Chromosome 5 Explained

Length Bp:	182,045,439 bp (CHM13)
Genes:	839 (CCDS)
Type:	Autosome
Centromere Position:	Submetacentric^[1] (48.8 Mbp^[2])
Chr:	5
Ensembl Id:	5
Entrez Id:	5
Ncbi Id:	5
Ucsc Id:	5
Refseq Id:	NC_000005
Genbank Id:	CM000667

Chromosome 5 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 5 spans about 182 million base pairs (the building blocks of DNA) and represents almost 6% of the total DNA in cells. Chromosome 5 is the 5th largest human chromosome, yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of non-coding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained.^[3]

Because chromosome 5 is responsible for many forms of growth and development (cell divisions) changes may cause cancers. One example would be acute myeloid leukemia (AML).^[4]

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 5. Because researchers use different approaches to genome annotation their predictions of the number of genes on each chromosome varies (for technical details, see gene prediction). Among various projects, the collaborative consensus coding sequence project (CCDS) takes an extremely conservative strategy. So CCDS's gene number prediction represents a lower bound on the total number of human protein-coding genes.^[5]

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes	Source	Release date
	839	—	—	^[6]	2016-09-08
HGNC	790	355	574	^[7]	2017-05-12
	882	1,207	707	^[8]	2017-03-29
	875	—	—	^[9]	2018-02-28
	886	981	785	^[10] ^[11] ^[12]	2017-05-19

Gene list

The following is a partial list of genes on human chromosome 5. For complete list, see the link in the infobox on the right.

Diseases and disorders

The following are some of the diseases related to genes located on chromosome 5:

• Attention-deficit/hyperactivity disorder
• Achondrogenesis type 1B
• Atelosteogenesis, type II
• Bipolar disorder
• Bosch-Boonstra-Schaaf optic atrophy syndrome
• Charcot–Marie–Tooth disease, type 4
• Cockayne syndrome
• Cornelia de Lange syndrome
• Corneal dystrophy of Bowman layer
• Cri du chat
• Diastrophic dysplasia
• Ehlers-Danlos syndrome
• Familial adenomatous polyposis
• Granular corneal dystrophy type I
• Granular corneal dystrophy type II
• GM2-gangliosidosis, AB variant
• Homocystinuria
• 3-Methylcrotonyl-CoA carboxylase deficiency
• Myelodysplastic syndrome
• Netherton syndrome
• Nicotine dependency
• Parkinson's disease
• Primary carnitine deficiency
• Recessive multiple epiphyseal dysplasia
• Sandhoff disease
• Spinal muscular atrophy
• Sotos Syndrome
• Survival motor neuron spinal muscular atrophy
• Treacher Collins syndrome
• Tricho-hepato-enteric syndrome
• Usher syndrome

Chromosomal conditions

The following conditions are caused by changes in the structure or number of copies of chromosome 5:

• Cri-du-chat syndrome is caused by a deletion of the end of the short (p) arm of chromosome 5. This chromosomal change is written as 5p-. The signs and symptoms of cri-du-chat syndrome are probably related to the loss of multiple genes in this region. Researchers have not identified all of these genes or determined how their loss leads to the features of the disorder. They have discovered, however, that a larger deletion tends to result in more severe mental retardation and developmental delays in people with cri-du-chat syndrome.^{[13] [14] [15]}

Researchers have defined narrow 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 mental retardation, small head (microcephaly), and distinctive facial features.

• Familial Adenomatous Polyposis is caused by a deletion of the APC tumor suppressor gene on the long (q) arm of chromosome 5. This chromosomal change results in thousands of colonic polyps which gives the patient a 100% risk of colon cancer if total colectomy is not done.
• Chromosome 5q deletion syndrome is caused by the deletion of the q arm (long arm) of chromosome 5. This deletion has been linked to several blood related disorders including Myelodysplastic syndrome and Erythroblastopenia. This is a different condition than Cri-du-chat which was mentioned above.
• 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 medical 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. A ring chromosome occurs when both ends of a broken chromosome are reunited.

Cytogenetic band

G-bands of human chromosome 5 in resolution 850 bphs^[16] ! Chr.! Arm^[17] ! Band^[18] ! ISCN
start^[19] ! ISCN
stop! Basepair
start! Basepair
stop! Stain^[20] ! Density

5	p	15.33	0	278			gneg
5	p	15.32	278	401			gpos	25
5	p	15.31	401	555			gneg
5	p	15.2	555	802			gpos	50
5	p	15.1	802	972			gneg
5	p	14.3	972	1234			gpos	100
5	p	14.2	1234	1281			gneg
5	p	14.1	1281	1543			gpos	100
5	p	13.3	1543	1836			gneg
5	p	13.2	1836	2068			gpos	25
5	p	13.1	2068	2253			gneg
5	p	12	2253	2407			gpos	50
5	p	11	2407	2592			acen
5	q	11.1	2592	2839			acen
5	q	11.2	2839	3271			gneg
5	q	12.1	3271	3518			gpos	75
5	q	12.2	3518	3580			gneg
5	q	12.3	3580	3765			gpos	75
5	q	13.1	3765	4012			gneg
5	q	13.2	4012	4197			gpos	50
5	q	13.3	4197	4397			gneg
5	q	14.1	4397	4752			gpos	50
5	q	14.2	4752	4907			gneg
5	q	14.3	4907	5400			gpos	100
5	q	15	5400	5678			gneg
5	q	21.1	5678	5879			gpos	100
5	q	21.2	5879	5987			gneg
5	q	21.3	5987	6295			gpos	100
5	q	22.1	6295	6419			gneg
5	q	22.2	6419	6527			gpos	50
5	q	22.3	6527	6666			gneg
5	q	23.1	6666	6943			gpos	100
5	q	23.2	6943	7267			gneg
5	q	23.3	7267	7468			gpos	100
5	q	31.1	7468	7807			gneg
5	q	31.2	7807	8008			gpos	25
5	q	31.3	8008	8316			gneg
5	q	32	8316	8625			gpos	75
5	q	33.1	8625	8887			gneg
5	q	33.2	8887	9072			gpos	50
5	q	33.3	9072	9304			gneg
5	q	34	9304	9690			gpos	100
5	q	35.1	9690	9952			gneg
5	q	35.2	9952	10183			gpos	25
5	q	35.3	10183	10600			gneg

Further reading

• Mainardi PC, Perfumo C, Cali A, Coucourde G, Pastore G, Cavani S, Zara F, Overhauser J, Pierluigi M, Bricarelli FD . Clinical and molecular characterisation of 80 patients with 5p deletion: genotype–phenotype correlation . J Med Genet . 2001 . 151–8 . 38 . 3 . 11238681 . 10.1136/jmg.38.3.151 . 1734829 .
• Schafer IA, Robin NH, Posch JJ, Clark BA, Izumo S, Schwartz S . Distal 5q deletion syndrome: phenotypic correlations . Am J Med Genet . 2001 . 63–8 . 103 . 1 . 11562936 . 10.1002/ajmg.1513.
• Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, Gordon LA, Scott D, Xie G, Huang W, Hellsten U, Tran-Gyamfi M, She X, Prabhakar S, Aerts A, Altherr M, Bajorek E, Black S, Branscomb E, Caoile C, Challacombe JF, Chan YM, Denys M, Detter JC, Escobar J, Flowers D, Fotopulos D, Glavina T, Gomez M, Gonzales E, Goodstein D, Grigoriev I, Groza M, Hammon N, Hawkins T, Haydu L, Israni S, Jett J, Kadner K, Kimball H, Kobayashi A, Lopez F, Lou Y, Martinez D, Medina C, Morgan J, Nandkeshwar R, Noonan JP, Pitluck S, Pollard M, Predki P, Priest J, Ramirez L, Retterer J, Rodriguez A, Rogers S, Salamov A, Salazar A, Thayer N, Tice H, Tsai M, Ustaszewska A, Vo N, Wheeler J, Wu K, Yang J, Dickson M, Cheng JF, Eichler EE, Olsen A, Pennacchio LA, Rokhsar DS, Richardson P, Lucas SM, Myers RM, Rubin EM. The DNA sequence and comparative analysis of human chromosome 5 . Nature . 431 . 7006 . 268–74 . September 2004 . 15372022 . 10.1038/nature02919 . 2004Natur.431..268S . free .
• Siddiqi R, Gilbert F . Chromosome 5 . Genet Test . 2003 . 169–87 . 7 . 2 . 12885343 . 10.1089/109065703322146902 .

External links

• Web site: National Institutes of Health . Chromosome 5 . Genetics Home Reference . https://web.archive.org/web/20041014230611/http://ghr.nlm.nih.gov/chromosome=5 . dead . October 14, 2004 . 2017-05-06 .
• Web site: Chromosome 5. Human Genome Project Information Archive 1990–2003. 2017-05-06.

Notes and References

1. Book: Tom Strachan. Andrew Read. Human Molecular Genetics. 2 April 2010. Garland Science. 978-1-136-84407-2. 45.
2. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
3. Web site: Home - Homo sapiens . 2007-02-07 . https://web.archive.org/web/20150402095423/http://genome.jgi-psf.org/chr5/chr5.home.html . 2015-04-02 . dead .
4. Web site: Chromosome 5 . December 2014 . Genetics Home Reference . Lister Hill National Center for Biomedical Communications. U.S. National Library of Medicine .
5. Pertea M, Salzberg SL. Between a chicken and a grape: estimating the number of human genes. . Genome Biol . 2010 . 11 . 5 . 206 . 20441615 . 10.1186/gb-2010-11-5-206 . 2898077 . free .
6. Web site: Search results - 5[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene . NCBI . CCDS Release 20 for Homo sapiens . 2016-09-08 . 2017-05-28.
7. Web site: Statistics & Downloads for chromosome 5 . HUGO Gene Nomenclature Committee . 2017-05-12 . 2017-05-19 . 2017-06-29 . https://web.archive.org/web/20170629104030/http://www.genenames.org/cgi-bin/statistics?c=5 . dead .
8. Web site: Chromosome 5: Chromosome summary - Homo sapiens . Ensembl Release 88 . 2017-03-29 . 2017-05-19.
9. Web site: Human chromosome 5: entries, gene names and cross-references to MIM . UniProt . 2018-02-28 . 2018-03-16.
10. Web site: Search results - 5[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene . NCBI . 2017-05-19 . 2017-05-20.
11. Web site: Search results - 5[CHR] AND "Homo sapiens"[Organism] AND (("genetype miscrna"[Properties] OR "genetype ncrna"[Properties] OR "genetype rrna"[Properties] OR "genetype trna"[Properties] OR "genetype scrna"[Properties] OR "genetype snrna"[Properties] OR "genetype snorna"[Properties]) NOT "genetype protein coding"[Properties] AND alive[prop]) - Gene . NCBI . 2017-05-19 . 2017-05-20.
12. Web site: Search results - 5[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene . NCBI . 2017-05-19 . 2017-05-20.
13. Cornish K, Bramble D . Cri du chat syndrome: genotype–phenotype correlations and recommendations for clinical management . Dev Med Child Neurol . 2002 . 494–7 . 44 . 7 . 12162388 . 10.1017/S0012162201002419. Bramble .
14. Wu Q, Niebuhr E, Yang H, Hansen L . Determination of the 'critical region' for cat-like cry of Cri-du-chat syndrome and analysis of candidate genes by quantitative PCR . Eur J Hum Genet . 2005 . 475–85 . 13 . 4 . 15657623 . 10.1038/sj.ejhg.5201345. free .
15. Zhang X, Snijders A, Segraves R, Zhang X, Niebuhr A, Albertson D, Yang H, Gray J, Niebuhr E, Bolund L, Pinkel D . High-resolution mapping of genotype–phenotype relationships in cri du chat syndrome using array comparative genomic hybridization . Am J Hum Genet . 2005 . 312–26 . 76 . 2 . 15635506 . 10.1086/427762 . 1196376 .
16. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
17. "p": Short arm; "q": Long arm.
18. For cytogenetic banding nomenclature, see article locus.
19. These values (ISCN start/stop) are based on the length of bands/ideograms from the ISCN book, An International System for Human Cytogenetic Nomenclature (2013). Arbitrary unit.
20. gpos: Region which is positively stained by G banding, generally AT-rich and gene poor; gneg: Region which is negatively stained by G banding, generally CG-rich and gene rich; acen Centromere. var: Variable region; stalk: Stalk.