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

Chromosome 5

Reviewed February 2013

What is chromosome 5?

Humans normally have 46 chromosomes in each cell, divided into 23 pairs. Two copies of chromosome 5, one copy inherited from each parent, form one of the pairs. Chromosome 5 spans about 181 million DNA building blocks (base pairs) and represents almost 6 percent of the total DNA in cells.

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. Chromosome 5 likely contains about 900 genes that provide instructions for making proteins. These proteins perform a variety of different roles in the body.

Genes on chromosome 5 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 chromosome 5:

  • ALDH7A1
  • ANKH
  • APC
  • ARSB
  • CSF1R
  • CTNND2
  • DNAH5
  • ERAP1
  • ERCC8
  • F12
  • FAM134B
  • FBN2
  • FGF10
  • FGFR4
  • FLT4
  • GABRA1
  • GLRA1
  • GM2A
  • GPR98
  • GRM6
  • HARS2
  • HEXB
  • HINT1
  • HSD17B4
  • IL7R
  • IRGM
  • MAP3K1
  • MATR3
  • MCCC2
  • MOCS2
  • MSX2
  • MTRR
  • MYOT
  • NNT
  • NPM1
  • NSD1
  • OXCT1
  • PIK3R1
  • PROP1
  • RAD50
  • RASA1
  • SAR1B
  • SDHA
  • SGCD
  • SH3TC2
  • SIL1
  • SLC1A3
  • SLC22A5
  • SLC26A2
  • SLC45A2
  • SMN1
  • SMN2
  • SPINK5
  • SQSTM1
  • TCOF1
  • TERT
  • TMEM173
  • TTC37
  • VCAN

How are changes in chromosome 5 related to health conditions?

Many genetic conditions are related to changes in particular genes on chromosome 5. This list of disorders associated with genes on chromosome 5 provides links to additional information.

Genetics Home Reference provides information about the following conditions related to genes on chromosome 5:

  • 3-methylcrotonyl-CoA carboxylase deficiency
  • achondrogenesis
  • acute promyelocytic leukemia
  • alpha-methylacyl-CoA racemase deficiency
  • amyotrophic lateral sclerosis
  • ankylosing spondylitis
  • atelosteogenesis type 2
  • autosomal recessive axonal neuropathy with neuromyotonia
  • autosomal recessive congenital stationary night blindness
  • breast cancer
  • capillary malformation-arteriovenous malformation syndrome
  • Charcot-Marie-Tooth disease
  • chylomicron retention disease
  • Cockayne syndrome
  • combined pituitary hormone deficiency
  • congenital contractural arachnodactyly
  • Cornelia de Lange syndrome
  • craniometaphyseal dysplasia
  • cri-du-chat syndrome
  • Crohn disease
  • cytogenetically normal acute myeloid leukemia
  • D-bifunctional protein deficiency
  • desmoid tumor
  • diastrophic dysplasia
  • distal myopathy 2
  • dyskeratosis congenita
  • Ehlers-Danlos syndrome
  • enlarged parietal foramina
  • episodic ataxia
  • familial adenomatous polyposis
  • familial dilated cardiomyopathy
  • familial glucocorticoid deficiency
  • familial idiopathic basal ganglia calcification
  • gastrointestinal stromal tumor
  • GM2-gangliosidosis, AB variant
  • hereditary angioedema
  • hereditary diffuse leukoencephalopathy with spheroids
  • hereditary hyperekplexia
  • hereditary sensory and autonomic neuropathy type II
  • homocystinuria
  • idiopathic pulmonary fibrosis
  • juvenile myoclonic epilepsy
  • lacrimo-auriculo-dento-digital syndrome
  • lattice corneal dystrophy type I
  • Leigh syndrome
  • limb-girdle muscular dystrophy
  • Marinesco-Sjögren syndrome
  • Milroy disease
  • molybdenum cofactor deficiency
  • mucopolysaccharidosis type VI
  • multiple epiphyseal dysplasia
  • multiple sclerosis
  • myofibrillar myopathy
  • Netherton syndrome
  • nonsyndromic paraganglioma
  • oculocutaneous albinism
  • Paget disease of bone
  • Parkes Weber syndrome
  • PDGFRB-associated chronic eosinophilic leukemia
  • Perrault syndrome
  • primary carnitine deficiency
  • primary ciliary dyskinesia
  • pyridoxine-dependent epilepsy
  • Sandhoff disease
  • short stature, hyperextensibility, hernia, ocular depression, Rieger anomaly, and teething delay
  • Sotos syndrome
  • spinal muscular atrophy
  • STING-associated vasculopathy with onset in infancy
  • succinyl-CoA:3-ketoacid CoA transferase deficiency
  • Swyer syndrome
  • Treacher Collins syndrome
  • trichohepatoenteric syndrome
  • Usher syndrome
  • UV-sensitive syndrome
  • Wagner syndrome
  • Weaver syndrome

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 chromosome 5.


Changes in the structure of chromosome 5 are associated with certain forms of cancer and conditions related to cancer. These changes are typically somatic, which means they are acquired during a person's lifetime and are present only in tumor cells. Deletions in the long (q) arm of the chromosome have been identified in a form of blood cancer known as acute myeloid leukemia (AML). These deletions also frequently occur in a disorder called myelodysplastic syndrome, which is a disease of the blood and bone marrow. People with this condition have a low number of red blood cells (anemia) and an increased risk of developing AML. When MDS is associated with a specific deletion in the long arm of chromosome 5, it is known as 5q- (5q minus) syndrome.

Studies suggest that some genes on chromosome 5 play critical roles in the growth and division of cells. When segments of the chromosome are deleted, as in some cases of AML and MDS, these important genes are missing. Without these genes, cells can grow and divide too quickly and in an uncontrolled way. Researchers are working to identify the specific genes on chromosome 5 that are related to AML and MDS.

cri-du-chat syndrome

Cri-du-chat (cat's cry) syndrome is caused by a deletion of the end of the short (p) arm of chromosome 5. This chromosomal change is written as 5p- (5p minus). The signs and symptoms of cri-du-chat syndrome are probably related to the loss of multiple genes in this region. Researchers are working to determine how the loss of these genes leads to the features of the disorder. They have discovered that in people with cri-du-chat syndrome, larger deletions tend to result in more severe intellectual disability and developmental delays than smaller deletions. Researchers have also defined regions of the short arm of chromosome 5 that are associated with particular features of cri-du-chat syndrome. A specific region designated 5p15.3 is associated with a cat-like cry, and a nearby region called 5p15.2 is associated with intellectual disability, small head size (microcephaly), and distinctive facial features.

Crohn disease

Several regions of chromosome 5 have been associated with the risk of developing Crohn disease. For example, a combination of genetic variations in a region of DNA on the long (q) arm of the chromosome (5q31) has been shown to increase a person's chance of developing Crohn disease. Together, these variations are known as the inflammatory bowel disease 5 (IBD5) locus. This region of chromosome 5 contains several related genes that may influence Crohn disease risk, including SLC22A4 and SLC22A5.

Variations in a region of the short (p) arm of chromosome 5 designated 5p13.1 are also associated with Crohn disease risk. Researchers refer to this part of chromosome 5 as a "gene desert" because it contains no known genes; however, it may contain stretches of DNA that help regulate nearby genes such as PTGER4. Research studies are under way to examine a possible connection between the PTGER4 gene and Crohn disease.

PDGFRB-associated chronic eosinophilic leukemia

Translocations involving chromosome 5 are involved in a type of blood cell cancer called PDGFRB-associated chronic eosinophilic leukemia. This condition is characterized by an increased number of eosinophils, a type of white blood cell. The most common translocation that causes this condition fuses part of the PDGFRB gene from chromosome 5 with part of the ETV6 gene from chromosome 12, written as t(5;12)(q31-33;p13). Translocations fusing the PDGFRB gene with one of more than 20 other genes have also been found to cause PDGFRB-associated chronic eosinophilic leukemia, but these other genetic changes are relatively uncommon. These translocations are acquired during a person's lifetime and are present only in cancer cells. This type of genetic change, called a somatic mutation, is not inherited.

The protein produced from the ETV6-PDGFRB fusion gene, called ETV6/PDGFRβ, functions differently than the proteins normally produced from the individual genes. The ETV6 protein normally turns off (represses) gene activity and the PDGFRβ protein plays a role in turning on (activating) signaling pathways. The ETV6/PDGFRβ protein is always turned on, activating signaling pathways and gene activity. When the ETV6-PDGFRB fusion gene mutation occurs in cells that develop into blood cells, the growth of eosinophils (and occasionally other white blood cells, such as neutrophils and mast cells) is poorly controlled, leading to PDGFRB-associated chronic eosinophilic leukemia. It is unclear why eosinophils are preferentially affected by this genetic change.

periventricular heterotopia

In a few cases, abnormalities in chromosome 5 have been associated with periventricular heterotopia, a disorder characterized by abnormal clumps of nerve cells (neurons) around fluid-filled cavities (ventricles) near the center of the brain. In each case, the affected individual had extra genetic material caused by an abnormal duplication of part of this chromosome. It is not known how this duplicated genetic material results in the signs and symptoms of periventricular heterotopia.

other chromosomal conditions

Other changes in the number or structure of chromosome 5 can have a variety of effects, including delayed growth and development, distinctive facial features, birth defects, and other health problems. Changes to chromosome 5 include an extra segment of the short (p) or long (q) arm of the chromosome in each cell (partial trisomy 5p or 5q), a missing segment of the long arm of the chromosome in each cell (partial monosomy 5q), and a circular structure called ring chromosome 5. Ring chromosomes occur when a chromosome breaks in two places and the ends of the chromosome arms fuse together to form a circular structure.

Is there a standard way to diagram chromosome 5?

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 chromosome 5
See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about chromosome 5?

You may find the following resources about chromosome 5 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 chromosome 5?

acute ; acute myelogenous leukemia ; acute myeloid leukemia ; AML ; anemia ; bone marrow ; cancer ; cell ; chromosome ; chronic ; deletion ; disability ; DNA ; duplication ; eosinophils ; fusion gene ; gene ; inherited ; leukemia ; locus ; mast cells ; microcephaly ; monosomy ; mutation ; myelodysplastic syndrome ; myelogenous ; myeloid ; neutrophils ; protein ; ring chromosomes ; somatic mutation ; syndrome ; translocation ; trisomy ; tumor ; white blood cells

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: February 2013
Published: March 23, 2015