Chromosome 6

Chromosome 6 is one of the 23 pairs of chromosomes in humans. People normally have two copies of this chromosome. Chromosome 6 spans more than 172 million base pairs (the building material of DNA) and represents between 5.5 and 6% of the total DNA in cells. It contains the major histocompatibility complex, which contains over 100 genes related to the immune response, and plays a vital role in organ transplantation.

Chromosome 6
Human chromosome 6 pair after G-banding.
One is from mother, one is from father.
Chromosome 6 pair
in human male karyogram.
Features
Length (bp)172,126,628 bp
(CHM13)
No. of genes996 (CCDS)[1]
TypeAutosome
Centromere positionSubmetacentric[2]
(59.8 Mbp[3])
Complete gene lists
CCDSGene list
HGNCGene list
UniProtGene list
NCBIGene list
External map viewers
EnsemblChromosome 6
EntrezChromosome 6
NCBIChromosome 6
UCSCChromosome 6
Full DNA sequences
RefSeqNC_000006 (FASTA)
GenBankCM000668 (FASTA)

The evolution of human centromere 6

The centromere of chromosome 6 illustrates an interesting example of centromere evolution. It was known that in a Catarrhini ancestor the chromosome 6 centromere was situated near position 26 Mb of the modern human chromosome. In Macaca mulatta, this old centromere went defunct and repositioned to a different chromosomal location. In case of humans, the old centromere went defunct and a more recent form emerged near the modern position of human cen6 (size of 60 Mb). Such cases are known as Evolutionary New Centromeres (ENC). This assembly phenomenon of the human chromosome 6 gives researchers an opportunity to investigate the origin of the ENC on chromosome 6. [4]

Genes

The human leukocyte antigen lies on chromosome 6, with the exception of the gene for β2-microglobulin (which is located on chromosome 15), and encodes cell-surface antigen-presenting proteins among other functions.

Number of genes

In 2003, the entirety of chromosome 6 was manually annotated for proteins, resulting in the identification of 1,557 genes, and 633 pseudogenes.[5]

The following are some of the newer gene count estimates. 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
CCDS996—— [1] 2016-09-08
HGNC1,007422736 [7] 2017-05-12
Ensembl1,038985800 [8] 2017-03-29
UniProt1,111—— [9] 2018-02-28
NCBI1,0531,188911 [10][11][12] 2017-05-19

Gene list

The following is a partial list of genes on human chromosome 6. For complete list, see the link in the infobox on the right.

p-arm

The following are some of the genes located on p-arm (short arm) of human chromosome 6:

  • ADTRP: encoding protein Androgen-dependent TFPI-regulating protein
  • APOM: encoding protein Apolipoprotein M (6p21.33)
  • ARMC12: encoding protein Armadillo repeat containing 12
  • ATXN1: encoding protein Ataxin 1 (6p16.3-p16.76)
  • TSBP1: encoding protein TSBP1 (6p21.32)
  • C6orf62: chromosome 6 open reading frame 62 (6p22.3)
  • C6orf89: chromosome 6 open reading frame 89 (6p21.2)
  • CDKAL1: CDK5 regulatory subunit associated protein 1 like 1 (6p22.3)
  • COL11A2: collagen, type XI, alpha 2(6p21.3)
  • CRIP3: encoding protein Cysteine rich protein 3
  • CYP21A2: cytochrome P450, family 21, subfamily A, polypeptide 2 (6p21.33)
  • DHX16: DEAH-box helicase 16 (6p21.33)
  • DOM3Z: Decapping exoribonuclease (6p21.33)
  • DSP: Desmoplakin gene linked to cardiomyopathy (6p24.3)
  • ELOVL5: ELOVL fatty acid elongase 5 (6p12.1)
  • FBXO9: F-box protein 9 (6p12.1)
  • FOXP4-AS1: encoding protein FOXP4 antisense RNA 1
  • FTH1P5: encoding protein Ferritin, heavy polypeptide 1 pseudogene 5
  • G6B: Protein G6b (6p21.33)
  • GCNT2: N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase (6p24.3)
  • GGNBP1: encoding protein Gametogenetin binding protein 1 (pseudogene)
  • GMDS: GDP-mannose 4,6-dehydratase (6p25.3)
  • GTPBP2: encoding protein Gtp binding protein 2
  • HCG4P11: HLA complex group 4 pseudogene 11
  • HFE: hemochromatosis (6p22.2)
  • HIST1H2AH: histone cluster 1 H2A family member h (6p22.1)
  • HLA-A, HLA-B, HLA-C: major histocompatibility complex (MHC), class I, A, B, and C loci. (6p21.3)
  • HLA-DQA1 and HLA-DQB1 form HLA-DQ heterodimer MHC class II, DQ: Celiac1, IDDM (6p21.3)
  • HLA-DRA, HLA-DRB1, HLA-DRB3, HLA-DRB4, HLA-DRB5 forms HLA-DR, heterodimer MHC class II, DR (6p21.3) Mold / Biotoxin Susceptibility
  • HLA-DPA1 and HLA-DPB1 forms HLA-DP, MHC class II, DP (6p21.3)
  • HLA-Cw*06:02: gene variation related to psoriasis (6p21.3)
  • KAAG1: encoding protein Kidney associated antigen 1
  • LOC100533655: encoding protein Aryl hydrocarbon receptor pseudogene
  • LST1: leukocyte specific transcript 1 (6p21.33)
  • LY6G6E encoding protein Lymphocyte antigen 6 complex, locus G6E (pseudogene) (6p21.33)
  • MIR4640: microRNA 4640 (6p21.33)
  • MLIP: muscular LMNA interaction protein (6p12.1)
  • MRPS18B: mitochondrial ribosomal protein S18B (6p21.33)
  • MUT: methylmalonyl Coenzyme A mutase (6p12.3)
  • NHLRC1: NHL repeat containing E3 ubiquitin protein ligase 1 (6p22.3)
  • NOL7: nucleolar protein 7 (6p23)
  • NQO2: N-ribosyldihydronicotinamide:quinone reductase 2 (6p25.2)
  • NRSN1: neurensin 1 (6p22.3)
  • NUDT3: nudix hydrolase 3 (6p21.31)
  • PFDN6: prefoldin subunit 6 (6p21.32)
  • PHACTR1: phosphatase and actin regulator 1 (6p24.1)
  • PKHD1: polycystic kidney and hepatic disease 1 (autosomal recessive) (6p21.2-p12)
  • PRICKLE4: prickle planar cell polarity protein 4 (6p21.1)
  • PRSS16: protease, serine 16 (6p22.1)
  • PSMB8-AS1: PSMB8 antisense RNA 1 (head to head) (6p21.32)
  • RAB44: encoding protein Rab44, member ras oncogene family
  • RIPOR2: RHO family interacting cell polarization regulator 2 (6p22.3)
  • RPL10A: encoding protein 60S ribosomal protein L10a (6p21.31)
  • SKIV2L: Ski2 like RNA helicase (6p21.33)
  • SSR1: signal sequence receptor subunit 1 (6p24.3)
  • TCF19: transcription factor 19 (6p21.33)
  • TCP11: t-complex 11 (6p21.31)
  • TJAP1: tight junction associated protein 1 (6p21.1)
  • TP53COR1 encoding protein Tumor protein p53 pathway corepressor 1 (non-protein coding)
  • TMEM151B: encoding protein Transmembrane protein 151B
  • TNXB: tenascin XB (6p21.3)
  • TRAM2: translocation associated membrane protein 2 (6p12.2)
  • TRIM38: encoding protein Tripartite motif containing 38
  • TTBK1: encoding protein Tau tubulin kinase 1
  • UBR2: ubiquitin protein ligase E3 component n-recognin 2 (6p21.2)
  • UNC5CL: encoding protein Unc-5 homolog C (C. elegans)-like
  • USP8P1: encoding protein Ubiquitin specific peptidase 8 pseudogene 1
  • VEGF: vascular endothelial growth factor A (angiogenic growth factor) (6p21.1)
  • VPS52: GARP complex subunit
  • VWA7: encoding protein Von willebrand factor a domain containing 7
  • ZKSCAN4: encoding protein zinc finger with KRAB and SCAN domains 4
  • ZNF76: zinc finger protein 76 (6p21.31)
  • ZNF193: zinc finger protein 193 (6p22.1)
  • ZNRD1: zinc ribbon domain containing 1 (6p22.1)

q-arm

The following are some of the genes located on q-arm (long arm) of human chromosome 6:

  • AIM1: encoding protein Absent in melanoma 1 protein (6q21)
  • AIG1: encoding protein Androgen-induced protein 1 (6q24.2)
  • AKIRIN2: akirin 2 (6q15)
  • ARG1: arginase 1 (6q23.2)
  • BCKDHB: branched-chain keto acid dehydrogenase E1, beta polypeptide (maple syrup urine disease) (6q14.1)
  • BMIQ3: body mass index QTL 3
  • TMEM242 encoding transmembrane protein TMEM242
  • C6orf203: encoding protein Chromosome 6 open reading frame 203
  • C6orf58: chromosome 6 open reading frame 58 (6q22.33)
  • CFAP206: encoding protein Cilia And Flagella Associated Protein 206
  • CMD1F: cardiomyopathy, dilated 1F
  • CMD1K: cardiomyopathy, dilated 1K
  • CNR1: cannabinoid 1 receptor (6q14-q15)[13]
  • DACT2: encoding protein Dishevelled binding antagonist of beta catenin 2
  • DFNB38: deafness, autosomal recessive 38
  • DYX4: dyslexia susceptibility 4
  • ECT2L: encoding protein Epithelial cell transforming sequence 2 oncogene-like
  • ESR1: Estrogen receptor 1 (6q25)
  • EYA4: eyes absent homolog 4 (Drosophila)(6q23.2)
  • FBXL4: F-box and leucine rich repeat protein 4 (6q16.1-q16.2)
  • FEB5: febrile convulsions 5
  • HACE1: HECT domain and Ankyrin repeat containing, E3 ubiquitin protein ligase 1 (6q21)
  • HEBP2: heme binding protein 2 (6q24.1)
  • IDDM8: insulin dependent diabetes mellitus 8
  • IDDM15: insulin dependent diabetes mellitus 15
  • IFNGR: interferon-γ receptor gene (6q23-q24)
  • IGF2R: insulin-like growth factor 2 receptor (6q25.3)
  • IMPG1: interphotoreceptor matrix proteoglylcan 1 (6q14.1)
  • KIAA0408
  • LGSN: encoding protein lengsin
  • LIN28B: lin-28 homolog B (6q16.3-q21)
  • MAN1A1: mannosidase alpha class 1A member 1 (6q22.31)
  • MB21D1: encoding protein Mab-21 domain containing 1
  • MCDR1: macular dystrophy, retinal, 1
  • MDN1: midasin AAA ATPase 1 (6q15)
  • MOXD1: monooxygenase DBH like 1 (6q23.2)
  • MTO1: mitochondrial tRNA translation optimization 1 (6q13)
  • MRT18: mental retardation, non-syndromic, autosomal recessive
  • MRT28: mental retardation, non-syndromic, autosomal recessive
  • MTRF1L: mitochondrial translational release factor 1 like (6q25.2)
  • MYO6: myosin VI (6q14.1)
  • NHEG1: encoding protein Neuroblastoma highly expressed 1
  • OA3: ocular albinism 3
  • OPRM1: μ-opioid receptors (6q24-q25)
  • OTSC7: otosclerosis 7
  • PLG: plasminogen (6q26)
  • PBCRA1
  • PARK2: Parkinson disease (autosomal recessive, juvenile) 2, parkin (6q26)
  • PCMT1: protein-L-isoaspartate (D-aspartate) O-methyltransferase (6q25.1)
  • PERP: p53 apoptosis effector related to PMP-22 (6q23.3)
  • PKIB: cAMP-dependent protein kinase inhibitor beta (6p22.31)
  • PLAGL1: (6q24.2)
  • QRSL1: encoding protein Glutaminyl-trna synthase (glutamine-hydrolyzing)-like 1
  • RCD1: retinal cone dystrophy 1
  • RFPL4B: Ret finger protein like 4B
  • RP63: retinitis pigmentosa 63
  • SASH1: SAM and SH3 domain containing 1 (6q24.3-q25.1)
  • SCZD5: schizophrenia disorder 5
  • SEN6: senescence (cellular)-related 6
  • SENP6: SUMO1/sentrin specific peptidase 6 (6q14.1)
  • SERAC1: serine active site containing 1 (6q25.3)
  • SERINC1: serine incorporator 1 (6q22.31)
  • SF3B5: splicing factor 3b subunit 5 (6q24.2)
  • SMAP1: small ArfGAP 1 (6q13)
  • SOBP: sine oculis binding protein homolog (6q21)
  • SPG25: spastic paraplegia 25
  • ST8: suppression of tumorigenicity 8
  • SYNJ2: synaptojanin 2 (6q25.3)
  • T: T brachyury transcription factor (more commonly known as the T gene) linked to Hepatocellular carcinoma and Chordoma (6q27)[14]
  • TAAR1: trace amine associated receptor 1 (6q23.1)
  • TAAR2: trace amine associated receptor 2 (6q24)
  • TMEM200A: encoding protein Transmembrane protein 200A
  • TSPYL1: TSPY like 1 (6q22.1)
  • UNC93A: encoding protein Unc-93 homolog A (C. elegans)
  • VNN1: vanin 1 (6q23.2)
  • VNN2: vanin 2 (6q23.2)
  • VTA1: Vesicle trafficking 1 (6q24.1-2)
  • ZC2HC1: encoding protein Zinc finger C2HC-type containing 1B
  • ZDHHC14: encoding protein Zinc finger, DHHC-type containing 14

Diseases and disorders

The following diseases are some of those related to genes on chromosome 6:

Cytogenetic band
G-banding ideograms of human chromosome 6
G-banding ideogram of human chromosome 6 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 6 in three different resolutions (400,[15] 550[16] and 850[3]). 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 6 in resolution 850 bphs[19]
Chr. Arm[20] Band[21] ISCN
start[22]		 ISCN
stop[22]		 Basepair
start		 Basepair
stop		 Stain[23] Density
6p 25.3011812,300,000 gneg
6p 25.21182072,300,0014,200,000 gpos25
6p 25.12073554,200,0017,100,000 gneg
6p 24.33555487,100,00110,600,000 gpos50
6p 24.254859210,600,00111,600,000 gneg
6p 24.159274011,600,00113,400,000 gpos25
6p 2374084413,400,00115,200,000 gneg
6p 22.3844118515,200,00125,200,000 gpos75
6p 22.21185134825,200,00127,100,000 gneg
6p 22.11348158527,100,00130,500,000 gpos50
6p 21.331585171830,500,00132,100,000 gneg
6p 21.321718183632,100,00133,500,000 gpos25
6p 21.311836216233,500,00136,600,000 gneg
6p 21.22162231036,600,00140,500,000 gpos25
6p 21.12310275540,500,00146,200,000 gneg
6p 12.32755308046,200,00151,800,000 gpos100
6p 12.23080314051,800,00153,000,000 gneg
6p 12.1314033775,300,000157,200,000 gpos100
6p 11.23377342157,200,00158,500,000 gneg
6p 11.13421355458,500,00159,800,000 acen
6q 11.13554365859,800,00162,600,000 acen
6q 11.23658373262,600,00162,700,000 gneg
6q 123732414762,700,00169,200,000 gpos100
6q 134147432469,200,00175,200,000 gneg
6q 14.14324462175,200,00183,200,000 gpos50
6q 14.24621470983,200,00184,200,000 gneg
6q 14.34709491784,200,00187,300,000 gpos50
6q 154917522887,300,00192,500,000 gneg
6q 16.15228561392,500,00198,900,000 gpos100
6q 16.25613568798,900,001100,000,000 gneg
6q 16.35687598310,000,0001105,000,000 gpos100
6q 215983653110,500,0001114,200,000 gneg
6q 22.165316753114,200,001117,900,000 gpos75
6q 22.267536872117,900,001118,100,000 gneg
6q 22.3168727168118,100,001125,800,000 gpos100
6q 22.3271687345125,800,001126,800,000 gneg
6q 22.3373457642126,800,001130,000,000 gpos75
6q 23.17642792313,000,0001130,900,000 gneg
6q 23.279238145130,900,001134,700,000 gpos50
6q 23.381458352134,700,001138,300,000 gneg
6q 24.183528560138,300,001142,200,000 gpos75
6q 24.285608708142,200,001145,100,000 gneg
6q 24.387088886145,100,001148,500,000 gpos75
6q 25.188869078148,500,001152,100,000 gneg
6q 25.290789241152,100,001155,200,000 gpos50
6q 25.392419596155,200,001160,600,000 gneg
6q 2695969774160,600,001164,100,000 gpos50
6q 27977410100164,100,001170,805,979 gneg

References
  1. "Search results - 6[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.
  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. Altemose, Nicolas; Logsdon, Glennis A.; Bzikadze, Andrey V.; Sidhwani, Pragya; Langley, Sasha A.; Caldas, Gina V.; Hoyt, Savannah J.; Uralsky, Lev; Ryabov, Fedor D.; Shew, Colin J.; Sauria, Michael E. G.; Borchers, Matthew; Gershman, Ariel; Mikheenko, Alla; Shepelev, Valery A. (April 2022). "Complete genomic and epigenetic maps of human centromeres". Science. 376 (6588): eabl4178. doi:10.1126/science.abl4178. ISSN 0036-8075. PMC 9233505. PMID 35357911.
  5. Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, et al. (October 2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805–11. Bibcode:2003Natur.425..805M. doi:10.1038/nature02055. PMID 14574404.
  6. 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.
  7. "Statistics & Downloads for chromosome 6". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19.
  8. "Chromosome 6: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19.
  9. "Human chromosome 6: entries, gene names and cross-references to MIM". UniProt. 2018-02-28. Retrieved 2018-03-16.
  10. "Search results - 6[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 - 6[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 - 6[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20.
  13. Matsuda LA, Lolait SJ, Brownstein MJ, Young AC, Bonner TI (August 1990). "Structure of a cannabinoid receptor and functional expression of the cloned cDNA". Nature. 346 (6284): 561–4. Bibcode:1990Natur.346..561M. doi:10.1038/346561a0. PMID 2165569. S2CID 4356509.
  14. "T brachyury transcription factor". T - T brachyury transcription factor - Genetics Home Reference.
  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". 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.
  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.
Notes

Further reading
Wikimedia Commons has media related to Human chromosome 6.
  • National Institutes of Health. "Chromosome 6". Genetics Home Reference. Archived from the original on 2007-08-12. Retrieved 2017-05-06.
  • "Chromosome 6". Human Genome Project Information Archive 1990–2003. Retrieved 2017-05-06.
  • "Chromosome 6 Research Project". Parent-driven research for genotype-phenotype studies on chromosome 6 disorders. Retrieved 2017-06-17
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