Chromosome 4

Genomics

The chromosome is ~193 megabases in length. In a 2012 paper, 775 protein-encoding genes were identified on this chromosome. 211 (27.9%) of these coding sequences did not have any experimental evidence at the protein level, in 2012. 271 appear to be membrane proteins. 54 have been classified as cancer-associated proteins.

Genes

Number of genes

The following are some of the gene count estimates of human chromosome 4. 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.

Gene list

The following is a partial list of genes on human chromosome 4. For complete list, see the link in the infobox on the right.

• AASDH: aminoadipate-semialdehyde dehydrogenase
• ACVR1: activin-like kinase 2 (ALK-2)
• ACOX3: encoding enzyme Peroxisomal acyl-coenzyme A oxidase 3
• AFAP1-AS1: encoding protein AFAP1 antisense RNA 1
• AGA: AGU syndrome (Finnish heritage disease) related gene
• AGPAT9: encoding enzyme Glycerol-3-phosphate acyltransferase 3 a.k.a. 1-acylglycerol-3-phosphate O-acyltransferase 9
• ANK2: ankyrin 2, neuronal
• APBB2: encoding protein Amyloid beta A4 precursor protein-binding family B member 2
• ART3: encoding enzyme Ecto-ADP-ribosyltransferase 3
• ASAHL: encoding enzyme N-acylethanolamine-hydrolyzing acid amidase
• BANK1: encoding protein B cell scaffold protein with ankyrin repeats 1
• BEND4: encoding protein BEN domain containing 4
• CCDC109B: Coiled-coil domain containing 109B
• CLNK: encoding protein Cytokine dependent hematopoietic cell linker
• Complement Factor I: Complement Factor I
• COL25A1-DT: encoding protein Zinc finger, cchc domain containing 23
• CRMP1: Collapsin response mediator protein 1, a member of CRMP family
• CSN2: Beta-casein
• CXCL1: chemokine (C-X-C motif) ligand 1, scyb1
• CXCL2: chemokine (C-X-C motif) ligand 2, scyb2
• CXCL3: chemokine (C-X-C motif) ligand 3, scyb3
• CXCL4: chemokine (C-X-C motif) ligand 4, Platelet factor-4, PF-4, scyb4
• CXCL5: chemokine (C-X-C motif) ligand 5, scyb5
• CXCL6: chemokine (C-X-C motif) ligand 6, scyb6
• CXCL7: chemokine (C-X-C motif) ligand 7, PPBP, scyb7
• CXCL8: chemokine (C-X-C motif) ligand 8, interleukin 8 (IL-8), scyb8
• CXCL9: chemokine (C-X-C motif) ligand 9, scyb9
• CXCL10: chemokine (C-X-C motif) ligand 10, scyb10
• CXCL11: chemokine (C-X-C motif) ligand 11, scyb11
• CXCL13: chemokine (C-X-C motif) ligand 13, scyb13
• CYTL1: Cytokine-like 1
• DCUN1D4: Defective in cullin neddylation 1 domain containing 4
• DHX15: DEAH-box helicase 15
• DKK2: Dickkopf-related protein 2
• DMAC1: encoding protein Transmembrane protein 261
• DUX4: Thought to be inactive but 2010 research shows a key role in FSHD
• ELMOD2: Elmo domain-containing 2
• EMCN: Endomucin
• EVC: Ellis–Van Creveld syndrome
• EVC2: Ellis–Van Creveld syndrome 2 (limbin)
• Factor XI: Mutations cause Haemophilia C
• FAM114A1: Family with sequence similarity 114, member A1
• FAM149A: Family with sequence similarity 149, member A
• FAM193A: Family with sequence similarity 193, member A
• FAM198B: encoding protein Protein ENED
• FAM221B: Family with sequence similarity 221, member B
• FAM47E-STBD1: FAM47E-STBD1 readthrough
• FGF2: Fibroblast growth factor 2 (basic fibroblast growth factor)
• FGFR3: fibroblast growth factor receptor 3 (achondroplasia, thanatophoric dwarfism, bladder cancer)
• FGFRL1: fibroblast growth factor receptor-like 1
• FRG1: FSHD region gene 1
• FRYL: encoding protein FRY like transcription coactivator
• FSTL5: encoding protein Follistatin like 5
• GUF1: GUF1 homolog, GTPase
• HDL3: encoding Huntington-like neurodegenerative disorder 2 protein
• HELQ: encoding protein Helicase, POLQ-like
• HTT (Huntingtin): huntingtin protein (Huntington's disease)
• IGJ: linker protein for immunoglobulin alpha and mu polypeptides
• INTS12: Integrator complex subunit 12
• KDR: Kinase insert domain receptor (Vascular endothelial growth factor receptor 2)
• KIAA1530: UV stimulated scaffold protein A
• KIT: tyrosine-protein kinase KIT, CD117; mast/stem cell growth factor receptor (SCFR)
• LCORL: Ligand dependent nuclear receptor corepressor like
• LDB2: LIM domain-binding protein 2
• LGI2: Leucine-rich repeat LGI family member 2
• LOC100505912 encoding protein Uncharacterized LOC100505912
• LSM6: U6 snRNA-associated Sm-like protein
• LTO1P1: encoding protein Oral cancer overexpressed 1 pseudogene 1
• LYAR: Cell growth-regulating nucleolar protein
• MAB21L2: Mab-21-like 2
• Marcksl1: encoding protein MARCKS-like 1
• MAML3: Mastermind-like 3
• MFSD7: encoding protein Major facilitator superfamily domain containing 7
• MIR1269A: microRNA 1269a
• MIR95: non-coding RNA MicroRNA 95
• MLF1IP: Centromere protein U
• MMAA: methylmalonic aciduria (cobalamin deficiency) cblA type
• MTHFD2L: NAD-dependent methylenetetrahydrofolate dehydrogenase 2-like protein
• MYL5: Myosin light chain 5
• NAP1L5: encoding protein Nucleosome assembly protein 1 like 5
• NDNF: encoding protein Neuron derived neurotrophic factor
• NOA1: encoding protein Nitric oxide associated 1
• NPNT: encoding protein Nephronectin
• NUDT6: nudix hydrolase 6
• NUDT9: nudix hydrolase 9
• OTUD4: OTU domain-containing protein 4
• PABPC4L: encoding protein Poly(A) binding protein, cytoplasmic 4-like
• PARM1: Prostate androgen-regulated mucin-like protein 1
• PHOX2B: codes for a homeodomain transcription factor
• PI4K2B: Phosphatidylinositol 4-kinase type 2-beta
• PKD2: polycystic kidney disease 2 (autosomal dominant)
• PLAC8: encoding protein Placenta specific 8
• PLK4: Serine/threonine-protein kinase PLK4
• PPEF2: encoding protein Protein phosphatase with ef-hand domain 2
• PSAPL1: encoding protein Prosaposin-like 1 (gene/pseudogene)
• QDPR: quinoid dihydropteridine reductase
• RBM47: RNA binding motif protein 47
• RG9MTD2: encoding protein RNA (guanine-9-) methyltransferase domain containing 2
• SCRG1: encoding protein Stimulator of chondrogenesis 1
• SDAD1: protein SDA1 homolog
• SEC24B: Sec24 homolog B
• SEC24D: Sec24 homolog D
• SEPT11: Septin-11
• SLC9B2: solute carrier family 9 member B2
• SLC10A4: solute carrier family 10 member 4
• SMIM20: encoding protein Small integral membrane protein 20
• SNCA: synuclein, alpha (non A4 component of amyloid precursor)
• SPATA5: Spermatogenesis-associated protein 5
• STATH: gene with protein product
• TACC3: Transforming acidic coiled-coil-containing protein 3
• TENM3: Teneurin transmembrane protein 3
• THAP6: THAP domain-containing protein 6
• TMEM155: encoding protein Transmembrane protein 155
• TMEM165: encoding protein Transmembrane protein 165
• TMEM175: encoding protein Transmembrane protein 175
• TMEM243: encoding protein Transmembrane protein 243
• TMPRSS11D: Transmembrane protease, serine 11D
• TMPRSS11F: encoding protein Transmembrane serine protease 11F
• TNIP2: TNFAIP3-interaction protein 2
• TNIP3: encoding protein TNFAIP3 interacting protein 3
• UCHL1: ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)
• UGDH-AS1: encoding protein UGDH antisense RNA 1
• UGT8: UDP glycosyltransferase 8
• UNC5C: netrin receptor UNC5C
• UPF0602: encoding UPF0602 Protein C4orf47
• USP38: encoding protein Ubiquitin specific peptidase 38
• USP53: ubiquitin specific peptidase 53
• UTP3: small subunit processome component
• VPS54
• WFS1: Wolfram syndrome 1 (wolframin)
• ZGRF1: zinc-finger GRF-type containing 1
• ZNF621: encoding protein Zinc finger protein 621

Diseases and disorders

The following are some of the diseases related to genes located on chromosome 4:

• Achondroplasia
• Autosomal dominant polycystic kidney disease (PKD-2)
• Bladder cancer
• Crouzonodermoskeletal syndrome
• Chronic lymphocytic leukemia
• Congenital central hypoventilation syndrome
• Ellis–Van Creveld syndrome
• Facioscapulohumeral muscular dystrophy
• Fibrodysplasia ossificans progressiva (FOP)
• Haemophilia C
• Huntington's disease
• Hemolytic uremic syndrome
• Hereditary benign intraepithelial dyskeratosis
• Hirschprung's disease
• Hypochondroplasia
• Mast cell activation syndrome
• Methylmalonic acidemia
• Mucopolysaccharidosis type I
• Muenke syndrome
• Nonsyndromic deafness
• Nonsyndromic deafness, autosomal dominant
• Parkinson's disease
• Polycystic kidney disease
• Romano–Ward syndrome
• SADDAN
• Tetrahydrobiopterin deficiency
• Thanatophoric dysplasia
  • Type 1
  • Type 2
• Wolfram syndrome
• Wolf–Hirschhorn syndrome

Cytogenetic band

References

References

1. (2 April 2010). "Human Molecular Genetics". Garland Science.
2. Genome Decoration Page, NCBI. [https://ftp.ncbi.nlm.nih.gov/pub/gdp/ideogram_9606_GCF_000001305.14_850_V1 Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3)]. Last update 2014-06-03. Retrieved 2017-04-26.
3. Chen LC, Liu MY, Hsiao YC, Choong WK, Wu HY, Hsu WL, Liao PC, Sung TY, Tsai SF, Yu JS, Chen YJ (2012) Decoding the disease-associated proteins encoded in the human chromosome 4. J Proteome Res
4. Pertea M, Salzberg SL. (2010). "Between a chicken and a grape: estimating the number of human genes.". Genome Biol.
5. (2016-09-08). "Search results - 4[CHR] AND "Homo sapiens"[Organism] AND ("has ccds"[Properties] AND alive[prop]) - Gene".
6. (2017-05-12). "Statistics & Downloads for chromosome 4".
7. (2017-03-29). "Chromosome 4: Chromosome summary - Homo sapiens".
8. (2018-02-28). "Human chromosome 4: entries, gene names and cross-references to MIM".
9. (2017-05-19). "Search results - 4[CHR] AND "Homo sapiens"[Organism] AND ("genetype protein coding"[Properties] AND alive[prop]) - Gene".
10. (2017-05-19). "Search results - 4[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".
11. (2017-05-19). "Search results - 4[CHR] AND "Homo sapiens"[Organism] AND ("genetype pseudo"[Properties] AND alive[prop]) - Gene".
12. (September 2010). "A unifying genetic model for facioscapulohumeral muscular dystrophy". Science.
13. Genome Decoration Page, NCBI. [https://ftp.ncbi.nlm.nih.gov/pub/gdp/ideogram_9606_GCF_000001305.14_400_V1 Ideogram data for Homo sapience (400 bphs, Assembly GRCh38.p3)]. Last update 2014-03-04. Retrieved 2017-04-26.
14. Genome Decoration Page, NCBI. [https://ftp.ncbi.nlm.nih.gov/pub/gdp/ideogram_9606_GCF_000001305.14_550_V1 Ideogram data for Homo sapience (550 bphs, Assembly GRCh38.p3)]. Last update 2015-08-11. Retrieved 2017-04-26.
15. International Standing Committee on Human Cytogenetic Nomenclature. (2013). "ISCN 2013: An International System for Human Cytogenetic Nomenclature (2013)". Karger Medical and Scientific Publishers.
16. (2012). "2012 Ninth International Conference on Computer Science and Software Engineering (JCSSE)".
17. Genome Decoration Page, NCBI. [https://ftp.ncbi.nlm.nih.gov/pub/gdp/ideogram_9606_GCF_000001305.14_850_V1 Ideogram data for Homo sapience (850 bphs, Assembly GRCh38.p3)]. Last update 2014-06-03. Retrieved 2017-04-26.
18. "'''p'''": Short arm; "'''q'''": Long arm.
19. For cytogenetic banding nomenclature, see article [[Locus (genetics). 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 [[GC-content. AT-rich]] and gene poor; '''gneg''': Region which is negatively stained by G banding, generally [[GC-content. CG-rich]] and gene rich; '''acen''' [[Centromere]]. '''var''': Variable region; '''stalk''': Stalk.