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Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®

X chromosome

Reviewed January 2012

What is the X chromosome?

The X chromosome is one of the two sex chromosomes in humans (the other is the Y chromosome). The sex chromosomes form one of the 23 pairs of human chromosomes in each cell. The X chromosome spans about 155 million DNA building blocks (base pairs) and represents approximately 5 percent of the total DNA in cells.

Each person normally has one pair of sex chromosomes in each cell. Females have two X chromosomes, while males have one X and one Y chromosome. Early in embryonic development in females, one of the two X chromosomes is randomly and permanently inactivated in cells other than egg cells. This phenomenon is called X-inactivation or Lyonization. X-inactivation ensures that females, like males, have one functional copy of the X chromosome in each body cell. Because X-inactivation is random, in normal females the X chromosome inherited from the mother is active in some cells, and the X chromosome inherited from the father is active in other cells.

Some genes on the X chromosome escape X-inactivation. Many of these genes are located at the ends of each arm of the X chromosome in areas known as the pseudoautosomal regions. Although many genes are unique to the X chromosome, genes in the pseudoautosomal regions are present on both sex chromosomes. As a result, men and women each have two functional copies of these genes. Many genes in the pseudoautosomal regions are essential for normal development.

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 X chromosome likely contains 800 to 900 genes that provide instructions for making proteins. These proteins perform a variety of different roles in the body.

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

Genetics Home Reference provides information about the following genes on the X chromosome:

  • ABCB7
  • ABCD1
  • AFF2
  • ALAS2
  • ANOS1
  • AR
  • ARSE
  • ARX
  • ATP7A
  • ATRX
  • AVPR2
  • BCOR
  • BTK
  • CASK
  • CD40LG
  • CDKL5
  • CHM
  • CLCN5
  • COL4A5
  • CYBB
  • DCX
  • DKC1
  • DMD
  • EBP
  • EDA
  • EMD
  • F8
  • F9
  • FGD1
  • FLNA
  • FMR1
  • FOXP3
  • FRMD7
  • G6PD
  • GATA1
  • GJB1
  • GLA
  • GPC3
  • GPR143
  • HCCS
  • HDAC8
  • HPRT1
  • HSD17B10
  • IDS
  • IL2RG
  • KDM6A
  • L1CAM
  • LAMP2
  • MAGT1
  • MECP2
  • MED12
  • MID1
  • MTM1
  • NDP
  • NR0B1
  • NYX
  • OCRL
  • OFD1
  • OPN1LW
  • OPN1MW
  • OTC
  • PDHA1
  • PGK1
  • PHEX
  • PHF8
  • PHKA1
  • PHKA2
  • PIGA
  • PLP1
  • POU3F4
  • PQBP1
  • PRPS1
  • RP2
  • RPGR
  • RPS6KA3
  • RS1
  • SH2D1A
  • SHOX
  • SLC6A8
  • SLC9A6
  • SLC16A2
  • SMC1A
  • SMS
  • TAF1
  • TAZ
  • TIMM8A
  • UBA1
  • WAS
  • XIAP
  • XK

How are changes in the X chromosome related to health conditions?

Many genetic conditions are related to changes in particular genes on the X chromosome. This list of disorders associated with genes on the X chromosome provides links to additional information.

Genetics Home Reference provides information about the following conditions related to genes on the X chromosome:

  • 17β-hydroxysteroid dehydrogenase type 10 deficiency
  • Aarskog-Scott syndrome
  • Allan-Herndon-Dudley syndrome
  • alpha thalassemia X-linked intellectual disability syndrome
  • Alport syndrome
  • amelogenesis imperfecta
  • androgenetic alopecia
  • androgen insensitivity syndrome
  • anhidrotic ectodermal dysplasia with immune deficiency
  • Arts syndrome
  • Barth syndrome
  • CASK-related intellectual disability
  • Charcot-Marie-Tooth disease
  • choroideremia
  • Christianson syndrome
  • chronic granulomatous disease
  • Coffin-Lowry syndrome
  • color vision deficiency
  • congenital hemidysplasia with ichthyosiform erythroderma and limb defects
  • Cornelia de Lange syndrome
  • cutis laxa
  • Danon disease
  • deafness-dystonia-optic neuronopathy syndrome
  • Dent disease
  • DMD-associated dilated cardiomyopathy
  • Duchenne and Becker muscular dystrophy
  • dyserythropoietic anemia and thrombocytopenia
  • dyskeratosis congenita
  • Emery-Dreifuss muscular dystrophy
  • Fabry disease
  • familial dilated cardiomyopathy
  • familial exudative vitreoretinopathy
  • FG syndrome
  • focal dermal hypoplasia
  • fragile X-associated primary ovarian insufficiency
  • fragile X-associated tremor/ataxia syndrome
  • fragile XE syndrome
  • fragile X syndrome
  • frontometaphyseal dysplasia
  • glucose-6-phosphate dehydrogenase deficiency
  • glycogen storage disease type IX
  • hemophilia
  • hereditary hypophosphatemic rickets
  • hypohidrotic ectodermal dysplasia
  • immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome
  • incontinentia pigmenti
  • inherited thyroxine-binding globulin deficiency
  • intestinal pseudo-obstruction
  • isolated growth hormone deficiency
  • isolated lissencephaly sequence
  • Joubert syndrome
  • Kabuki syndrome
  • Kallmann syndrome
  • L1 syndrome
  • Langer mesomelic dysplasia
  • Leigh syndrome
  • Lenz microphthalmia syndrome
  • Léri-Weill dyschondrosteosis
  • Lesch-Nyhan syndrome
  • Lowe syndrome
  • Lujan syndrome
  • McLeod neuroacanthocytosis syndrome
  • MECP2 duplication syndrome
  • MECP2-related severe neonatal encephalopathy
  • Melnick-Needles syndrome
  • Menkes syndrome
  • microphthalmia
  • microphthalmia with linear skin defects syndrome
  • mucopolysaccharidosis type II
  • nephrogenic diabetes insipidus
  • nonsyndromic hearing loss
  • Norrie disease
  • ocular albinism
  • oculofaciocardiodental syndrome
  • Ohdo syndrome, Maat-Kievit-Brunner type
  • Opitz G/BBB syndrome
  • oral-facial-digital syndrome
  • ornithine transcarbamylase deficiency
  • osteopetrosis
  • otopalatodigital syndrome type 1
  • otopalatodigital syndrome type 2
  • paroxysmal nocturnal hemoglobinuria
  • Partington syndrome
  • Pelizaeus-Merzbacher disease
  • periventricular heterotopia
  • phosphoglycerate kinase deficiency
  • phosphoribosylpyrophosphate synthetase superactivity
  • porphyria
  • PPM-X syndrome
  • primary ciliary dyskinesia
  • prostate cancer
  • pyruvate dehydrogenase deficiency
  • Renpenning syndrome
  • retinitis pigmentosa
  • Rett syndrome
  • severe congenital neutropenia
  • Simpson-Golabi-Behmel syndrome
  • Snyder-Robinson syndrome
  • spastic paraplegia type 2
  • spinal and bulbar muscular atrophy
  • spinal muscular atrophy
  • Swyer syndrome
  • Turner syndrome
  • type 1 diabetes
  • warfarin sensitivity
  • Wiskott-Aldrich syndrome
  • X-linked adrenal hypoplasia congenita
  • X-linked adrenoleukodystrophy
  • X-linked agammaglobulinemia
  • X-linked chondrodysplasia punctata 1
  • X-linked chondrodysplasia punctata 2
  • X-linked congenital stationary night blindness
  • X-linked creatine deficiency
  • X-linked dystonia-parkinsonism
  • X-linked hyper IgM syndrome
  • X-linked immunodeficiency with magnesium defect, Epstein-Barr virus infection, and neoplasia
  • X-linked infantile nystagmus
  • X-linked infantile spasm syndrome
  • X-linked intellectual disability, Siderius type
  • X-linked juvenile retinoschisis
  • X-linked lissencephaly with abnormal genitalia
  • X-linked lymphoproliferative disease
  • X-linked myotubular myopathy
  • X-linked severe combined immunodeficiency
  • X-linked sideroblastic anemia
  • X-linked sideroblastic anemia and ataxia
  • X-linked spondyloepiphyseal dysplasia tarda
  • X-linked thrombocytopenia

Changes in the structure or number of copies of a chromosome can also cause problems with health and development. The following chromosomal conditions are associated with such changes in the X chromosome.

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.

48,XXYY syndrome

48,XXYY syndrome is caused by the presence of an extra X chromosome and an extra Y chromosome in a male's cells. Extra genetic material from the X chromosome interferes with male sexual development, preventing the testes from functioning normally and reducing the levels of testosterone in adolescent and adult males. Extra copies of genes from the pseudoautosomal regions of the extra X and Y chromosome contribute to the signs and symptoms of 48,XXYY syndrome; however, the specific genes have not been identified.

intestinal pseudo-obstruction

Intestinal pseudo-obstruction, a condition characterized by impairment of the muscle contractions that move food through the digestive tract (peristalsis), can be caused by genetic changes within the X chromosome.

Some individuals with intestinal pseudo-obstruction have mutations, duplications, or deletions of genetic material in the X chromosome that affect the FLNA gene. Researchers believe that these genetic changes may impair the function of the filamin A protein, causing abnormalities in the cytoskeleton of nerve cells (neurons) in the gastrointestinal tract. These abnormalities result in impaired peristalsis, which causes abdominal pain and the other gastrointestinal symptoms of intestinal pseudo-obstruction.

Deletions or duplications of genetic material that affect the FLNA gene can also include adjacent genes on the X chromosome. Changes in adjacent genes may account for some of the other signs and symptoms, such as neurological abnormalities and unusual facial features, that occur in some affected individuals.

Klinefelter syndrome

Klinefelter syndrome is caused by the presence of one or more extra copies of the X chromosome in a male's cells. Extra genetic material from the X chromosome interferes with male sexual development, preventing the testes from functioning normally and reducing the levels of testosterone (a hormone that directs male sexual development). A shortage of testosterone can lead to delayed or incomplete puberty, genital abnormalities, breast enlargement (gynecomastia), reduced facial and body hair, and an inability to have biological children (infertility). Children with Klinefelter syndrome may also have learning disabilities, delayed speech and language development, and a shy and unassuming personality.

Typically, people with Klinefelter syndrome have one extra copy of the X chromosome in each cell, for a total of two X chromosomes and one Y chromosome (47,XXY). Less commonly, affected individuals may have two or three extra X chromosomes (48,XXXY or 49,XXXXY). As the number of extra sex chromosomes increases, so does the risk of learning problems, intellectual disability, birth defects, and other health issues.

Some people with features of Klinefelter syndrome have the extra X chromosome in only some of their cells; in these individuals, the condition is described as mosaic Klinefelter syndrome (46,XY/47,XXY). Individuals with mosaic Klinefelter syndrome may have milder signs and symptoms, depending on how many cells have an additional X chromosome.

microphthalmia with linear skin defects syndrome

A deletion of genetic material in a region of the X chromosome called Xp22 causes microphthalmia with linear skin defects syndrome. This region includes a gene called HCCS, which carries instructions for producing an enzyme called holocytochrome c-type synthase. This enzyme helps produce a molecule called cytochrome c. Cytochrome c is involved in a process called oxidative phosphorylation, by which mitochondria generate adenosine triphosphate (ATP), the cell's main energy source. It also plays a role in the self-destruction of cells (apoptosis).

A deletion of genetic material that includes the HCCS gene prevents the production of the holocytochrome c-type synthase enzyme. In females (who have two X chromosomes), some cells produce a normal amount of the enzyme and other cells produce none. The resulting overall reduction in the amount of this enzyme leads to the signs and symptoms of microphthalmia with linear skin defects syndrome.

In males (who have only one X chromosome), a deletion that includes the HCCS gene results in a total loss of the holocytochrome c-type synthase enzyme. A lack of this enzyme appears to be lethal very early in development, so almost no males are born with microphthalmia with linear skin defects syndrome. A few affected individuals with male appearance but who have two X chromosomes have been identified.

A reduced amount of the holocytochrome c-type synthase enzyme can damage cells by impairing their ability to generate energy. In addition, without the holocytochrome c-type synthase enzyme, the damaged cells may not be able to undergo apoptosis. These cells may instead die in a process called necrosis that causes inflammation and damages neighboring cells. During early development this spreading cell damage may lead to the eye and skin abnormalities characteristic of microphthalmia with linear skin defects syndrome.

triple X syndrome

Triple X syndrome (also called 47,XXX or trisomy X) results from an extra copy of the X chromosome in each of a female's cells. Females with triple X syndrome have three X chromosomes, for a total of 47 chromosomes per cell. An extra copy of the X chromosome is associated with tall stature, learning problems, and other features in some girls and women.

Some females with triple X syndrome have an extra X chromosome in only some of their cells. This phenomenon is called 46,XX/47,XXX mosaicism.

Females with more than one extra copy of the X chromosome (48,XXXX or 49,XXXXX) have been identified, but these chromosomal changes are rare. As the number of extra sex chromosomes increases, so does the risk of learning problems, intellectual disability, birth defects, and other health issues.

Turner syndrome

Turner syndrome results when one normal X chromosome is present in a female's cells and the other sex chromosome is missing or structurally altered. The missing genetic material affects development before and after birth, leading to short stature, ovarian malfunction, and the other features of Turner syndrome.

About half of individuals with Turner syndrome have monosomy X (45,X), which means each cell in an individual's body has only one copy of the X chromosome instead of the usual two sex chromosomes. Turner syndrome can also occur if one of the sex chromosomes is partially missing or rearranged rather than completely absent.

Some women with Turner syndrome have a chromosomal change in only some of their cells, which is known as mosaicism. Some cells have the usual two sex chromosomes (either two X chromosomes or one X chromosome and one Y chromosome), and other cells have only one copy of the X chromosome. Women with Turner syndrome caused by X chromosome mosaicism (45,X/46,XX or 45,X/46,XY) are said to have mosaic Turner syndrome.

Researchers have not determined which genes on the X chromosome are responsible for most of the features of Turner syndrome. They have, however, identified one gene called SHOX that is important for bone development and growth. The SHOX gene is located in the pseudoautosomal regions of the sex chromosomes. Missing one copy of this gene likely causes short stature and skeletal abnormalities in women with Turner syndrome.

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 the chromosomes.

Is there a standard way to diagram the X 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 X chromosome
See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about the X chromosome?

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

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

What glossary definitions help with understanding the X chromosome?

adenosine triphosphate ; adolescent ; aneuploidy ; apoptosis ; ATP ; cell ; chromosome ; cytoskeleton ; deletion ; digestive ; disabilities ; disability ; DNA ; egg ; embryonic ; enzyme ; fertility ; fetus ; gastrointestinal ; gene ; gene dosage ; gynecomastia ; hormone ; infertility ; inflammation ; inherited ; lyonization ; mitochondria ; molecule ; monosomy ; mosaic ; mosaicism ; necrosis ; neurological ; obstruction ; ovarian ; oxidative phosphorylation ; phosphorylation ; protein ; puberty ; sex chromosomes ; sex determination ; short stature ; sperm ; stature ; syndrome ; testes ; testosterone ; translocation ; trisomy ; X-inactivation

You may find definitions for these and many other terms in the Genetics Home Reference Glossary.


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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? ( in the Handbook.

Reviewed: January 2012
Published: February 1, 2016