Rozen S, Page DC. The male-specific region of the human Y chromosome is a mosaic of discrete sequence classes. Nature. 2003 Jun 19;423(6942):825-37. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=12815422)
  • Tyler-Smith C. An evolutionary perspective on Y-chromosomal variation and male infertility. Int J Androl. 2008 Aug;31(4):376-82. Review. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=18399979)
  • UCSC Genome Browser: Statistics from NCBI Build 36, March 2006 (http://genome.cse.ucsc.edu/goldenPath/stats.html)
  • Vogt PH, Falcao CL, Hanstein R, Zimmer J. The AZF proteins. Int J Androl. 2008 Aug;31(4):383-94. Review. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=18462373)
  • Vogt PH. Azoospermia factor (AZF) in Yq11: towards a molecular understanding of its function for human male fertility and spermatogenesis. Reprod Biomed Online. 2005 Jan;10(1):81-93. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=15705299)
  • Walzer S, Bashir AS, Silbert AR. Cognitive and behavioral factors in the learning disabilities of 47,XXY and 47,XYY boys. Birth Defects Orig Artic Ser. 1990;26(4):45-58. No abstract available. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=2090328)
  • Waters PD, Wallis MC, Marshall Graves JA. Mammalian sex--Origin and evolution of the Y chromosome and SRY. Semin Cell Dev Biol. 2007 Jun;18(3):389-400. Epub 2007 Feb 24. Review. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=17400006)
  • Willard HF. Tales of the Y chromosome. Nature. 2003 Jun 19;423(6942):810-1, 813. No abstract available. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=12815408)

 

The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? (http://ghr.nlm.nih.gov/handbook/consult/findingprofessional) in the Handbook.

 
Reviewed: January 2009
Published: January 23, 2009