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

Chromosome 9

Reviewed September 2012

What is chromosome 9?

Humans normally have 46 chromosomes in each cell, divided into 23 pairs. Two copies of chromosome 9, one copy inherited from each parent, form one of the pairs. Chromosome 9 is made up of about 141 million DNA building blocks (base pairs) and represents approximately 4.5 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 9 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 chromosome 9 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 9:

  • ABCA1
  • ADAMTS13
  • AGPAT2
  • ALAD
  • APTX
  • ASS1
  • AUH
  • C9orf72
  • CDKN2A
  • COL5A1
  • DBH
  • DNAI1
  • DOCK8
  • EHMT1
  • ENG
  • EXOSC3
  • FKTN
  • FREM1
  • FXN
  • GALT
  • GLDC
  • GNE
  • GSN
  • HSD17B3
  • JAK2
  • KCNT1
  • LMX1B
  • NOTCH1
  • NR5A1
  • PIGO
  • POMT1
  • PTCH1
  • RMRP
  • ROR2
  • SETX
  • SPTLC1
  • SURF1
  • TEK
  • TGFBR1
  • TOR1A
  • TPM2
  • TRPM6
  • TSC1
  • TYRP1
  • VCP
  • VPS13A
  • XPA

How are changes in chromosome 9 related to health conditions?

Many genetic conditions are related to changes in particular genes on chromosome 9. This list of disorders associated with genes on chromosome 9 provides links to additional information.

Genetics Home Reference provides information about the following conditions related to genes on chromosome 9:

  • 3-methylglutaconyl-CoA hydratase deficiency
  • 9q22.3 microdeletion
  • 17-beta hydroxysteroid dehydrogenase 3 deficiency
  • Adams-Oliver syndrome
  • amyotrophic lateral sclerosis
  • ataxia with oculomotor apraxia
  • autosomal dominant nocturnal frontal lobe epilepsy
  • autosomal recessive hyper-IgE syndrome
  • benign essential blepharospasm
  • bladder cancer
  • cap myopathy
  • cartilage-hair hypoplasia
  • chorea-acanthocytosis
  • citrullinemia
  • congenital generalized lipodystrophy
  • critical congenital heart disease
  • cytochrome c oxidase deficiency
  • distal arthrogryposis type 1
  • dopamine beta-hydroxylase deficiency
  • early-onset primary dystonia
  • Ehlers-Danlos syndrome
  • essential thrombocythemia
  • familial dysautonomia
  • familial HDL deficiency
  • familial thoracic aortic aneurysm and dissection
  • Fanconi anemia
  • Friedreich ataxia
  • Fukuyama congenital muscular dystrophy
  • galactosemia
  • geleophysic dysplasia
  • glycine encephalopathy
  • Gorlin syndrome
  • head and neck squamous cell carcinoma
  • hereditary fructose intolerance
  • hereditary hemorrhagic telangiectasia
  • hereditary sensory neuropathy type IA
  • heterotaxy syndrome
  • hypomagnesemia with secondary hypocalcemia
  • inclusion body myopathy 2
  • inclusion body myopathy with early-onset Paget disease and frontotemporal dementia
  • Kleefstra syndrome
  • lattice corneal dystrophy type II
  • Leigh syndrome
  • limb-girdle muscular dystrophy
  • Loeys-Dietz syndrome
  • lymphangioleiomyomatosis
  • Mabry syndrome
  • malignant migrating partial seizures of infancy
  • Manitoba oculotrichoanal syndrome
  • multiple cutaneous and mucosal venous malformations
  • nail-patella syndrome
  • nemaline myopathy
  • Nicolaides-Baraitser syndrome
  • nonsyndromic holoprosencephaly
  • oculocutaneous albinism
  • polycythemia vera
  • pontocerebellar hypoplasia
  • porphyria
  • primary ciliary dyskinesia
  • primary hyperoxaluria
  • primary myelofibrosis
  • prostate cancer
  • pulmonary arterial hypertension
  • Robinow syndrome
  • Sheldon-Hall syndrome
  • sialuria
  • Swyer syndrome
  • Tangier disease
  • thrombotic thrombocytopenic purpura
  • tuberous sclerosis complex
  • VLDLR-associated cerebellar hypoplasia
  • Walker-Warburg syndrome
  • xeroderma pigmentosum

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 9.

9q22.3 microdeletion

9q22.3 microdeletion is a chromosomal change in which a small piece of the long (q) arm of chromosome 9 is deleted in each cell. Affected individuals are missing at least 352,000 base pairs, also written as 352 kilobases (kb), in the q22.3 region of chromosome 9. This 352-kb segment is known as the minimum critical region because it is the smallest deletion that has been found to cause the signs and symptoms related to 9q22.3 microdeletions. These signs and symptoms include delayed development, intellectual disability, certain physical abnormalities, and the characteristic features of a genetic condition called Gorlin syndrome (also known as nevoid basal cell carcinoma syndrome). 9q22.3 microdeletions can also be much larger; the largest reported deletion included 20.5 million base pairs (20.5 Mb).

People with a 9q22.3 microdeletion are missing from two to more than 270 genes on chromosome 9. All known 9q22.3 microdeletions include the PTCH1 gene. Researchers believe that many of the features associated with 9q22.3 microdeletions, particularly the signs and symptoms of Gorlin syndrome, result from a loss of the PTCH1 gene. Other signs and symptoms related to 9q22.3 microdeletions probably result from the loss of additional genes in the q22.3 region. Researchers are working to determine which missing genes contribute to the other features associated with the deletion.

bladder cancer

Deletions of part or all of chromosome 9 are commonly found in bladder cancers. These chromosomal changes are seen only in cancer cells and typically occur early in tumor formation. Researchers believe that several genes that play a role in bladder cancer may be located on chromosome 9. They suspect that these genes may be tumor suppressors, which means they normally help prevent cells from growing and dividing in an uncontrolled way. Researchers are working to determine which genes, when altered or missing, are involved in the development and progression of bladder tumors.

Kleefstra syndrome

Most people with Kleefstra syndrome, a disorder with signs and symptoms involving many parts of the body, are missing a sequence of about 1 million DNA building blocks (base pairs) on one copy of chromosome 9 in each cell. The deletion occurs near the end of the long (q) arm of the chromosome at a location designated q34.3, a region containing a gene called EHMT1. Some affected individuals have shorter or longer deletions in the same region.

The loss of the EHMT1 gene from one copy of chromosome 9 in each cell is believed to be responsible for the characteristic features of Kleefstra syndrome in people with the 9q34.3 deletion. However, the loss of other genes in the same region may lead to additional health problems in some affected individuals.

The EHMT1 gene provides instructions for making an enzyme called euchromatic histone methyltransferase 1. Histone methyltransferases are enzymes that modify proteins called histones. Histones are structural proteins that attach (bind) to DNA and give chromosomes their shape. By adding a molecule called a methyl group to histones, histone methyltransferases can turn off (suppress) the activity of certain genes, which is essential for normal development and function. A lack of euchromatic histone methyltransferase 1 enzyme impairs proper control of the activity of certain genes in many of the body's organs and tissues, resulting in the abnormalities of development and function characteristic of Kleefstra syndrome.

other cancers

Changes in the structure of chromosome 9 have been found in many types of cancer. These changes, which occur only in cancer cells, usually involve a loss of part of the chromosome or a rearrangement of chromosomal material. For example, a loss of part of the long (q) arm of chromosome 9 has been identified in some types of brain tumor. It is unclear how these chromosomal changes are related to the development and growth of cancers.

A rearrangement (translocation) of genetic material between chromosomes 9 and 22 is associated with several types of blood cancer known as leukemias. This chromosomal abnormality, which is commonly called the Philadelphia chromosome, is found only in cancer cells. It fuses part of a specific gene from chromosome 22 (the BCR gene) with part of another gene from chromosome 9 (the ABL1 gene). The protein produced from these fused genes signals tumor cells to continue dividing abnormally and prevents them from adequately repairing DNA damage.

The Philadelphia chromosome has been identified in most cases of a slowly progressing form of blood cancer called chronic myeloid leukemia (CML). It also has been found in some cases of more rapidly progressing blood cancers known as acute leukemias. The presence of the Philadelphia chromosome can help predict how a cancer will progress and provides a target for molecular therapies.

other chromosomal conditions

Other changes in the structure or number of copies of chromosome 9 can have a variety of effects. Intellectual disability, delayed development, distinctive facial features, and an unusual head shape are common features. Changes to chromosome 9 include an extra piece of the chromosome in each cell (partial trisomy), a missing segment of the chromosome in each cell (partial monosomy), and a circular structure called a ring chromosome 9. A ring chromosome occurs when both ends of a broken chromosome are reunited. Rearrangements (translocations) of genetic material between chromosome 9 and other chromosomes can also lead to extra or missing chromosome segments.

Is there a standard way to diagram chromosome 9?

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 9
See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about chromosome 9?

You may find the following resources about chromosome 9 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 9?

acute ; biomarker ; cancer ; carcinoma ; cell ; chromosome ; chronic ; critical region ; deletion ; disability ; DNA ; DNA damage ; enzyme ; gene ; histone ; inherited ; kb ; leukemia ; Mb ; methyl ; methyltransferase ; molecule ; monosomy ; myeloid ; progression ; protein ; rearrangement ; syndrome ; translocation ; trisomy ; tumor

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


  • Coco S, Valdora F, Bonassi S, Scaruffi P, Stigliani S, Oberthuer A, Berthold F, Andolfo I, Servidei T, Riccardi R, Basso E, Iolascon A, Tonini GP. Chromosome 9q and 16q loss identified by genome-wide pooled-analysis are associated with tumor aggressiveness in patients with classic medulloblastoma. OMICS. 2011 May;15(5):273-80. doi: 10.1089/omi.2010.0103. Epub 2011 Feb 24. (
  • Ensembl Human Map View (;r=9:1-138394717)
  • Gilbert F, Kauff N. Disease genes and chromosomes: disease maps of the human genome. Chromosome 9. Genet Test. 2001 Summer;5(2):157-74. (
  • Hoischen A, Ehrler M, Fassunke J, Simon M, Baudis M, Landwehr C, Radlwimmer B, Lichter P, Schramm J, Becker AJ, Weber RG. Comprehensive characterization of genomic aberrations in gangliogliomas by CGH, array-based CGH and interphase FISH. Brain Pathol. 2008 Jul;18(3):326-37. doi: 10.1111/j.1750-3639.2008.00122.x. Epub 2008 Mar 26. (
  • Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE, Howe KL, Andrews TD, Searle S, Hunt SE, Scott CE, Jones MC, Ainscough R, Almeida JP, Ambrose KD, Ashwell RI, Babbage AK, Babbage S, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beasley H, Beasley O, Bird CP, Bray-Allen S, Brown AJ, Brown JY, Burford D, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Chen Y, Clarke G, Clark SY, Clee CM, Clegg S, Collier RE, Corby N, Crosier M, Cummings AT, Davies J, Dhami P, Dunn M, Dutta I, Dyer LW, Earthrowl ME, Faulkner L, Fleming CJ, Frankish A, Frankland JA, French L, Fricker DG, Garner P, Garnett J, Ghori J, Gilbert JG, Glison C, Grafham DV, Gribble S, Griffiths C, Griffiths-Jones S, Grocock R, Guy J, Hall RE, Hammond S, Harley JL, Harrison ES, Hart EA, Heath PD, Henderson CD, Hopkins BL, Howard PJ, Howden PJ, Huckle E, Johnson C, Johnson D, Joy AA, Kay M, Keenan S, Kershaw JK, Kimberley AM, King A, Knights A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd C, Lloyd DM, Lovell J, Martin S, Mashreghi-Mohammadi M, Matthews L, McLaren S, McLay KE, McMurray A, Milne S, Nickerson T, Nisbett J, Nordsiek G, Pearce AV, Peck AI, Porter KM, Pandian R, Pelan S, Phillimore B, Povey S, Ramsey Y, Rand V, Scharfe M, Sehra HK, Shownkeen R, Sims SK, Skuce CD, Smith M, Steward CA, Swarbreck D, Sycamore N, Tester J, Thorpe A, Tracey A, Tromans A, Thomas DW, Wall M, Wallis JM, West AP, Whitehead SL, Willey DL, Williams SA, Wilming L, Wray PW, Young L, Ashurst JL, Coulson A, Blöcker H, Durbin R, Sulston JE, Hubbard T, Jackson MJ, Bentley DR, Beck S, Rogers J, Dunham I. DNA sequence and analysis of human chromosome 9. Nature. 2004 May 27;429(6990):369-74. (
  • Kurzrock R, Kantarjian HM, Druker BJ, Talpaz M. Philadelphia chromosome-positive leukemias: from basic mechanisms to molecular therapeutics. Ann Intern Med. 2003 May 20;138(10):819-30. Review. (
  • Map Viewer: Genes on Sequence (,ugHs,genes&CHR=9)
  • Mhawech-Fauceglia P, Cheney RT, Schwaller J. Genetic alterations in urothelial bladder carcinoma: an updated review. Cancer. 2006 Mar 15;106(6):1205-16. Review. (
  • Muller EA, Aradhya S, Atkin JF, Carmany EP, Elliott AM, Chudley AE, Clark RD, Everman DB, Garner S, Hall BD, Herman GE, Kivuva E, Ramanathan S, Stevenson DA, Stockton DW, Hudgins L. Microdeletion 9q22.3 syndrome includes metopic craniosynostosis, hydrocephalus, macrosomia, and developmental delay. Am J Med Genet A. 2012 Feb;158A(2):391-9. doi: 10.1002/ajmg.a.34216. Epub 2011 Dec 21. (
  • Redon R, Baujat G, Sanlaville D, Le Merrer M, Vekemans M, Munnich A, Carter NP, Cormier-Daire V, Colleaux L. Interstitial 9q22.3 microdeletion: clinical and molecular characterisation of a newly recognised overgrowth syndrome. Eur J Hum Genet. 2006 Jun;14(6):759-67. (
  • Stewart DR, Kleefstra T. The chromosome 9q subtelomere deletion syndrome. Am J Med Genet C Semin Med Genet. 2007 Nov 15;145C(4):383-92. Review. (
  • UCSC Genome Browser: Statistics (
  • Willemsen MH, Beunders G, Callaghan M, de Leeuw N, Nillesen WM, Yntema HG, van Hagen JM, Nieuwint AW, Morrison N, Keijzers-Vloet ST, Hoischen A, Brunner HG, Tolmie J, Kleefstra T. Familial Kleefstra syndrome due to maternal somatic mosaicism for interstitial 9q34.3 microdeletions. Clin Genet. 2011 Jul;80(1):31-8. doi: 10.1111/j.1399-0004.2010.01607.x. Epub 2011 Jan 10. (
  • Wolff EM, Liang G, Jones PA. Mechanisms of Disease: genetic and epigenetic alterations that drive bladder cancer. Nat Clin Pract Urol. 2005 Oct;2(10):502-10. Review. (
  • Yatsenko SA, Brundage EK, Roney EK, Cheung SW, Chinault AC, Lupski JR. Molecular mechanisms for subtelomeric rearrangements associated with the 9q34.3 microdeletion syndrome. Hum Mol Genet. 2009 Jun 1;18(11):1924-36. doi: 10.1093/hmg/ddp114. Epub 2009 Mar 17. (


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: September 2012
Published: February 1, 2016