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.
Human chromosome 5 pair after G-banding.
One is from mother, one is from father.
Chromosome 5 pair
in human male karyogram.
|Length (bp)||181,538,259 bp|
|No. of genes||839 (CCDS)|
|Complete gene lists|
|External map viewers|
|Full DNA sequences|
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).
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.
|Estimated by||Protein-coding genes||Non-coding RNA genes||Pseudogenes||Source||Release date|
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
- C5orf3: encoding protein FAM114A2
- C5orf13: Neuronal regeneration related protein
- C5orf21/FAM172A: encoding protein UPF0528 protein FAM172A
- C5orf42: Chromosome 5 open reading frame 42
- 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
- FAM71B: encoding protein Family with sequence similarity 71 member B
- FAM105B: encoding protein Family with sequence similarity 105, 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
- 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)
- 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
- MIR146A: microRNA 146a
- MTRR: 5-methyltetrahydrofolate-homocysteine methyltransferase reductase
- MZB1: Marginal zone B and B1 cell-specific protein
- NIPBL: Nipped-B homolog (Drosophila)
- NSA2 encoding protein TGF beta-inducible nuclear protein 1
- NSD1: Transcription coregulator protein
- NSUN2: NOP2/Sun domain family, member 2
- NUDCD2: NudC domain-containing protein 2
- P4HA2: Prolyl 4-hydroxylase subunit alpha-2
- PCBD2: Pterin-4-alpha-carbinolamine dehydratase 2
- PELO: Pelota homolog
- 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
- 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
- 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 (NR2F1, BBSOAS)
- 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
- 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
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.
- 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.
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- Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
- Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
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- Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
- "p": Short arm; "q": Long arm.
- For cytogenetic banding nomenclature, see article locus.
- 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.
- 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.
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- 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. PMID 11562936.
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