Chromosome 22

Chromosome 22
Human chromosome 22 pair after G-banding. One is from mother, one is from father.
Chromosome 22 pair in human male karyogram.
Features
Length (bp)	51,324,926 bp (CHM13)
No. of genes	417 (CCDS) [1]
Type	Autosome
Centromere position	Acrocentric [2] (15.0 Mbp [3] )
Complete gene lists
CCDS	Gene list
HGNC	Gene list
UniProt	Gene list
NCBI	Gene list
External map viewers
Ensembl	Chromosome 22
Entrez	Chromosome 22
NCBI	Chromosome 22
UCSC	Chromosome 22
Full DNA sequences
RefSeq	NC_000022 (FASTA)
GenBank	CM000684 (FASTA)

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, spanning about 51 million DNA base pairs and representing between 1.5 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. ^[4]

Human chromosomes are numbered by their apparent size in the karyotype, with chromosome 1 being the largest and chromosome 22 having originally been identified as the smallest. However, genome sequencing has revealed that chromosome 21 is actually smaller than chromosome 22.

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. ^[5]

Estimated by	Protein-coding genes	Non-coding RNA genes	Pseudogenes	Source	Release date
CCDS	417	—	—	[1]	2016-09-08
HGNC	424	161	295	[6]	2019-07-08
Ensembl	489	515	325	[7]	2017-03-29
UniProt	496	—	—	[8]	2018-02-28
NCBI	474	392	379	[9] [10] [11]	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) encoding protein cyclic AMP-dependent transcription factor ATF-4
• BCR (22q11) encoding breakpoint cluster region protein
• CARD10 (22q13) encoding caspase recruitment domain-containing protein 10
• CBX7 (22q13) encoding chromobox protein homolog 7
• CDC42EP1: CDC42 effector protein 1
• CECR1: cat eye syndrome critical region protein 1
• CHEK2 (22q12)
• COMT: Catechol-O-methyltransferase
• 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
• EP300-AS1
• EWSR1
• TAFA5: family with sequence similarity 19 member A5
• FAM227A: encoding protein FAM227A
• FBLN1
• GTPBP1: GTP-binding protein 1
• HMGXB4: encoding protein HMG-box containing 4
• IFT27: encoding protein intraflagellar transport 27
• IGL@
• IGLJ3 encoding protein immunoglobulin lambda joining 3
• IGLL5: encoding protein immunoglobulin lambda like polypeptide 5
• KIAA0930: encoding uncharacterized protein KIAA0930
• 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
• RNU12: encoding protein RNA, U12 small nuclear
• RRP7A: encoding protein ribosomal RNA-processing protein 7 homolog A
• RTCB: encoding protein RNA 2',3'-cyclic phosphate and 5'-OH ligase
• RTL6: encoding protein retrotransposon Gag Like 6
• 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: encoding protein Ku70

Locus	Gene	Description	Condition
22 q11.1-q11.2	IGL@	Asymmetric crying facies (Cayler cardiofacial syndrome)
22 q11.21	TBX1	T-box 1
22 q11	RTN4R	Reticulon 4 receptor	Schizophrenia
22 q11.21-q11.23	COMT	catechol-O-methyltransferase gene
22 q12.1-q13.1	NEFH	neurofilament, heavy polypeptide 200kDa
22 q12.1 [12]	CHEK2	CHK2 checkpoint homolog (S. pombe)
22 q12.2	NF2	neurofibromin 2	bilateral acoustic neuroma
22 q13	SOX10	SRY (sex determining region Y)-box 10
22 q13.1	APOL1	Apolipoprotein L1
22 q13.2	EP300	E1A binding protein p300
22 q13.3	WNT7B	Wingless-type MMTV integration site family, member 7B	22q13 deletion syndrome
22 q13.3	SHANK3	SH3 and multiple ankyrin repeat domains 3	22q13 deletion syndrome
22 q13.3	SULT4A1	sulfotransferase family 4A, member 1	22q13 deletion syndrome
22 q13.3	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
• 22q11.2 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
• Renal medullary carcinoma
• Rubinstein-Taybi syndrome
• Waardenburg syndrome
• Schizophrenia ^[13]

Chromosomal conditions

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

• 22q11.2 deletion syndrome: Most people with 22q11.2 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 q11.2. 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 22q11.2 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 22q11.2 deletion syndrome.
• 22q11.2 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 intellectual disability, 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 der (22) syndrome, it occurs when an individual has an extra chromosome composed of pieces of the 11th and 22nd chromosomes.

Cytogenetic band

G-banding ideograms of human chromosome 22

G-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 (e.g. Ensembl, UCSC Genome Browser).

G-banding patterns of human chromosome 22 in three different resolutions (400, ^[14] 550 ^[15] and 850 ^[3] ). Band length in this diagram is based on the ideograms from ISCN (2013). ^[16] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process. ^[17]

G-bands of human chromosome 22 in resolution 850 bphs ^[3]

Chr.	Arm [18]	Band [19]	ISCN start [20]	ISCN stop [20]	Basepair start	Basepair stop	Stain [21]	Density
22	p	13	0	260	1	4,300,000	gvar
22	p	12	260	576	4,300,001	9,400,000	stalk
22	p	11.2	576	836	9,400,001	13,700,000	gvar
22	p	11.1	836	1015	13,700,001	15,000,000	acen
22	q	11.1	1015	1234	15,000,001	17,400,000	acen
22	q	11.21	1234	1563	17,400,001	21,700,000	gneg
22	q	11.22	1563	1700	21,700,001	23,100,000	gpos	25
22	q	11.23	1700	1878	23,100,001	25,500,000	gneg
22	q	12.1	1878	2029	25,500,001	29,200,000	gpos	50
22	q	12.2	2029	2194	29,200,001	31,800,000	gneg
22	q	12.3	2194	2413	31,800,001	37,200,000	gpos	50
22	q	13.1	2413	2687	37,200,001	40,600,000	gneg
22	q	13.2	2687	2852	40,600,001	43,800,000	gpos	50
22	q	13.31	2852	3181	43,800,001	48,100,000	gneg
22	q	13.32	3181	3290	48,100,001	49,100,000	gpos	50
22	q	13.33	3290	3400	49,100,001	50,818,468	gneg

References

1. "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene". NCBI. CCDS Release 20 for Homo sapiens. 8 September 2016. Retrieved 28 May 2017.
2. Tom Strachan; Andrew Read (2 April 2010). Human Molecular Genetics. Garland Science. p. 45. ISBN   978-1-136-84407-2.
3. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
4. Mayor, Susan (1999). "First human chromosome is sequenced". BMJ. 319 (7223). BMJ Group: 1453. doi:10.1136/bmj.319.7223.1453a. PMC   1117192 . PMID   10582915.
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 22". HUGO Gene Nomenclature Committee. 8 July 2019. Archived from the original on 18 August 2017. Retrieved 7 August 2019.
7. "Chromosome 22: Chromosome summary - Homo sapiens". Ensembl Release 88. 29 March 2017. Retrieved 19 May 2017.
8. "Human chromosome 22: entries, gene names and cross-references to MIM". UniProt. 28 February 2018. Retrieved 16 March 2018.
9. "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene". NCBI. 19 May 2017. Retrieved 20 May 2017.
10. "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. 19 May 2017. Retrieved 20 May 2017.
11. "Search results - 22[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 19 May 2017. Retrieved 20 May 2017.
12. 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 22q12.1 microdeletions involving the gene". American Journal of Medical Genetics Part A. 167 (5): 1047–1053. doi:10.1002/ajmg.a.36839. PMID   25810350. S2CID   205319722.
13. 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. U.S.A. 99 (26): 16859–64. Bibcode:2002PNAS...9916859L. doi: 10.1073/pnas.232186099 . PMC   139234 . PMID   12477929.
14. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
15. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
16. 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.
17. Sethakulvichai, W.; Manitpornsut, S.; Wiboonrat, M.; Lilakiatsakun, W.; Assawamakin, A.; Tongsima, S. (2012). "Estimation of band level resolutions of human chromosome images". 2012 Ninth International Conference on Computer Science and Software Engineering (JCSSE). pp. 276–282. doi:10.1109/JCSSE.2012.6261965. ISBN   978-1-4673-1921-8. S2CID   16666470.
18. "p": Short arm; "q": Long arm.
19. For cytogenetic banding nomenclature, see article locus.
20. 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.
21. 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. Bibcode:1999Natur.402..489D. doi: 10.1038/990031 . PMID   10591208.
• Gilbert F (1998). "Disease genes and chromosomes: disease maps of the human genome. Chromosome 22". Genet Test. 2 (1): 89–97. doi:10.1089/gte.1998.2.89. 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:10.7326/0003-4819-138-10-200305200-00010. PMID   12755554. S2CID   25865321.
• 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:10.1016/S0736-5748(02)00050-3. PMID   12175881. S2CID   22941004.
• McDermid HE, Morrow BE (2002). "Genomic disorders on 22q11". Am J Hum Genet. 70 (5): 1077–88. doi:10.1086/340363. 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 22q11.2 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:10.1101/gad.1055203. 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:10.1136/jmg.40.8.575. PMC   1735560 . PMID   12920066.

External links

• National Institutes of Health. "Chromosome 22". Genetics Home Reference. Archived from the original on 5 June 2011. Retrieved 6 May 2017.
• "Chromosome 22". Human Genome Project Information Archive 1990–2003. Retrieved 6 May 2017.