Chromosome 5

Chromosome 5

Human chromosome 5 pair after G-banding.

One is from mother, one is from father.

Chromosome 5 pair

in human male karyogram.

Features
Length 181,538,259 bp
(bp) (GRCh38)[1]
No. of 839 (CCDS)[2]
genes
Type Autosome
Centromere Submetacentric[3]
position (48.8 Mbp[4])
Complete gene lists
CCDS Gene list (https://www.ncbi.nlm.nih.gov/gene?term=5%5BChr%5D%20AND%20%22Ho
mo%20sapiens%22%5BOrganism%5D%20AND%20%28%22has%20ccds%22%5BPro
perties%5D%20AND%20alive%5Bprop%5D%29&cmd=DetailsSearch)
HGNC Gene list (https://www.genenames.org/cgi-bin/statistics?c=5)
UniProt Gene list (https://www.uniprot.org/docs/humchr05.txt)
NCBI Gene list (https://www.ncbi.nlm.nih.gov/gene/?term=5%5BCHR%5D+AND+human%5B
ORGN%5D)
External map viewers
Ensembl Chromosome 5 (http://www.ensembl.org/Homo_sapiens/Location/Chromosome?r=5)
 Entrez Chromosome 5 (https://www.ncbi.nlm.nih.gov/mapview/maps.cgi?TAXID=9606&chr=5)
NCBI Chromosome 5 (https://www.ncbi.nlm.nih.gov/genome/gdv/browser/?context=genome
&acc=GCF_000001405.36&chr=5)
UCSC Chromosome 5 (https://genome.ucsc.edu/cgi-bin/hgTracks?db=hg38&position=chr5)
Full DNA sequences
RefSeq NC_000005 (https://www.ncbi.nlm.nih.gov/nuccore/NC_000005?report=fasta) (FASTA)
GenBank CM000667 (https://www.ncbi.nlm.nih.gov/nuccore/CM000667?report=fasta) (FASTA)

Chromosome 5 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this
chromosome. Chromosome 5 spans about 181 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.[5]

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).[6]

Contents
Genes
Number of genes
Gene list
Diseases and disorders
Chromosomal conditions
Cytogenetic band
References
Further reading
External links

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.[7]
 Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date

CCDS 839 — — [2] 2016-09-08

HGNC 790 355 574 [8] 2017-05-12

Ensembl 882 1,207 707 [9] 2017-03-29

UniProt 875 — — [10] 2018-02-28

NCBI 886 981 785 [11][12][13] 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.

ABLIM3: encoding protein Actin-binding LIM protein 3

ADAMTS2: ADAM metallopeptidase with thrombospondin type 1 motif, 2
AGXT2: Alanine-glyoxylate aminotransferase 2
ANKRD31: encoding protein Ankyrin repeat domain 31
APBB3: encoding protein Amyloid beta A4 precursor protein-binding family B member 3
APC: adenomatosis polyposis coli
ARL15: encoding protein ADP-ribosylation factor-like 15
BRIX1: Ribosome biogenesis protein BRX1 homolog (also BXDC2)
C1QTNF3: Complement C1q tumor necrosis factor-related protein 3
C5orf45: Chromosome 5 open reading frame 45
CPLANE1: Ciliogenesis And Planar Polarity Effector 1
CAST: Calpastatin
CPLX2: Complexin-2
CREBRF: encoding protein CREB3 regulatory factor
CXXC5: CXXC-type zing finger protein 5
DPYSL3: Dihydropyrimidinase-like protein 3
EGR1: early growth response protein 1
ERAP1: endoplasmic reticulum aminopeptidase 1 (previously called ARTS-1)
ERAP2: endoplasmic reticulum aminopeptidase 2
ESM1: Endothelial cell-specific molecule 1
DTDST: diastrophic dysplasia sulfate transporter
EIF4E1B: encoding protein Eukaryotic translation initiation factor 4E family member 1B
ERCC8: excision repair cross-complementing rodent repair deficiency, complementation
group 8
FAF2: encoding protein Fas associated factor family member 2
FAM172A: encoding protein UPF0528 protein FAM172A
FAM105B: encoding protein Family with sequence similarity 105, member B
FAM114A2: encoding protein FAM114A2
FAM71B: encoding protein Family with sequence similarity 71 member B
FASTKD3: FAST kinase domain-containing protein 3
FBXL7: F-box/LRR-repeat protein 7
FCHSD1: FCH and double SH3 domain protein 1
FGF1: fibroblast growth factor 1 (acidic fibroblast growth factor)
FGFR4: fibroblast growth factor receptor 4
GM2A: GM2 ganglioside activator
GNPDA1: Glucosamine-6-phosphate isomerase 1
GPBP1: Vasculin
HEXB: hexosaminidase B (beta polypeptide)
HMGXB3: encoding protein HMG-box containing 3
IK: Protein Red
IRX1: Iroquois-class homeodomain protein (human)
LARP1: La-related protein 1
LMAN2: Lectin mannose binding 2
LNCR3 encoding protein Lung cancer susceptibility 3
LPCAT1: Lysophosphatidylcholine acyltransferase 1
LYRM7: encoding protein LYR motif containing 7
LYSMD3: LysM and putative peptidoglycan-binding domain-containing protein 3
MAN2A1: Alpha-mannosidase 2
MASS1: monogenic, audiogenic seizure susceptibility 1 homolog (mouse)
MCC: Colorectal mutant cancer protein
MCCC2: methylcrotonoyl-Coenzyme A carboxylase 2 (beta)
MCEF: transcription factor AF4/FMR2 family, member 4
MEF2C: Myocyte-specific enhancer factor 2C
MEF2C-AS1: encoding protein MEF2C antisense RNA 1
MGAT1: Mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase
MIR1271: encoding MicroRNA 1271
MIR146A: microRNA 146a
MTRR: 5-methyltetrahydrofolate-homocysteine methyltransferase reductase
MZB1: Marginal zone B and B1 cell-specific protein
NIPBL: Nipped-B homolog (Drosophila)
NREP: Neuronal regeneration related protein
NSA2 encoding protein TGF beta-inducible nuclear protein 1
NSD1: Transcription coregulator protein
NSUN2: NOP2/Sun domain family, member 2
NR2F1: Nuclear hormone receptor
NUDCD2: NudC domain-containing protein 2
P4HA2: Prolyl 4-hydroxylase subunit alpha-2
PCBD2: Pterin-4-alpha-carbinolamine dehydratase 2
PELO: Pelota homolog
PGGT1B: encoding protein Protein geranylgeranyltransferase type I subunit beta
PHAX: Phosphorylated adapter for RNA export
Pikachurin: Responsible for the functioning of the ribbon synapses; allows the eye to track
moving objects
PFDN1: Prefoldin subunit 1
POLR3G: encoding protein Polymerase (RNA) III (DNA directed) polypeptide G (32kD)
PPIP5K2: Diphosphoinositol pentakisphosphate kinase 2
PRCC1: Proline-rich coiled coil 1
 PRR16: encoding protein Proline-rich protein 16
PURA: Purine-rich element-binding protein A
PWWP2A: encoding protein PWWP domain containing 2A
RANBP3L: encoding protein RAN binding protein 3-like
RMND5B: Required for meiotic nuclear division 5 homolog B
SFXN1: Sideroflexin-1
SKIV2L2: Ski2 like RNA helicase 2
SLC22A5: solute carrier family 22 (organic cation transporter), member 5
SLC26A2: solute carrier family 26 (sulfate transporter), member 2
SH3TC2: domain and tetratricopeptide repeats 2
SLCO4C1: Solute carrier organic anion transporter family member 4c1
SLU7: pre-mRNA-splicing factor SLU7
SMN1: survival motor neuron 1, telomeric
SMN2: survival motor neuron 2, centromeric
SNCAIP: synuclein, alpha interacting protein (synphilin)
SPEF2: Sperm flagellar protein 2
SPINK5: serine protease inhibitor Kazal-type 5 (LEKTI)
SPINK6: serine protease inhibitor Kazal-type 6
SPINK9: serine protease inhibitor Kazal-type 9 (LEKTI-2)
SPZ1: Spermatogenic leucine zipper protein 1
STC2: Stanniocalcin-2
TBCA: Tubulin-specific chaperone A
TCOF1: Treacher Collins-Franceschetti syndrome 1
TGFBI: keratoepithelin
THG1L: Probable tRNA(His) guanylyltransferase
TICAM2: TIR domain-containing adapter molecule 2
TMEM171: encoding protein Transmembrane protein 171
TNFAIP8: Tumor necrosis factor, alpha-induced protein 8
TTC37: Tetratricopeptide repeat domain 37
UPF0488: encodes G protein-coupled receptor protein signaling pathway
YIPF5: Yip1 domain family member 5
YTHDC2: encoding protein YTH domain containing 2
ZBED3: Zinc finger BED domain-containing protein 3
ZNF608: encoding protein Zinc finger protein 608

Diseases and disorders

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

Achondrogenesis type 1B
Atelosteogenesis, type II
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.[14][15][16]

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-banding ideograms of human chromosome 5

G-banding ideogram G-banding patterns of human

of human chromosome 5 in three different
chromosome 5 in resolutions (400,[17] 550[18] and 850[4]).
resolution 850 bphs. Band length in this diagram is based on
Band length in this the ideograms from ISCN (2013).[19] This
diagram is type of ideogram represents actual
proportional to base- relative band length observed under a
pair length. This type microscope at the different moments
of ideogram is during the mitotic process.[20]
generally used in
genome browsers
(e.g. Ensembl, UCSC
Genome Browser).
 G-bands of human chromosome 5 in resolution 850 bphs[21]
ISCN ISCN Basepair
Basepair

Chr. Arm[22] Band[23] Stain[25] Density

start[24] stop[24] start stop

5 p 15.33 0 278 1 4,400,000 gneg

5 p 15.32 278 401 4,400,001 6,300,000 gpos 25
5 p 15.31 401 555 6,300,001 9,900,000 gneg
5 p 15.2 555 802 9,900,001 15,000,000 gpos 50
5 p 15.1 802 972 15,000,001 18,400,000 gneg
5 p 14.3 972 1234 18,400,001 23,300,000 gpos 100
5 p 14.2 1234 1281 23,300,001 24,600,000 gneg
5 p 14.1 1281 1543 24,600,001 28,900,000 gpos 100
5 p 13.3 1543 1836 28,900,001 33,800,000 gneg
5 p 13.2 1836 2068 33,800,001 38,400,000 gpos 25
5 p 13.1 2068 2253 38,400,001 42,500,000 gneg
5 p 12 2253 2407 42,500,001 46,100,000 gpos 50
5 p 11 2407 2592 46,100,001 48,800,000 acen
5 q 11.1 2592 2839 48,800,001 51,400,000 acen
5 q 11.2 2839 3271 51,400,001 59,600,000 gneg
5 q 12.1 3271 3518 59,600,001 63,600,000 gpos 75
5 q 12.2 3518 3580 63,600,001 63,900,000 gneg
5 q 12.3 3580 3765 63,900,001 67,400,000 gpos 75
5 q 13.1 3765 4012 67,400,001 69,100,000 gneg
5 q 13.2 4012 4197 69,100,001 74,000,000 gpos 50
5 q 13.3 4197 4397 74,000,001 77,600,000 gneg
5 q 14.1 4397 4752 77,600,001 82,100,000 gpos 50
5 q 14.2 4752 4907 82,100,001 83,500,000 gneg
5 q 14.3 4907 5400 83,500,001 93,000,000 gpos 100
5 q 15 5400 5678 93,000,001 98,900,000 gneg
5 q 21.1 5678 5879 98,900,001 103,400,000 gpos 100
5 q 21.2 5879 5987 103,400,001 105,100,000 gneg
5 q 21.3 5987 6295 105,100,001 110,200,000 gpos 100
5 q 22.1 6295 6419 110,200,001 112,200,000 gneg
5 q 22.2 6419 6527 112,200,001 113,800,000 gpos 50
5 q 22.3 6527 6666 113,800,001 115,900,000 gneg
5 q 23.1 6666 6943 115,900,001 122,100,000 gpos 100
5 q 23.2 6943 7267 122,100,001 127,900,000 gneg
5 q 23.3 7267 7468 127,900,001 131,200,000 gpos 100
5 q 31.1 7468 7807 131,200,001 136,900,000 gneg
5 q 31.2 7807 8008 136,900,001 140,100,000 gpos 25
 5 q 31.3 8008 8316 140,100,001 145,100,000 gneg
5 q 32 8316 8625 145,100,001 150,400,000 gpos 75
5 q 33.1 8625 8887 150,400,001 153,300,000 gneg
5 q 33.2 8887 9072 153,300,001 156,300,000 gpos 50
5 q 33.3 9072 9304 156,300,001 160,500,000 gneg
5 q 34 9304 9690 160,500,001 169,000,000 gpos 100
5 q 35.1 9690 9952 169,000,001 173,300,000 gneg
5 q 35.2 9952 10183 173,300,001 177,100,000 gpos 25
5 q 35.3 10183 10600 177,100,001 181,538,259 gneg

References
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20. Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.;
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_V1). Last update 2014-06-03. Retrieved 2017-04-26.
22. "p": Short arm; "q": Long arm.
23. For cytogenetic banding nomenclature, see article locus.
24. 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.
25. 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.

Further reading
Mainardi PC, Perfumo C, Cali A, Coucourde G, Pastore G, Cavani S, Zara F, Overhauser J,
Pierluigi M, Bricarelli FD (2001). "Clinical and molecular characterisation of 80 patients with
5p deletion: genotype–phenotype correlation" (https://www.ncbi.nlm.nih.gov/pmc/articles/PM
C1734829). J Med Genet. 38 (3): 151–8. doi:10.1136/jmg.38.3.151 (https://doi.org/10.1136%
2Fjmg.38.3.151). PMC 1734829 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1734829).
PMID 11238681 (https://pubmed.ncbi.nlm.nih.gov/11238681).
Schafer IA, Robin NH, Posch JJ, Clark BA, Izumo S, Schwartz S (2001). "Distal 5q deletion
syndrome: phenotypic correlations". Am J Med Genet. 103 (1): 63–8. doi:10.1002/ajmg.1513
(https://doi.org/10.1002%2Fajmg.1513). PMID 11562936 (https://pubmed.ncbi.nlm.nih.gov/1
1562936).
Schmutz J, Martin J, Terry A, Couronne O, Grimwood J, Lowry S, et al. (September 2004).
"The DNA sequence and comparative analysis of human chromosome 5" (https://doi.org/10.
1038%2Fnature02919). Nature. 431 (7006): 268–74. Bibcode:2004Natur.431..268S (https://
ui.adsabs.harvard.edu/abs/2004Natur.431..268S). doi:10.1038/nature02919 (https://doi.org/1
0.1038%2Fnature02919). PMID 15372022 (https://pubmed.ncbi.nlm.nih.gov/15372022).
Siddiqi R, Gilbert F (2003). "Chromosome 5". Genet Test. 7 (2): 169–87.
doi:10.1089/109065703322146902 (https://doi.org/10.1089%2F109065703322146902).
PMID 12885343 (https://pubmed.ncbi.nlm.nih.gov/12885343).

External links
National Institutes of Health. "Chromosome 5" (https://web.archive.org/web/2004101423061
1/http://ghr.nlm.nih.gov/chromosome=5). Genetics Home Reference. Archived from the
original (http://ghr.nlm.nih.gov/chromosome=5) on October 14, 2004. Retrieved 2017-05-06.
"Chromosome 5" (http://web.ornl.gov/sci/techresources/Human_Genome/posters/chromoso
me/chromo05.shtml). Human Genome Project Information Archive 1990–2003. Retrieved
2017-05-06.

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