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 genes	996 (CCDS)^[1]
Type	Autosome
Centromere position	Submetacentric^[2] (59.8 Mbp^[3])
Complete gene lists
CCDS	Gene list
HGNC	Gene list
UniProt	Gene list
NCBI	Gene list
External map viewers
Ensembl	Chromosome 6
Entrez	Chromosome 6
NCBI	Chromosome 6
UCSC	Chromosome 6
Full DNA sequences
RefSeq	NC_000006 (FASTA)
GenBank	CM000668 (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
CCDS	996	—	—	^[1]	2016-09-08
HGNC	1,007	422	736	^[7]	2017-05-12
Ensembl	1,038	985	800	^[8]	2017-03-29
UniProt	1,111	—	—	^[9]	2018-02-28
NCBI	1,053	1,188	911	^[10]^[11]^[12]	2017-05-19

Gene list

See also: Category:Genes on human chromosome 6

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)
• 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)
• 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)
• GMDS: GDP-mannose 4,6-dehydratase (6p25.3)
• 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)
• 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
• VEGF: vascular endothelial growth factor A (angiogenic growth factor) (6p21.1)
• VPS52: GARP complex subunit
• 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
• 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]
• 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)
• 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)
• 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:

• ankylosing spondylitis, HLA-B
• collagenopathy, types II and XI
• Coeliac disease HLA-DQA1 & DQB1
• Ehlers-Danlos syndrome, classical, hypermobility, and Tenascin-X types
• Hashimoto's thyroiditis
• hemochromatosis
• Hemochromatosis type 1
• 21-hydroxylase deficiency
• maple syrup urine disease
• methylmalonic acidemia
• Autosomal nonsyndromic deafness
• North Carolina macular dystrophy
• otospondylomegaepiphyseal dysplasia
• Parkinson disease
• polycystic kidney disease
• porphyria
• porphyria cutanea tarda
• Rheumatoid arthritis, HLA-DR
• CIRS (Chronic Inflammatory Response Syndrome ), Sick Building Syndrome, Mold Toxin Susceptibility / Poisoning, HLA-DR/DQ
• Spinocerebellar ataxia type 1, ATXN1
• Stickler syndrome, COL11A2
• Systemic lupus erythematosus
• Diabetes mellitus type 1, HLA-DR, DQA1 & DQB1
• X-linked sideroblastic anemia
• Epilepsy
• Guillain Barre Syndrome
• Chordoma
• Hepatocellular carcinoma
• Schizophrenia

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
6	p	25.3	0	118	1	2,300,000	gneg
6	p	25.2	118	207	2,300,001	4,200,000	gpos	25
6	p	25.1	207	355	4,200,001	7,100,000	gneg
6	p	24.3	355	548	7,100,001	10,600,000	gpos	50
6	p	24.2	548	592	10,600,001	11,600,000	gneg
6	p	24.1	592	740	11,600,001	13,400,000	gpos	25
6	p	23	740	844	13,400,001	15,200,000	gneg
6	p	22.3	844	1185	15,200,001	25,200,000	gpos	75
6	p	22.2	1185	1348	25,200,001	27,100,000	gneg
6	p	22.1	1348	1585	27,100,001	30,500,000	gpos	50
6	p	21.33	1585	1718	30,500,001	32,100,000	gneg
6	p	21.32	1718	1836	32,100,001	33,500,000	gpos	25
6	p	21.31	1836	2162	33,500,001	36,600,000	gneg
6	p	21.2	2162	2310	36,600,001	40,500,000	gpos	25
6	p	21.1	2310	2755	40,500,001	46,200,000	gneg
6	p	12.3	2755	3080	46,200,001	51,800,000	gpos	100
6	p	12.2	3080	3140	51,800,001	53,000,000	gneg
6	p	12.1	3140	3377	5,300,0001	57,200,000	gpos	100
6	p	11.2	3377	3421	57,200,001	58,500,000	gneg
6	p	11.1	3421	3554	58,500,001	59,800,000	acen
6	q	11.1	3554	3658	59,800,001	62,600,000	acen
6	q	11.2	3658	3732	62,600,001	62,700,000	gneg
6	q	12	3732	4147	62,700,001	69,200,000	gpos	100
6	q	13	4147	4324	69,200,001	75,200,000	gneg
6	q	14.1	4324	4621	75,200,001	83,200,000	gpos	50
6	q	14.2	4621	4709	83,200,001	84,200,000	gneg
6	q	14.3	4709	4917	84,200,001	87,300,000	gpos	50
6	q	15	4917	5228	87,300,001	92,500,000	gneg
6	q	16.1	5228	5613	92,500,001	98,900,000	gpos	100
6	q	16.2	5613	5687	98,900,001	100,000,000	gneg
6	q	16.3	5687	5983	10,000,0001	105,000,000	gpos	100
6	q	21	5983	6531	10,500,0001	114,200,000	gneg
6	q	22.1	6531	6753	114,200,001	117,900,000	gpos	75
6	q	22.2	6753	6872	117,900,001	118,100,000	gneg
6	q	22.31	6872	7168	118,100,001	125,800,000	gpos	100
6	q	22.32	7168	7345	125,800,001	126,800,000	gneg
6	q	22.33	7345	7642	126,800,001	130,000,000	gpos	75
6	q	23.1	7642	7923	13,000,0001	130,900,000	gneg
6	q	23.2	7923	8145	130,900,001	134,700,000	gpos	50
6	q	23.3	8145	8352	134,700,001	138,300,000	gneg
6	q	24.1	8352	8560	138,300,001	142,200,000	gpos	75
6	q	24.2	8560	8708	142,200,001	145,100,000	gneg
6	q	24.3	8708	8886	145,100,001	148,500,000	gpos	75
6	q	25.1	8886	9078	148,500,001	152,100,000	gneg
6	q	25.2	9078	9241	152,100,001	155,200,000	gpos	50
6	q	25.3	9241	9596	155,200,001	160,600,000	gneg
6	q	26	9596	9774	160,600,001	164,100,000	gpos	50
6	q	27	9774	10100	164,100,001	170,805,979	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

• Some text in this article was taken from http://ghr.nlm.nih.gov/chromosome=6 2007-08-12 at the Wayback Machine (public domain)

Further reading

• Gilbert F (2002). "Chromosome 6". Genet Test. 6 (4): 341–58. doi:10.1089/10906570260471912. PMID 12537662.

External links

 

Wikimedia Commons has media related to Human chromosome 6.

• National Institutes of Health. . 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