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Chromosome 22

chromosome 22, chromosome 22 disorders
Chromosome 22 is one of the 23 pairs of chromosomes in human cells Humans normally have two copies of chromosome 22 in each cell Chromosome 22 is the second smallest human chromosome chromosome 21 being smaller, spanning about 49 million DNA base pairs and representing between 15 and 2% of the total DNA in cells

In 1999, researchers working on the Human Genome Project announced they had determined the sequence of base pairs that make up this chromosome Chromosome 22 was the first human chromosome to be fully sequenced[5]

Chromosome 22 was originally identified as the smallest chromosome After extensive research, however, researchers concluded that chromosome 21 was smaller The numbering of these chromosomes wasn't rearranged because of chromosome 21 being known by that designation as the chromosome that can lead to Down syndrome, or trisomy 21[citation needed]

Contents

  • 1 Genes
    • 11 Number of genes
    • 12 Gene list
  • 2 Diseases and disorders
  • 3 Chromosomal conditions
  • 4 Cytogenetic band
  • 5 References
  • 6 Further reading
  • 7 External links

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 22 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[6]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 417 - - [2] 2016-09-08
HGNC 424 148 288 [7] 2017-05-12
Ensembl 489 515 325 [8] 2017-03-29
UniProt 496 - - [9] 2018-02-28
NCBI 474 392 379 [10][11][12] 2017-05-19

Gene list

See also: Category:Genes on human chromosome 22

The following is a partial list of genes on human chromosome 22 For complete list, see the link in the infobox on the right

  • ADM2: encoding protein ADM2
  • APOBEC3B: encoding protein Probable DNA dC->dU-editing enzyme APOBEC-3B
  • ARFGAP3: encoding protein ADP-ribosylation factor GTPase-activating protein 3
  • ASCC2: encoding protein Activating signal cointegrator 1 complex subunit 2
  • ATF4 22q13
  • BCR 22q11
  • CARD10 22q13
  • CBX7 22q13
  • C22orf9: encoding protein Uncharacterized protein
  • CDC42EP1: CDC42 effector protein 1
  • CECR1: Cat eye syndrome critical region protein 1
  • CHEK2 22q12
  • COMT
  • CRELD2: Cysteine-rich with EGF-like domain protein 2
  • CSDC2: Cold shock domain-containing protein D2
  • CSNK1E: encoding enzyme Casein kinase I isoform epsilon or CK1ε,
  • DGCR5: encoding a long non-coding RNA
  • DGCR6: DiGeorge Syndrome critical region gene 6
  • EP300
  • EWSR1
  • FAM19A5: Family with sequence similarity 19 member A5
  • FAM227a: encoding protein FAM227A
  • FAM227A: encoding protein FAM227A
  • FBLN1
  • GTPBP1: GTP-binding protein 1
  • IGL@
  • IGLJ3 encoding protein Immunoglobulin lambda joining 3
  • LINC00899 encoding protein Long intergenic non-protein coding RNA 899
  • MAPK1
  • MAPK12
  • MCAT: encoding enzyme Malonyl CoA-acyl carrier protein transacylase, mitochondrial
  • MCM5
  • MIF
  • MIRLET7BHG: encoding protein MIRLET7B host gene non-protein coding
  • MKL1
  • MMP11
  • MN1
  • MTP18:
  • MYH9
  • NF2
  • NOL12: encoding protein Nucleolar protein 12
  • PARVB
  • PDGFB
  • PI4KA: encoding enzyme Phosphatidylinositol 4-kinase alpha
  • PI4KAP2: pseudogene phosphatidylinositol 4-kinase alpha pseudogene 2
  • PISD: encoding enzyme Phosphatidylserine decarboxylase proenzyme
  • PNPLA3: encoding enzyme Patatin-like phospholipase domain-containing protein 3
  • PRAME: encoding protein Melanoma antigen preferentially expressed in tumors
  • RAC2
  • RBX1
  • RNR5: encoding RNA, ribosomal 45S cluster 5
  • RRP7A: encoding protein Ribosomal RNA-processing protein 7 homolog A
  • SAMM50: encoding protein Sorting and assembly machinery component 50 homolog
  • SEPT3: encoding protein Neuronal-specific septin-3
  • SEPT5
  • SHFM3P1:
  • SOX10
  • SYNGR1: encoding protein Synaptogyrin-1
  • TBC1D10A: encoding protein TBC1 domain family member 10A
  • TEF: encoding protein Thyrotroph embryonic factor
  • THAP7: encoding protein THAP domain-containing protein 7
  • THOC5: encoding protein THO complex subunit 5 homolog
  • TRMU: encoding enzyme Mitochondrial tRNA-specific 2-thiouridylase 1
  • TTC28: encoding protein Tetratricopeptide repeat domain 28
  • TTLL1: encoding enzyme Probable tubulin polyglutamylase TTLL1
  • XRCC6
Locus Gene Description Condition
22q111-q112 IGL@ Asymmetric crying facies Cayler cardiofacial syndrome
22q1121 TBX1 T-box 1
22q11 RTN4R Reticulon 4 receptor Schizophrenia
22q1121-q1123 COMT catechol-O-methyltransferase gene
22q121-q131 NEFH neurofilament, heavy polypeptide 200kDa
22q121[13] CHEK2 CHK2 checkpoint homolog S pombe
22q122 NF2 neurofibromin 2 bilateral acoustic neuroma
22q13 SOX10 SRY sex determining region Y-box 10
22q131 APOL1 Apolipoprotein L1
22q132 EP300 E1A binding protein p300
22q133 WNT7B Wingless-type MMTV integration site family, member 7B 22q13 deletion syndrome
22q133 SHANK3 SH3 and multiple ankyrin repeat domains 3 22q13 deletion syndrome
22q133 SULT4A1 sulfotransferase family 4A, member 1 22q13 deletion syndrome
22q133 PARVB parvin beta cytoskeleton organization and cell adhesion 22q13 deletion syndrome

Diseases and disorders

The following diseases are some of those related to genes on chromosome 22:

  • Amyotrophic lateral sclerosis
  • Breast cancer
  • Cat eye syndrome
  • Chronic myeloid leukemia
  • DiGeorge Syndrome
  • Desmoplastic small round cell tumor
  • 22q112 distal deletion syndrome
  • 22q13 deletion syndrome or Phelan-McDermid syndrome
  • Emanuel syndrome
  • Ewing sarcoma
  • Focal Segmental Glomerulosclerosis
  • Li-Fraumeni syndrome
  • Metachromatic leukodystrophy
  • Methemoglobinemia
  • Neurofibromatosis type 2
  • Opitz G/BBB syndrome
  • Rubinstein-Taybi syndrome
  • Waardenburg syndrome
  • Schizophrenia[14]

Chromosomal conditions

The following conditions are caused by changes in the structure or number of copies of chromosome 22:

  • 22q112 deletion syndrome: Most people with 22q112 deletion syndrome are missing about 3 million base pairs on one copy of chromosome 22 in each cell The deletion occurs near the middle of the chromosome at a location designated as q112 This region contains about 30 genes, but many of these genes have not been well characterized A small percentage of affected individuals have shorter deletions in the same region
    The loss of one particular gene, TBX1, is thought to be responsible for many of the characteristic features of 22q112 deletion syndrome, such as heart defects, an opening in the roof of the mouth a cleft palate, distinctive facial features, and low calcium levels A loss of this gene does not appear to cause learning disabilities, however Other genes in the deleted region are also likely to contribute to the signs and symptoms of 22q112 deletion syndrome
  • 22q112 distal deletion syndrome
  • 22q13 deletion syndrome
  • Other chromosomal conditions: Other changes in the number or structure of chromosome 22 can have a variety of effects, including mental retardation, delayed development, physical abnormalities, and other medical problems These changes include an extra piece of chromosome 22 in each cell partial trisomy, a missing segment of the chromosome in each cell partial monosomy, and a circular structure called ring chromosome 22 that is caused by the breakage and reattachment of both ends of the chromosome
  • Cat-eye syndrome is a rare disorder most often caused by a chromosomal change called an inverted duplicated 22 A small extra chromosome is made up of genetic material from chromosome 22 that has been abnormally duplicated copied The extra genetic material causes the characteristic signs and symptoms of cat-eye syndrome, including an eye abnormality called ocular iris coloboma a gap or split in the colored part of the eye, small skin tags or pits in front of the ear, heart defects, kidney problems, and, in some cases, delayed development
  • A rearrangement translocation of genetic material between chromosomes 9 and 22 is associated with several types of blood cancer leukemia This chromosomal abnormality, which is commonly called the Philadelphia chromosome, is found only in cancer cells The Philadelphia chromosome has been identified in most cases of a slowly progressing form of blood cancer called chronic myeloid leukemia, or CML It also has been found in some cases of more rapidly progressing blood cancers acute leukemias The presence of the Philadelphia chromosome can help predict how the cancer will progress and provides a target for molecular therapies
  • Emanuel Syndrome is a translocation of chromosomes 11 and 22 Originally known as Supernumerary der22 Syndrome, it occurs when an individual has an extra chromosome composed of pieces of the 11th and 22nd chromosomes
  • the 22q11 locus contains the subgenes for immunoglobulin light chain lambda: the immunoglobulin lambda light chain locus contains protein-coding genes that can be lost with its rearrangement[15] This is based on a physiological mechanism and is not pathogenetic for leukemias or lymphomas[15] However, the rearrangement of several lambda variable subgenes can activate expression of an overlapping miRNA gene, which has consequences for gene expression regulation[16]

Cytogenetic band

G-banding ideograms of human chromosome 22G-banding ideogram of human chromosome 22 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 eg Ensembl, UCSC Genome BrowserG-banding patterns of human chromosome 22 in three different resolutions 400,[17] 550[18] and 850[4] Band length in this diagram is based on the ideograms from ISCN 2013[19] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process[20] G-bands of human chromosome 22 in resolution 850 bphs[21]
Chr Arm[22] Band[23] ISCN
start[24]
ISCN
stop[24]
Basepair
start
Basepair
stop
Stain[25] Density
22 p 13 0 260 7000100000000000000♠1 7006430000000000000♠4,300,000 gvar
22 p 12 260 576 7006430000100000000♠4,300,001 7006940000000000000♠9,400,000 stalk
22 p 112 576 836 7006940000100000000♠9,400,001 7007137000000000000♠13,700,000 gvar
22 p 111 836 1015 7007137000010000000♠13,700,001 7007150000000000000♠15,000,000 acen
22 q 111 1015 1234 7007150000010000000♠15,000,001 7007174000000000000♠17,400,000 acen
22 q 1121 1234 1563 7007174000010000000♠17,400,001 7007217000000000000♠21,700,000 gneg
22 q 1122 1563 1700 7007217000010000000♠21,700,001 7007231000000000000♠23,100,000 gpos 25
22 q 1123 1700 1878 7007231000010000000♠23,100,001 7007255000000000000♠25,500,000 gneg
22 q 121 1878 2029 7007255000010000000♠25,500,001 7007292000000000000♠29,200,000 gpos 50
22 q 122 2029 2194 7007292000010000000♠29,200,001 7007318000000000000♠31,800,000 gneg
22 q 123 2194 2413 7007318000010000000♠31,800,001 7007372000000000000♠37,200,000 gpos 50
22 q 131 2413 2687 7007372000010000000♠37,200,001 7007406000000000000♠40,600,000 gneg
22 q 132 2687 2852 7007406000010000000♠40,600,001 7007438000000000000♠43,800,000 gpos 50
22 q 1331 2852 3181 7007438000010000000♠43,800,001 7007481000000000000♠48,100,000 gneg
22 q 1332 3181 3290 7007481000010000000♠48,100,001 7007491000000000000♠49,100,000 gpos 50
22 q 1333 3290 3400 7007491000010000000♠49,100,001 7007508184680000000♠50,818,468 gneg

References

  1. ^ "Human Genome AssemblGenome Reference Consortium" National Center for Biotechnology Information 2013-12-24 Retrieved 2017-03-04 
  2. ^ a b "Search results - 22[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. ^ a b Genome Decoration Page, NCBI Ideogram data for Homo sapience 850 bphs, Assembly GRCh38p3 Last update 2014-06-03 Retrieved 2017-04-26
  5. ^ Mayor, Susan 1999 "First human chromosome is sequenced" BMJ BMJ Group 319 7223: 1453 doi:101136/bmj31972231453a PMC 1117192  PMID 10582915 
  6. ^ Pertea M, Salzberg SL 2010 "Between a chicken and a grape: estimating the number of human genes" Genome Biol 11 5: 206 doi:101186/gb-2010-11-5-206 PMC 2898077  PMID 20441615 
  7. ^ "Statistics & Downloads for chromosome 22" HUGO Gene Nomenclature Committee 2017-05-12 Retrieved 2017-05-19 
  8. ^ "Chromosome 22: Chromosome summary - Homo sapiens" Ensembl Release 88 2017-03-29 Retrieved 2017-05-19 
  9. ^ "Human chromosome 22: entries, gene names and cross-references to MIM" UniProt 2018-02-28 Retrieved 2018-03-16 
  10. ^ "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND "genetype protein coding"[Properties] AND alive[prop] - Gene" NCBI 2017-05-19 Retrieved 2017-05-20 
  11. ^ "Search results - 22[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 
  12. ^ "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND "genetype pseudo"[Properties] AND alive[prop] - Gene" NCBI 2017-05-19 Retrieved 2017-05-20 
  13. ^ Beck, Megan; Peterson, Jess F; McConnell, Juliann; McGuire, Marianne; Asato, Miya; Losee, Joseph E; Surti, Urvashi; Madan-Khetarpal, Suneeta; Rajkovic, Aleksandar; Yatsenko, Svetlana A May 2015 "Craniofacial abnormalities and developmental delay in two families with overlapping 22q121 microdeletions involving the gene" American Journal of Medical Genetics Part A 167 5: 1047–1053 doi:101002/ajmga36839 PMID 25810350 
  14. ^ Liu H, Abecasis GR, Heath SC, Knowles A, Demars S, Chen YJ, Roos JL, Rapoport JL, Gogos JA, Karayiorgou M December 2002 "Genetic variation in the 22q11 locus and susceptibility to schizophrenia" Proc Natl Acad Sci USA 99 26: 16859–64 doi:101073/pnas232186099 PMC 139234  PMID 12477929 
  15. ^ a b Mraz, M; Stano Kozubik, K; Plevova, K; Musilova, K; Tichy, B; Borsky, M; Kuglik, P; Doubek, M; Brychtova, Y; Mayer, J; Pospisilova, S 2013 "The origin of deletion 22q11 in chronic lymphocytic leukemia is related to the rearrangement of immunoglobulin lambda light chain locus" Leukemia Research 37 7: 802–808 doi:101016/jleukres201303018 PMID 23608880 
  16. ^ Mraz, M; Dolezalova, D; Plevova, K; Stano Kozubik, K; Mayerova, V; Cerna, K; Musilova, K; Tichy, B; Pavlova, S; Borsky, M; Verner, J; Doubek, M; Brychtova, Y; Trbusek, M; Hampl, A; Mayer, J; Pospisilova, S 2012 "MicroRNA-650 expression is influenced by immunoglobulin gene rearrangement and affects the biology of chronic lymphocytic leukemia" Blood 119 9: 2110–2113 doi:101182/blood-2011-11-394874 PMID 22234685 
  17. ^ Genome Decoration Page, NCBI Ideogram data for Homo sapience 400 bphs, Assembly GRCh38p3 Last update 2014-03-04 Retrieved 2017-04-26
  18. ^ Genome Decoration Page, NCBI Ideogram data for Homo sapience 550 bphs, Assembly GRCh38p3 Last update 2015-08-11 Retrieved 2017-04-26
  19. ^ 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 
  20. ^ Sethakulvichai, W; Manitpornsut, S; Wiboonrat, M; Lilakiatsakun, W; Assawamakin, A; Tongsima, S 2012 "Estimation of band level resolutions of human chromosome images" PDF In Computer Science and Software Engineering JCSSE, 2012 International Joint Conference on: 276–282 doi:101109/JCSSE20126261965 
  21. ^ Genome Decoration Page, NCBI Ideogram data for Homo sapience 850 bphs, Assembly GRCh38p3 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. ^ a b 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

  • Dunham I, Shimizu N, Roe BA, Chissoe S, Hunt AR, Collins JE, Bruskiewich R, Beare DM, Clamp M, Smink LJ, Ainscough R, Almeida JP, Babbage A, Bagguley C, Bailey J, Barlow K, Bates KN, Beasley O, Bird CP, Blakey S, Bridgeman AM, Buck D, Burgess J, Burrill WD, O'Brien KP 1999 "The DNA sequence of human chromosome 22" Nature 402 6761: 489–95 doi:101038/990031 PMID 10591208 
  • Gilbert F 1998 "Disease genes and chromosomes: disease maps of the human genome Chromosome 22" Genet Test 2 1: 89–97 doi:101089/gte1998289 PMID 10464604 
  • Kurzrock R, Kantarjian HM, Druker BJ, Talpaz M 2003 "Philadelphia chromosome-positive leukemias: from basic mechanisms to molecular therapeutics" Ann Intern Med 138 10: 819–30 doi:107326/0003-4819-138-10-200305200-00010 PMID 12755554 
  • Maynard TM, Haskell GT, Lieberman JA, LaMantia AS 2002 "22q11 DS: genomic mechanisms and gene function in DiGeorge/velocardiofacial syndrome" Int J Dev Neurosci 20 3–5: 407–19 doi:101016/S0736-57480200050-3 PMID 12175881 
  • McDermid HE, Morrow BE 2002 "Genomic disorders on 22q11" Am J Hum Genet 70 5: 1077–88 doi:101086/340363 PMC 447586  PMID 11925570 
  • McDonald-McGinn DM, Kirschner R, Goldmuntz E, Sullivan K, Eicher P, Gerdes M, Moss E, Solot C, Wang P, Jacobs I, Handler S, Knightly C, Heher K, Wilson M, Ming JE, Grace K, Driscoll D, Pasquariello P, Randall P, Larossa D, Emanuel BS, Zackai EH 1999 "The Philadelphia story: the 22q112 deletion: report on 250 patients" Genet Couns 10 1: 11–24 PMID 10191425 
  • Rinn JL, Euskirchen G, Bertone P, Martone R, Luscombe NM, Hartman S, Harrison PM, Nelson FK, Miller P, Gerstein M, Weissman S, Snyder M 2003 "The transcriptional activity of human Chromosome 22" Genes Dev 17 4: 529–40 doi:101101/gad1055203 PMC 195998  PMID 12600945 
  • Wilson HL, Wong AC, Shaw SR, Tse WY, Stapleton GA, Phelan MC, Hu S, Marshall J, McDermid HE, et al 2003 "Molecular characterisation of the 22q13 deletion syndrome supports the role of haploinsufficiency of SHANK3/PROSASP2 in the major neurological symptoms" J Med Genet 40 8: 575–584 doi:101136/jmg408575 PMC 1735560  PMID 12920066 

External links

  • National Institutes of Health "Chromosome 22" Genetics Home Reference Retrieved 2017-05-06 
  • "Chromosome 22" Human Genome Project Information Archive 1990–2003 Retrieved 2017-05-06 

chromosome 22, chromosome 22 central, chromosome 22 deficiency, chromosome 22 deletion, chromosome 22 deletion syndrome, chromosome 22 disorders, chromosome 22 duplication, chromosome 22 trisomy, chromosome 22q, chromosome 22q11


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