Chromosome 15

Chromosome 15 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 15 spans about 101 million base pairs (the building material of DNA) and represents between 3% and 3.5% of the total DNA in cells.

Chromosome 15
Human chromosome 15 pair after G-banding.
One is from mother, one is from father.
Chromosome 15 pair
in human male karyogram.
Features
Length (bp)101,991,189 bp
(GRCh38)[1]
No. of genes561 (CCDS)[2]
TypeAutosome
Centromere positionAcrocentric[3]
(19.0 Mbp[4])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome 15
EntrezChromosome 15
NCBIChromosome 15
UCSCChromosome 15
Full DNA sequences
RefSeqNC_000015 (FASTA)
GenBankCM000677 (FASTA)

The human leukocyte antigen gene for β2-microglobulin is found at chromosome 15.

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 15. 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
CCDS561—— [2] 2016-09-08
HGNC559328433 [6] 2017-05-12
Ensembl605992508 [7] 2017-03-29
UniProt601—— [8] 2018-02-28
NCBI629716594 [9][10][11] 2017-05-19

Gene list

The following is a partial list of genes on human chromosome 15. For complete list, see the link in the infobox on the right.

  • AAGAB: alpha- and gamma-adaptin binding protein
  • ACSBG1: encoding enzyme Acyl-CoA Synthetase, Bubblegum Family, member 1
  • ARPP-19: encoding protein cAMP-regulated phosphoprotein 19
  • C15orf15: encoding protein Probable ribosome biogenesis protein RLP24
  • CAPN3: Calpain 3 (limb-girdle muscular dystrophy type 2A)
  • CHP: Calcium binding protein P22
  • CHSY1: Chondroitin sulfate synthase 1
  • CLK3: CDC like kinase 3
  • ClpX: encoding enzyme ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial
  • COMMD4: encoding protein COMM domain-containing protein 4
  • CPEB1: Cytoplasmic polyladenylation element binding protein 1
  • DTWD1:
  • ELL3: encoding protein Elongation factor RNA polymerase II-like 3
  • FAH: fumarylacetoacetate hydrolase (fumarylacetoacetase)
  • FAM214A: encoding protein Protein FAM214A
  • FBN1: fibrillin 1 (Marfan syndrome)
  • FOXB1: encoding protein Forkhead box B1
  • GATM: Glycine aminotransferase, mitochondrial
  • GCHFR: GTP cyclohydrolase 1 feedback regulatory protein
  • GLCE: D-glucuronyl C5-epimerase
  • HDGFRP3:
  • HEXA: hexosaminidase A (alpha polypeptide)(Tay–Sachs disease)
  • HMG20A: encoding protein High mobility group protein 20A
  • IDDM3 encoding protein Insulin dependent diabetes mellitus 3
  • IMP3: encoding protein U3 small nucleolar ribonucleoprotein protein IMP3
  • ITPKA: encoding enzyme Inositol-trisphosphate 3-kinase A
  • IVD: isovaleryl Coenzyme A dehydrogenase
  • KATNBL1: encoding protein KATNBL1
  • LARP6 encoding protein La-related protein 6 also known as acheron or La ribonucleoprotein domain family member 6 (LARP6),
  • LCMT2: encoding enzyme Leucine carboxyl methyltransferase 2
  • LINC00926 encoding protein Long intergenic non-protein coding RNA 926
  • MESDC2: encoding protein LDLR chaperone MESD
  • MESP1: encoding protein Mesoderm posterior 1 homolog (mouse)
  • MFAP1: encoding protein Microfibrillar-associated protein 1
  • MCPH4: microcephaly, primary autosomal recessive 4
  • MIR7-2: encoding protein MicroRNA 7-2
  • MIR627: encoding protein MicroRNA 627
  • NIPA2: encoding protein Non-imprinted in Prader-Willi/Angelman syndrome region protein 2
  • OCA2: oculocutaneous albinism II (pink-eye dilution homolog, mouse)
  • PDCD7: encoding protein Programmed cell death protein 7
  • PML: promyelocytic leukemia protein (involved in t(15,17) with RARalpha, predominant cause of acute promyelocytic leukemia.
  • PTPLAD1: encoding enzyme Protein tyrosine phosphatase-like protein PTPLAD1
  • PYGO1: encoding protein Pygopus homolog 1 (Drosophila)
  • RAD51: RAD51 homolog (RecA homolog, E. coli) (S. cerevisiae)
  • RMDN3: encoding protein Regulator of microtubule dynamics protein 3
  • RNR3: encoding RNA, ribosomal 45S cluster 3
  • RTF1: encoding protein Rtf1, Paf1/RNA polymerase II complex component, homolog (S. cerevisiae)
  • SCAMP2: encoding protein Secretory carrier-associated membrane protein 2
  • SCAMP5: encoding protein Secretory carrier-associated membrane protein 5
  • SCZD10: encoding protein Schizophrenia disorder 10 (periodic catatonia)
  • SCAPER: S-phase CyclinA Associated Protein residing in the Endoplasmic Reticulum
  • SENP8: encoding enzyme Sentrin-specific protease 8
  • SERF2: encoding protein Small EDRK-rich factor 2
  • SLC24A5: the gene responsible for at least 1/3 of the skin color differences between races, expressed in the brain and the nervous system
  • SNAPC5: encoding protein snRNA-activating protein complex subunit 5
  • SPN1: encoding protein Snurportin1
  • STRC: stereocilin
  • SUHW4: encoding protein Zinc finger protein 280D
  • SYNM: encoding protein Synemin
  • TGFBR2: location 3p24.2-p25 due to a inactivation mutation
  • TMC3: encoding protein Transmembrane channel like 3
  • TMCO5A: encoding protein Transmembrane and coiled-coil domains 5A
  • TMED3: encoding protein Transmembrane p24 trafficking protein 3
  • UBE3A: ubiquitin protein ligase E3A (human papilloma virus E6-associated protein, Angelman syndrome)
  • Ube3a-ATS:
  • VPS39: encoding protein hVam6p/Vps39-like protein
  • ZNF592: encoding protein Zinc finger protein 592
  • UNC13C: encoding protein unc-13 homolog C

Chromosomal conditions

The following conditions are caused by mutations in chromosome 15. Two of the conditions (Angelman syndrome and Prader–Willi syndrome) involve a loss of gene activity in the same part of chromosome 15, the 15q11.2-q13.1 region. This discovery provided the first evidence in humans that something beyond genes could determine how the genes are expressed.[12]

Angelman syndrome
Main article: Angelman syndrome

The main characteristics of Angelman syndrome are severe intellectual disability, ataxia, lack of speech, and excessively happy demeanor. Angelman syndrome results from a loss of gene activity in a specific part of chromosome 15, the 15q11-q13 region. This region contains a gene called UBE3A that, when mutated or absent, likely causes the characteristic features of this condition. People normally have two copies of the UBE3A gene, one from each parent. Both copies of this gene are active in many of the body's tissues. In the brain, however, only the copy inherited from a person's mother (the maternal copy) is active. If the maternal copy is lost because of a chromosomal change or a gene mutation, a person will have no working copies of the UBE3A gene in the brain.

In most cases (about 70%), people with Angelman syndrome have a deletion in the maternal copy of chromosome 15. This chromosomal change deletes the region of chromosome 15 that includes the UBE3A gene. Because the copy of the UBE3A gene inherited from a person's father (the paternal copy) is normally inactive in the brain, a deletion in the maternal chromosome 15 results in no active copies of the UBE3A gene in the brain.

In 3% to 7% of cases, Angelman syndrome occurs when a person has two copies of the paternal chromosome 15 instead of one copy from each parent. This phenomenon is called paternal uniparental disomy (UPD). People with paternal UPD for chromosome 15 have two copies of the UBE3A gene, but they are both inherited from the father and are therefore inactive in the brain.

About 10% of Angelman syndrome cases are caused by a mutation in the UBE3A gene, and another 3% result from a defect in the DNA region that controls the activation of the UBE3A gene and other genes on the maternal copy of chromosome 15. In a small percentage of cases, Angelman syndrome may be caused by a chromosomal rearrangement called a translocation or by a mutation in a gene other than UBE3A. These genetic changes can abnormally inactivate the UBE3A gene.

Angelman syndrome can be hereditary, as evidenced by one case where a patient became pregnant with a daughter who also had the condition.[13]

Prader–Willi syndrome
Main article: Prader–Willi syndrome

The main characteristics of this condition include polyphagia (extreme, insatiable appetite), mild to moderate developmental delay, hypogonadism resulting in delayed to no puberty, and hypotonia. Prader-Willi syndrome is caused by the loss of active genes in a specific part of chromosome 15, the 15q11-q13 region. People normally have two copies of this chromosome in each cell, one copy from each parent. Prader–Willi syndrome occurs when the paternal copy is partly or entirely missing.

In about 70% of cases, Prader–Willi syndrome occurs when the 15q11-q13 region of the paternal chromosome 15 is deleted. The genes in this region are normally active on the paternal copy of the chromosome and are inactive on the maternal copy. Therefore, a person with a deletion in the paternal chromosome 15 will have no active genes in this region.

In about 25% of cases, a person with Prader–Willi syndrome has two maternal copies of chromosome 15 in each cell instead of one copy from each parent. This phenomenon is called maternal uniparental disomy. Because some genes are normally active only on the paternal copy of this chromosome, a person with two maternal copies of chromosome 15 will have no active copies of these genes.

In a small percentage of cases, Prader–Willi syndrome is not caused by a chromosomal rearrangement called a trans location. Rarely, the condition is caused by an abnormality in the DNA region that controls the activity of genes on the paternal chromosome 15. Because patients almost always have difficulty reproducing, Prader–Willi syndrome is generally not hereditary.

Isodicentric chromosome 15
Main article: Isodicentric 15

A specific chromosomal change called an isodicentric chromosome 15 (IDIC15) (also known by a number of other names) can affect growth and development. The patient possesses an "extra" or "marker" chromosome. This small extra chromosome is made up of genetic material from chromosome 15 that has been abnormally duplicated (copied) and attached end-to-end. In some cases, the extra chromosome is very small and has no effect on a person's health. A larger isodicentric chromosome 15 can result in weak muscle tone (hypotonia), mental retardation, seizures, and behavioral problems.[14] Signs and symptoms of autism (a developmental disorder that affects communication and social interaction) have also been associated with the presence of an isodicentric chromosome 15.

Other chromosomal conditions

Other changes in the number or structure of chromosome 15 can cause mental retardation, delayed growth and development, hypotonia, and characteristic facial features. These changes include an extra copy of part of chromosome 15 in each cell (partial trisomy 15) or a missing segment of the chromosome in each cell (partial monosomy 15). In some cases, several of the chromosome's DNA building blocks (nucleotides) are deleted or duplicated.

The following diseases are some of those related to genes on chromosome 15:

Cytogenetic band
G-banding ideograms of human chromosome 15
G-banding ideogram of human chromosome 15 in resolution 850 bphs. Band length in this diagram is proportional to base-pair length. This type of ideogram is generally used in genome browsers (e.g. Ensembl, UCSC Genome Browser).
G-banding patterns of human chromosome 15 in three different resolutions (400,[15] 550[16] and 850[4]). Band length in this diagram is based on the ideograms from ISCN (2013).[17] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[18]
G-bands of human chromosome 15 in resolution 850 bphs[19]
Chr. Arm[20] Band[21] ISCN
start[22]		 ISCN
stop[22]		 Basepair
start		 Basepair
stop		 Stain[23] Density
15p 13027014,200,000 gvar
15p 122706314,200,0019,700,000 stalk
15p 11.263111429,700,00117,500,000 gvar
15p 11.11142138217,500,00119,000,000 acen
15q 11.11382148719,000,00120,500,000 acen
15q 11.21487177320,500,00125,500,000 gneg
15q 121773196825,500,00127,800,000 gpos50
15q 13.11968216427,800,00130,000,000 gneg
15q 13.22164228430,000,00130,900,000 gpos50
15q 13.32284252430,900,00133,400,000 gneg
15q 142524276533,400,00139,800,000 gpos75
15q 15.12765297539,800,00142,500,000 gneg
15q 15.22975306542,500,00143,300,000 gpos25
15q 15.33065324543,300,00144,500,000 gneg
15q 21.13245347144,500,00149,200,000 gpos75
15q 21.23471362149,200,00152,600,000 gneg
15q 21.33621384652,600,00158,800,000 gpos75
15q 22.13846398258,800,00159,000,000 gneg
15q 22.23982408759,000,00163,400,000 gpos25
15q 22.314087425263,400,00166,900,000 gneg
15q 22.324252435766,900,00167,000,000 gpos25
15q 22.334357450767,000,00167,200,000 gneg
15q 234507461367,200,00172,400,000 gpos25
15q 24.14613474872,400,00174,900,000 gneg
15q 24.24748480874,900,00176,300,000 gpos25
15q 24.34808492876,300,00178,000,000 gneg
15q 25.14928504878,000,00181,400,000 gpos50
15q 25.25048516981,400,00184,700,000 gneg
15q 25.35169537984,700,00188,500,000 gpos50
15q 26.15379564988,500,00193,800,000 gneg
15q 26.25649586093,800,00198,000,000 gpos50
15q 26.35860607098,000,001101,991,189 gneg

References

Specific references:

  1. "Human Genome Assembly GRCh38 – Genome Reference Consortium". National Center for Biotechnology Information. 2013-12-24. Retrieved 2017-03-04.
  2. "Search results – 15[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) – Gene". NCBI. CCDS Release 20 for Homo sapiens. 2016-09-08. Retrieved 2017-05-28.
  3. Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN 978-1-136-84407-2.
  4. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  5. Pertea M, Salzberg SL (2010). "Between a chicken and a grape: estimating the number of human genes". Genome Biol. 11 (5): 206. doi:10.1186/gb-2010-11-5-206. PMC 2898077. PMID 20441615.
  6. "Statistics & Downloads for chromosome 15". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  7. "Chromosome 15: Chromosome summary – Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  8. "Human chromosome 15: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  9. "Search results – 15[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) – Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  10. "Search results – 15[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. Retrieved 2017-05-20.
  11. "Search results – 15[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) – Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  12. "Teacher's Guide". Ghost in Your Genes (season 35). Nova (TV series). October 16, 2007. Retrieved 2009-09-26. The program...recounts how one scientist determined how the deletion of a key sequence of DNA on human chromosome 15 could lead to two different syndromes depending on whether the deletion originated from the mother or the father [and] explains that this was the first human evidence that something other than genes themselves could determine how genes are expressed.
  13. Lossie A, Driscoll D (1999). "Transmission of Angelman syndrome by an affected mother". Genet Med. 1 (6): 262–6. doi:10.1097/00125817-199909000-00004. PMID 11258627.
  14. "What is Dup15q Syndrome? – Dup15q". www.dup15q.org. Archived from the original on 2017-09-06. Retrieved 2017-09-05.
  15. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  16. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  17. International Standing Committee on Human Cytogenetic Nomenclature (2013). ISCN 2013: An International System for Human Cytogenetic Nomenclature (2013). Karger Medical and Scientific Publishers. ISBN 978-3-318-02253-7.
  18. Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.; Tongsima, S. (2012). "Estimation of band level resolutions of human chromosome images". In Computer Science and Software Engineering (JCSSE), 2012 International Joint Conference on: 276–282. doi:10.1109/JCSSE.2012.6261965. ISBN 978-1-4673-1921-8.
  19. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  20. "p": Short arm; "q": Long arm.
  21. For cytogenetic banding nomenclature, see article locus.
  22. 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.
  23. 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.

General references:

  • National Institutes of Health. "Chromosome 15". Genetics Home Reference. Retrieved 2017-05-06.
  • "Chromosome 15". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
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