Chromosome 6 (human)

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Template:Infobox chromosome 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 170 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.

Genes

Template:Category see also 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.[1]

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.[2]

Estimated by Protein-coding genes Non-coding RNA genes Pseudogenes Source Release date
CCDS 996 - - [3] 2016-09-08
HGNC 1,007 422 736 [4] 2017-05-12
Ensembl 1,038 985 800 [5] 2017-03-29
NCBI 1,053 1,188 911 [6][7][8] 2017-05-19

Some genes requiring arm identification are:

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)
  • C6orf10: encoding protein Uncharacterized protein C6orf10 (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)
  • 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)
  • G6B: Protein G6b (6p21.33)
  • GCNT2: N-acetyllactosaminide beta-1,6-N-acetylglucosaminyl-transferase (6p24.3)
  • GMDS: GDP-mannose 4,6-dehydratase (6p25.3)
  • HCG4P11: HLA complex group 4 pseudogene 11
  • HFE: hemochromatosis (6p21.3)
  • 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)
  • HLA-DPA1 and HLA-DPB1 forms HLA-DR, MHC class II, DP (6p21.3)
  • HLA-Cw*06:02: gene variation related to psoriasis (6p21.3)
  • LST1: leukocyte specific transcript 1 (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)
  • RIPOR2: RHO family interacting cell polarization regulator 2 (6p22.3)
  • RPL10A: encoding protein 60S ribosomal protein L10a (6p21.31)
  • SASH1: SAM and SH3 domain containing 1 (6q24.3-q25.1)
  • 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)
  • TMEM151B: encoding protein Transmembrane protein 151B
  • TNXB: tenascin XB (6p21.3)
  • TRAM2: translocation associated membrane protein 2 (6p12.2)
  • UBR2: ubiquitin protein ligase E3 component n-recognin 2 (6p21.2)
  • UNC5CL: encoding protein Unc-5 homolog C (C. elegans)-like
  • VEGF: vascular endothelial growth factor A (angiogenic growth factor) (6p21.1)
  • VPS52: GARP complex subunit
  • 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)
  • C6orf58: chromosome 6 open reading frame 58 (6q22.33)
  • C6orf165: encoding protein DUF3508 (6q15)
  • CNR1: cannabinoid 1 receptor (6q14-q15)[9]
  • 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)
  • HACE1: HECT domain and Ankyrin repeat containing, E3 ubiquitin protein ligase 1 (6q21)
  • HEBP2: heme binding protein 2 (6q24.1)
  • IFNGR: interferon-γ receptor gene (6q23-q24)
  • IGF2R: insulin-like growth factor 2 receptor (6q25.3)
  • IMPG1: interphotoreceptor matrix proteoglylcan 1 (6q14.1)
  • 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
  • MDN1: midasin AAA ATPase 1 (6q15)
  • MOXD1: monooxygenase DBH like 1 (6q23.2)
  • MTO1: mitochondrial tRNA translation optimization 1 (6q13)
  • MTRF1L: mitochondrial translational release factor 1 like (6q25.2)
  • MYO6: myosin VI (6q14.1)
  • OPRM1: μ-opioid receptors (6q24-q25)
  • PLG: plasminogen (6q26)
  • 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)
  • 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)
  • SYNJ2: synaptojanin 2 (6q25.3)
  • T: T brachyury transcription factor (more commonly known as the T gene) linked to Hepatocellular carcinoma and Chordoma (6q27)[10]
  • 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:

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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,[11] 550[12] and 850[13]). Band length in this diagram is based on the ideograms from ISCN (2013).[14] This type of ideogram represents actual relative band length observed under a microscope at the different moments during the mitotic process.[15]
G-bands of human chromosome 6 in resolution 850 bphs[16]
Chr. Arm[17] Band[18] ISCN
start[19]
ISCN
stop[19]
Basepair
start
Basepair
stop
Stain[20] Density
6 p 25.3 0 118 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 25.2 118 207 Template:Val/delimitnum Template:Val/delimitnum gpos 25
6 p 25.1 207 355 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 24.3 355 548 Template:Val/delimitnum Template:Val/delimitnum gpos 50
6 p 24.2 548 592 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 24.1 592 740 Template:Val/delimitnum Template:Val/delimitnum gpos 25
6 p 23 740 844 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 22.3 844 1185 Template:Val/delimitnum Template:Val/delimitnum gpos 75
6 p 22.2 1185 1348 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 22.1 1348 1585 Template:Val/delimitnum Template:Val/delimitnum gpos 50
6 p 21.33 1585 1718 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 21.32 1718 1836 Template:Val/delimitnum Template:Val/delimitnum gpos 25
6 p 21.31 1836 2162 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 21.2 2162 2310 Template:Val/delimitnum Template:Val/delimitnum gpos 25
6 p 21.1 2310 2755 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 12.3 2755 3080 Template:Val/delimitnum Template:Val/delimitnum gpos 100
6 p 12.2 3080 3140 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 12.1 3140 3377 Template:Val/delimitnum1 Template:Val/delimitnum gpos 100
6 p 11.2 3377 3421 Template:Val/delimitnum Template:Val/delimitnum gneg
6 p 11.1 3421 3554 Template:Val/delimitnum Template:Val/delimitnum acen
6 q 11.1 3554 3658 Template:Val/delimitnum Template:Val/delimitnum acen
6 q 11.2 3658 3732 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 12 3732 4147 Template:Val/delimitnum Template:Val/delimitnum gpos 100
6 q 13 4147 4324 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 14.1 4324 4621 Template:Val/delimitnum Template:Val/delimitnum gpos 50
6 q 14.2 4621 4709 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 14.3 4709 4917 Template:Val/delimitnum Template:Val/delimitnum gpos 50
6 q 15 4917 5228 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 16.1 5228 5613 Template:Val/delimitnum Template:Val/delimitnum gpos 100
6 q 16.2 5613 5687 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 16.3 5687 5983 Template:Val/delimitnum1 Template:Val/delimitnum gpos 100
6 q 21 5983 6531 Template:Val/delimitnum1 Template:Val/delimitnum gneg
6 q 22.1 6531 6753 Template:Val/delimitnum Template:Val/delimitnum gpos 75
6 q 22.2 6753 6872 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 22.31 6872 7168 Template:Val/delimitnum Template:Val/delimitnum gpos 100
6 q 22.32 7168 7345 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 22.33 7345 7642 Template:Val/delimitnum Template:Val/delimitnum gpos 75
6 q 23.1 7642 7923 Template:Val/delimitnum1 Template:Val/delimitnum gneg
6 q 23.2 7923 8145 Template:Val/delimitnum Template:Val/delimitnum gpos 50
6 q 23.3 8145 8352 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 24.1 8352 8560 Template:Val/delimitnum Template:Val/delimitnum gpos 75
6 q 24.2 8560 8708 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 24.3 8708 8886 Template:Val/delimitnum Template:Val/delimitnum gpos 75
6 q 25.1 8886 9078 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 25.2 9078 9241 Template:Val/delimitnum Template:Val/delimitnum gpos 50
6 q 25.3 9241 9596 Template:Val/delimitnum Template:Val/delimitnum gneg
6 q 26 9596 9774 Template:Val/delimitnum Template:Val/delimitnum gpos 50
6 q 27 9774 10100 Template:Val/delimitnum Template:Val/delimitnum gneg

Research

The Chromosome 6 Research Project is a parent-driven research project for phenotype-genotype studies on chromosome 6 disorders.

Chromosomal anomalies, such as chromosome 6 deletions (too little chromosomal material) or duplications (too much chromosomal material), are a cause of significant congenital birth defects and developmental delays in children. There are many different chromosome 6 aberrations possible, each with different symptoms, and all of them are extremely rare. Because of the broad variety of chromosome 6 alterations, there is little information available for each specific aberration, leading to uncertainty for parents and doctors and sub-optimal treatment for children with these aberrations.

The Chromosome 6 Research Project compares the exact alterations in chromosome 6 (the genotype) with the effect they have on the appearance and other clinical features of affected individuals (the phenotype). Data about chromosome 6 deletions and duplications from patients from all over the world are being collected.

First results, further information and the possibility to sign up and participate in the Chromosome 6 Research Project is available on: www.chromosome6.org[21]

References

  1. Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL, Wilming L, Jones MC, Horton R, Hunt SE, Scott CE, Gilbert JG, Clamp ME, Bethel G, Milne S, Ainscough R, Almeida JP, Ambrose KD, Andrews TD, Ashwell RI, Babbage AK, Bagguley CL, Bailey J, Banerjee R, Barker DJ, Barlow KF, Bates K, Beare DM, Beasley H, Beasley O, Bird CP, Blakey S, Bray-Allen S, Brook J, Brown AJ, Brown JY, Burford DC, Burrill W, Burton J, Carder C, Carter NP, Chapman JC, Clark SY, Clark G, Clee CM, Clegg S, Cobley V, Collier RE, Collins JE, Colman LK, Corby NR, Coville GJ, Culley KM, Dhami P, Davies J, Dunn M, Earthrowl ME, Ellington AE, Evans KA, Faulkner L, Francis MD, Frankish A, Frankland J, French L, Garner P, Garnett J, Ghori MJ, Gilby LM, Gillson CJ, Glithero RJ, Grafham DV, Grant M, Gribble S, Griffiths C, Griffiths M, Hall R, Halls KS, Hammond S, Harley JL, Hart EA, Heath PD, Heathcott R, Holmes SJ, Howden PJ, Howe KL, Howell GR, Huckle E, Humphray SJ, Humphries MD, Hunt AR, Johnson CM, Joy AA, Kay M, Keenan SJ, Kimberley AM, King A, Laird GK, Langford C, Lawlor S, Leongamornlert DA, Leversha M, Lloyd CR, Lloyd DM, Loveland JE, Lovell J, Martin S, Mashreghi-Mohammadi M, Maslen GL, Matthews L, McCann OT, McLaren SJ, McLay K, McMurray A, Moore MJ, Mullikin JC, Niblett D, Nickerson T, Novik KL, Oliver K, Overton-Larty EK, Parker A, Patel R, Pearce AV, Peck AI, Phillimore B, Phillips S, Plumb RW, Porter KM, Ramsey Y, Ranby SA, Rice CM, Ross MT, Searle SM, Sehra HK, Sheridan E, Skuce CD, Smith S, Smith M, Spraggon L, Squares SL, Steward CA, Sycamore N, Tamlyn-Hall G, Tester J, Theaker AJ, Thomas DW, Thorpe A, Tracey A, Tromans A, Tubby B, Wall M, Wallis JM, West AP, White SS, Whitehead SL, Whittaker H, Wild A, Willey DJ, Wilmer TE, Wood JM, Wray PW, Wyatt JC, Young L, Younger RM, Bentley DR, Coulson A, Durbin R, Hubbard T, Sulston JE, Dunham I, Rogers J, Beck S; Palmer; Sims; Edwards; Ashurst; Wilming; Jones; Horton; Hunt; Scott; Gilbert; Clamp; Bethel; Milne; Ainscough; Almeida; Ambrose; Andrews; Ashwell; Babbage; Bagguley; Bailey; Banerjee; Barker; Barlow; Bates; Beare; Beasley; Beasley; et al. (October 2003). "The DNA sequence and analysis of human chromosome 6". Nature. 425 (6960): 805–11. PMID 14574404. doi:10.1038/nature02055. 
  2. Pertea M, Salzberg SL (2010). "Between a chicken and a grape: estimating the number of human genes.". Genome Biol. 11 (5): 206. PMC 2898077Freely accessible. PMID 20441615. doi:10.1186/gb-2010-11-5-206. 
  3. "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. 
  4. "Statistics & Downloads for chromosome 6". HUGO Gene Nomenclature Committee. 2017-05-12. Retrieved 2017-05-19. 
  5. "Chromosome 6: Chromosome summary - Homo sapiens". Ensembl Release 88. 2017-03-29. Retrieved 2017-05-19. 
  6. "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. 
  7. "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. 
  8. "Search results - 6[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene". NCBI. 2017-05-19. Retrieved 2017-05-20. 
  9. Matsuda LA, Lolait SJ, Brownstein MJ, Young AC, Bonner TI; Lolait; Brownstein; Young; Bonner (August 1990). "Structure of a cannabinoid receptor and functional expression of the cloned cDNA". Nature. 346 (6284): 561–4. Bibcode:1990Natur.346..561M. PMID 2165569. doi:10.1038/346561a0. 
  10. "T brachyury transcription factor". T - T brachyury transcription factor - Genetics Home Reference. 
  11. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3). Last update 2014-03-04. Retrieved 2017-04-26.
  12. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3). Last update 2015-08-11. Retrieved 2017-04-26.
  13. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  14. 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. 
  15. 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:10.1109/JCSSE.2012.6261965. 
  16. Genome Decoration Page, NCBI. Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3). Last update 2014-06-03. Retrieved 2017-04-26.
  17. "p": Short arm; "q": Long arm.
  18. For cytogenetic banding nomenclature, see article locus.
  19. 19.0 19.1 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.
  20. 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.
  21. "Chromosome 6 Project - Chromosome 6 Research Project". Chromosome 6 Research Project. Retrieved 2017-06-17. 
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External links

Template:Commons category

  • National Institutes of Health. "Chromosome 6". Genetics Home Reference. 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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