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Chromosome 9

Reviewed January 2007

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 140 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 between 800 and 1,300 genes.

Genes on chromosome 9 are among the estimated 20,000 to 25,000 total genes in the human genome.

Genetics Home Reference includes these genes on chromosome 9:

  • ABCA1:ATP-binding cassette, sub-family A (ABC1), member 1
  • ADAMTS13:ADAM metallopeptidase with thrombospondin type 1 motif, 13
  • AGPAT2:1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)
  • ALAD:aminolevulinate, delta-, dehydratase
  • APTX:aprataxin
  • ASS1:argininosuccinate synthetase 1
  • AUH:AU RNA binding protein/enoyl-Coenzyme A hydratase
  • COL5A1:collagen, type V, alpha 1
  • DBH:dopamine beta-hydroxylase (dopamine beta-monooxygenase)
  • DFNB31:deafness, autosomal recessive 31
  • ENG:endoglin (Osler-Rendu-Weber syndrome 1)
  • FKTN:fukutin
  • FXN:frataxin
  • GALT:galactose-1-phosphate uridylyltransferase
  • GLDC:glycine dehydrogenase (decarboxylating)
  • GNE:glucosamine (UDP-N-acetyl)-2-epimerase/N-acetylmannosamine kinase
  • GRHPR:glyoxylate reductase/hydroxypyruvate reductase
  • HSD17B3:hydroxysteroid (17-beta) dehydrogenase 3
  • IKBKAP:inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase complex-associated protein
  • LMX1B:LIM homeobox transcription factor 1, beta
  • NR5A1:nuclear receptor subfamily 5, group A, member 1
  • PTCH1:patched homolog 1 (Drosophila)
  • RMRP:RNA component of mitochondrial RNA processing endoribonuclease
  • ROR2:receptor tyrosine kinase-like orphan receptor 2
  • SETX:senataxin
  • TMC1:transmembrane channel-like 1
  • TOR1A:torsin family 1, member A (torsin A)
  • TSC1:tuberous sclerosis 1
  • TYRP1:tyrosinase-related protein 1
  • VCP:valosin-containing protein
  • VPS13A:vacuolar protein sorting 13 homolog A (S. cerevisiae)

GeneCards provides a table of genes on chromosome 9 and disorders related to those genes (http://www.genecards.org/cgi-bin/listdiseasecards.pl?type=chrom&search=9).

There are many genetic conditions related to genes on chromosome 9.

Genetics Home Reference includes these conditions related to genes on chromosome 9:

  • amyotrophic lateral sclerosis
  • ataxia with oculomotor apraxia
  • Berardinelli-Seip congenital lipodystrophy
  • 17-beta hydroxysteroid dehydrogenase 3 deficiency
  • bladder cancer
  • cartilage-hair hypoplasia
  • chorea-acanthocytosis
  • citrullinemia
  • dopamine beta-hydroxylase deficiency
  • early-onset primary dystonia
  • Ehlers-Danlos syndrome
  • familial dysautonomia
  • Friedreich ataxia
  • Fukuyama congenital muscular dystrophy
  • galactosemia
  • glycine encephalopathy
  • Gorlin syndrome
  • hereditary hemorrhagic telangiectasia
  • inclusion body myopathy 2
  • inclusion body myopathy with early-onset Paget disease and frontotemporal dementia
  • 3-methylglutaconic aciduria
  • nail-patella syndrome
  • nonsyndromic deafness
  • oculocutaneous albinism
  • porphyria
  • primary hyperoxaluria
  • Robinow syndrome
  • sialuria
  • Swyer syndrome
  • Tangier disease
  • thrombotic thrombocytopenic purpura
  • tuberous sclerosis

GeneCards provides a table of genes on chromosome 9 and disorders related to those genes (http://www.genecards.org/cgi-bin/listdiseasecards.pl?type=chrom&search=9).

What chromosomal conditions are related to chromosome 9?

The following conditions are caused by changes in the structure or number of copies of chromosome 9.

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.

other 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 ABL gene). The protein produced from this fused gene 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? (http://ghr.nlm.nih.gov/handbook/howgeneswork/genelocation) 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.

  • Additional NIH Resources - National Institutes of Health
    National Human Genome Research Institute: Chromosome Abnormalities (http://www.genome.gov/11508982)
  • Educational resources - Information pages
    Genome News Network: Human Chromosomes 9 and 10 Are Complete (May 26, 2004) (http://www.genomenewsnetwork.org/articles/2004/05/26/chromosomes.php)
  • 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.

  • Research Resources - Tools for researchers
    • Cancer Genetics Web (http://www.cancerindex.org/geneweb/clinkc09.htm)
    • Database of Genomic Variants: Chromosome 9 (http://projects.tcag.ca/variation/cgi-bin/tbrowse/tbrowse?source=hg17&table=Locus&show=table&keyword=&flop=AND&fcol=_C19&fcomp==&fkwd=chr9&cols=)
    • DNA sequence and analysis of human chromosome 9. Nature. 2004 May 27;429(6990):369-74. (http://www.nature.com/nature/journal/v429/n6990/full/nature02465.html)
    • Ensembl Human Map View: Chromosome 9 (http://www.ensembl.org/Homo_sapiens/mapview?chr=9)
    • Oak Ridge National Laboratory: Chromosome 9 Overview (http://genome.ornl.gov/cgi-bin/GCat/GetChrom.cgi?org=human&chr=9)
    • The Sanger Institute: Human Chromosome 9 Project Overview (http://www.sanger.ac.uk/HGP/Chr9/)
    • U.S. Department of Energy: Human Chromosome Launchpad (http://www.ornl.gov/sci/techresources/Human_Genome/launchpad/chrom09.shtml)
  • PubMed - Recent literature (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=PubMed&term=(Chromosomes,+Human,+Pair+9[MAJR])+AND+(Chromosome+9[TI])+AND+english[la]+AND+human[mh]&orig_db=PubMed&filters=ON&pmfilter_EDatLimit=1080+Days)
  • Map Viewer - Genetic maps (http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?org=human&maps=ideogr,morbid,pheno&zoom=100&chr=9)

What glossary definitions help with understanding chromosome 9?

acute ; base pair ; cancer ; cell ; chromosome ; chronic ; deletion ; DNA ; DNA damage ; gene ; leukemia ; monosomy ; myeloid ; progression ; protein ; rearrangement ; ring chromosomes ; translocation ; trisomy ; tumor

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: Chromosome 9 (http://www.ensembl.org/Homo_sapiens/mapview?chr=9)
  • Gilbert F, Kauff N. Disease genes and chromosomes: disease maps of the human genome. Chromosome 9. Genet Test. 2001 Summer;5(2):157-74. No abstract available. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=11551106)
  • 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, Blocker 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. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=15164053)
  • 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. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=12755554)
  • Map Viewer: Genes on Sequence (http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=human&MAPS=ideogr,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. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=16470587)
  • Pai, G Shashidhar; Lewandowski, Raymond C; Borgaonkar, Digamber S; Handbook of chromosomal syndromes; Hoboken, N.J. : Wiley-Liss, c2003. p132-146.
  • UCSC Genome Browser: Statistics from NCBI Build 35, May 2004 (http://genome.cse.ucsc.edu/goldenPath/stats.html)
  • 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. (http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=retrieve&db=pubmed&dopt=Abstract&list_uids=16474624)

 

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 2007
Published: January 23, 2009