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{{Short description|Committee for human gene name standards}} |
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|citation = Braschi et al. (2019)<ref name="pmid30304474">{{cite journal | vauthors = Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, Yates B, Bruford E | display-authors = 6 | title = Genenames.org: the HGNC and VGNC resources in 2019 | journal = Nucleic Acids Research | volume = 47 | issue = D1 | pages = D786–D792 | date = January 2019 | pmid = 30304474 | pmc = 6324057 | doi = 10.1093/nar/gky930 }}</ref> |
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|url = {{URL|www.genenames.org}}<br>{{URL|www.genenames.org/news}} |
|url = {{URL|www.genenames.org}}<br>{{URL|www.genenames.org/news}} |
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|download = {{URL|https://www.genenames.org/ |
|download = {{URL|https://www.genenames.org/download/statistics-and-files/|Statistics & Downloads}}<br />{{URL|https://www.genenames.org/download/custom/|Custom Downloads}}<br />{{URL|https://biomart.genenames.org/|HGNC Biomart}} |
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|webservice = {{URL|rest.genenames.org}} |
|webservice = {{URL|rest.genenames.org}} |
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|webapp = {{URL|www.genenames.org/ |
|webapp = {{URL|https://www.genenames.org/tools/hcop/|HGNC Comparison of Orthology Predictions}},<ref>{{cite journal | vauthors = Wright MW, Eyre TA, Lush MJ, Povey S, Bruford EA | title = HCOP: the HGNC comparison of orthology predictions search tool | journal = Mammalian Genome | volume = 16 | issue = 11 | pages = 827–8 | date = November 2005 | pmid = 16284797 | doi = 10.1007/s00335-005-0103-2 | s2cid = 1091618 }}</ref><ref>{{cite journal | vauthors = Eyre TA, Wright MW, Lush MJ, Bruford EA | title = HCOP: a searchable database of human orthology predictions | journal = Briefings in Bioinformatics | volume = 8 | issue = 1 | pages = 2–5 | date = January 2007 | pmid = 16951416 | doi = 10.1093/bib/bbl030 | doi-access = }}</ref> {{URL|https://www.genenames.org/tools/search/|Search}} |
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The '''HUGO Gene Nomenclature Committee''' ('''HGNC''') is a committee of the [[Human Genome Organisation]] (HUGO) that sets the [[standardization|standards]] for human [[gene nomenclature]]. The HGNC approves a ''unique'' and ''meaningful'' name for every known human [[gene]],<ref>https://www.genenames.org/about/overview</ref> based on a query of experts. In addition to the name, which is usually 1 to 10 words long, the HGNC also assigns a symbol (a short group of characters) to every gene. As with an [[International System of Units|SI]] symbol, a gene symbol is like an abbreviation but is more than that, being a second unique name that can stand on its own just as much as substitute for the longer name. It may not necessarily "stand for" the initials of the name, although many gene symbols do reflect that origin. |
The '''HUGO Gene Nomenclature Committee''' ('''HGNC''') is a committee of the [[Human Genome Organisation]] (HUGO) that sets the [[standardization|standards]] for human [[gene nomenclature]]. The HGNC approves a ''unique'' and ''meaningful'' name for every known human [[gene]],<ref>{{Cite web | url=https://www.genenames.org/about/overview | title=About the HGNC | HUGO Gene Nomenclature Committee | access-date=2018-03-23 | archive-date=2023-03-26 | archive-url=https://web.archive.org/web/20230326032945/https://www.genenames.org/about/overview | url-status=dead }}</ref><ref name="bruford">{{cite journal |last1=Bruford |first1=Elspeth A. |last2=Braschi |first2=Bryony |last3=Denny |first3=Paul |last4=Jones |first4=Tamsin E. M. |last5=Seal |first5=Ruth L. |last6=Tweedie |first6=Susan |title=Guidelines for human gene nomenclature |journal=Nature Genetics |date=August 2020 |volume=52 |issue=8 |pages=754–758 |doi=10.1038/s41588-020-0669-3|pmid=32747822 |pmc=7494048 }}</ref> based on a query of experts. In addition to the name, which is usually 1 to 10 words long, the HGNC also assigns a symbol (a short group of characters) to every gene. As with an [[International System of Units|SI]] symbol, a gene symbol is like an abbreviation but is more than that, being a second unique name that can stand on its own just as much as substitute for the longer name. It may not necessarily "stand for" the initials of the name, although many gene symbols do reflect that origin. |
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== Purpose == |
== Purpose == |
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Full gene names, and especially gene abbreviations and symbols, are often not specific to a single gene. A marked example is CAP which can refer to any of 6 different genes (''[https://www.genenames.org/data/hgnc_data.php?hgnc_id=13575 BRD4] {{Webarchive|url=https://web.archive.org/web/20131027084955/http://www.genenames.org/data/hgnc_data.php?hgnc_id=13575 |date=2013-10-27 }}'', ''[https://www.genenames.org/data/hgnc_data.php?hgnc_id=20040 CAP1] {{Webarchive|url=https://web.archive.org/web/20131102135041/http://www.genenames.org/data/hgnc_data.php?hgnc_id=20040 |date=2013-11-02 }}'', ''[https://www.genenames.org/data/hgnc_data.php?hgnc_id=9639 HACD1] {{Webarchive|url=https://web.archive.org/web/20131007140055/http://www.genenames.org/data/hgnc_data.php?hgnc_id=9639 |date=2013-10-07 }}'', ''[https://www.genenames.org/data/hgnc_data.php?hgnc_id=6656 LNPEP] {{Webarchive|url=https://web.archive.org/web/20120913231946/http://www.genenames.org/data/hgnc_data.php?hgnc_id=6656 |date=2012-09-13 }}'', ''[https://www.genenames.org/data/hgnc_data.php?hgnc_id=8950 SERPINB6] {{Webarchive|url=https://web.archive.org/web/20131008024537/http://www.genenames.org/data/hgnc_data.php?hgnc_id=8950 |date=2013-10-08 }}'', and ''[https://www.genenames.org/data/hgnc_data.php?hgnc_id=14565 SORBS1] {{Webarchive|url=https://web.archive.org/web/20121012033246/http://www.genenames.org/data/hgnc_data.php?hgnc_id=14565 |date=2012-10-12 }}''). |
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The HGNC short gene names, or gene symbols, unlike previously used or published symbols, are specifically assigned to one gene only. This can result in less common abbreviations being selected but reduces confusion as to which gene is referred to. |
The HGNC short gene names, or gene symbols, unlike previously used or published symbols, are specifically assigned to one gene only. This can result in less common abbreviations being selected but reduces confusion as to which gene is referred to. |
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== Naming guidelines == |
== Naming guidelines == |
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The HGNC published its latest human gene naming guidelines in 2020.<ref name="bruford" /> These may be summarized as:<ref name="guidelines">{{cite web |title=HGNC Guidelines {{!}} HUGO Gene Nomenclature Committee |url=https://www.genenames.org/about/guidelines/ |website=www.genenames.org |access-date=26 April 2021}}</ref> |
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The HGNC summarises its approach to naming genes and assigning ''symbols'' (gene name abbreviations) as follows: |
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# ''gene symbols must be unique'' |
# ''gene symbols must be unique'' |
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# symbols should only contain [[Latin letters]] and [[Arabic numerals]] |
# symbols should only contain [[Latin letters]] and [[Arabic numerals]] |
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# symbols should not contain [[punctuation]] or "G" for gene |
# symbols should not contain [[punctuation]] or "G" for gene |
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# symbols do not contain any reference to the [[species]] they are encoded in, i.e. "H/h" for human |
# symbols do not contain any reference to the [[species]] they are encoded in, i.e. "H/h" for human |
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The full description of HGNC's nomenclature guidelines can be found on their web site [https://www.genenames.org/guidelines.html]. HGNC advocates the appendices ''_v1, _v2,..'' to distinguish between different [[Alternative splicing|splice variants]] and ''_pr1, _pr2,..'' for [[Promoter (biology)|promoter]] variants of a single gene. |
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The HGNC states that "gene nomenclature should ''evolve with new technology'' rather than be restrictive, as sometimes occurs when historical and single gene nomenclature systems are applied."<ref>{{cite journal | vauthors = Shows TB, McAlpine PJ, Boucheix C, Collins FS, Conneally PM, Frézal J, Gershowitz H, Goodfellow PN, Hall JG, Issitt P, Jones CA, Knowles BB, Lewis M, McKusick VA, Meisler M, Morton NE, Rubenstein P, Schanfield MS, Schmickel RD, Skolnick MH, Spence MA, Sutherland GR, Traver M, Van Cong N, Willard HF | display-authors = 6 | title = Guidelines for human gene nomenclature. An international system for human gene nomenclature (ISGN, 1987) | journal = Cytogenetics and Cell Genetics | volume = 46 | issue = 1–4 | pages = 11–28 | year = 1987 | pmid = 3507270 | doi = 10.1159/000132471 | pmc = 7494048 }}</ref> The HGNC has also issued guides to specific locus types such as endogenous retroviral loci,<ref>{{cite journal | vauthors = Mayer J, Blomberg J, Seal RL | title = A revised nomenclature for transcribed human endogenous retroviral loci | journal = Mobile DNA | volume = 2 | issue = 1 | pages = 7 | date = May 2011 | pmid = 21542922 | pmc = 3113919 | doi = 10.1186/1759-8753-2-7 | doi-access = free }}</ref> structural variants<ref>{{cite journal | vauthors = Seal RL, Wright MW, Gray KA, Bruford EA | title = Vive la différence: naming structural variants in the human reference genome | journal = Human Genomics | volume = 7 | pages = 12 | date = May 2013 | issue = 1 | pmid = 23634723 | pmc = 3648363 | doi = 10.1186/1479-7364-7-12 | doi-access = free }}</ref> and non-coding RNAs.<ref>{{cite journal | vauthors = Wright MW, Bruford EA | title = Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature | journal = Human Genomics | volume = 5 | issue = 2 | pages = 90–8 | date = January 2011 | pmid = 21296742 | pmc = 3051107 | doi = 10.1186/1479-7364-5-2-90 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Wright MW | title = A short guide to long non-coding RNA gene nomenclature | journal = Human Genomics | volume = 8 | issue = 1 | pages = 7 | date = April 2014 | pmid = 24716852 | pmc = 4021045 | doi = 10.1186/1479-7364-8-7 | doi-access = free }}</ref><ref>{{cite journal | vauthors = Seal R, Chen L, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA | title = A guide to naming human non-coding RNA genes | journal = EMBO J | volume = 39 | date = Feb 2020 | issue = 6 | pages = e103777 | pmid = 32090359 | pmc = 7073466 | doi = 10.15252/embj.2019103777 }}</ref> |
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HGNC also states that "gene nomenclature should ''evolve with new technology'' rather than be restrictive as sometimes occurs when historical and single gene nomenclature systems are applied."<ref>{{cite journal|url=https://www.genenames.org/sites/genenames.org/files/documents/PMID3507270.pdf|pmid=3507270|year=1987|last1=Shows|first1=TB|last2=McAlpine|first2=PJ|last3=Boucheix|first3=C|last4=Collins|first4=FS|last5=Conneally|first5=PM|last6=Frézal|first6=J|last7=Gershowitz|first7=H|last8=Goodfellow|first8=PN|last9=Hall|first9=JG|last10=Issitt|first10=P|last11=Jones|first11=C. A.|last12=Knowles|first12=B. B.|last13=Lewis|first13=M|last14=McKusick|first14=V. A.|last15=Meisler|first15=M|last16=Morton|first16=N. E.|last17=Rubenstein|first17=P|last18=Schanfield|first18=M. S.|last19=Schmickel|first19=R. D.|last20=Skolnick|first20=M. H.|last21=Spence|first21=M. A.|last22=Sutherland|first22=G. R.|last23=Traver|first23=M|last24=Van Cong|first24=N|last25=Willard|first25=H. F.|title=Guidelines ''for human'' gene nomenclature. An international system ''for human'' gene nomenclature (ISGN, 1987)|volume=46|issue=1–4|pages=11–28|journal=Cytogenetics and Cell Genetics|display-authors=8|doi=10.1159/000132471}}</ref> |
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Comprehensive human gene naming guidelines were last published in 2002,<ref>{{cite journal|last=Wain|first=HM|author2=Bruford, EA |author3=Lovering, RC |author4=Lush, MJ |author5=Wright, MW |author6= Povey, S |title=Guidelines for human gene nomenclature.|journal=Genomics|date=Apr 2002|volume=79|issue=4|pages=464–70|pmid=11944974 |doi=10.1006/geno.2002.6748}}</ref> but the HGNC has subsequently issued guides to specific locus types such as endogenous retroviral loci,<ref>{{cite journal|last=Mayer|first=J|author2=Blomberg, J |author3=Seal, RL |title=A revised nomenclature for transcribed human endogenous retroviral loci.|journal=Mobile DNA|date=May 4, 2011|volume=2|issue=1|pages=7|pmid=21542922|doi=10.1186/1759-8753-2-7|pmc=3113919}}</ref> structural variants <ref>{{cite journal|last=Seal|first=RL|author2=Wright, MW |author3=Gray, KA |author4= Bruford, EA |title=Vive la différence: naming structural variants in the human reference genome.|journal=Human genomics|date=May 1, 2013|volume=7|pages=12|pmid=23634723 |doi=10.1186/1479-7364-7-12 |pmc=3648363}}</ref> and non-coding RNAs.<ref>{{cite journal|last=Wright|first=MW|author2=Bruford, EA|title=Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature.|journal=Human genomics|date=Jan 2011|volume=5|issue=2|pages=90–8|pmid=21296742|pmc=3051107|doi=10.1186/1479-7364-5-2-90}}</ref><ref>{{cite journal|last=Wright|first=MW|title=A short guide to long non-coding RNA gene nomenclature.|journal=Human genomics|date=Apr 9, 2014|volume=8|issue=1|pages=7|pmid=24716852|doi=10.1186/1479-7364-8-7|pmc=4021045}}</ref> |
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== Naming procedure == |
== Naming procedure == |
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== Revision == |
== Revision == |
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The gene name revision procedure is similar to the naming procedure, but changing a |
The gene name revision procedure is similar to the naming procedure, but changing a standardized gene name after establishment of a consensus can create confusion, therefore the merit of this is controversial. For this reason the HGNC aims to change a gene name only if agreement for that change can be reached among a majority of researchers working on that gene. |
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== See also == |
== See also == |
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{{col-begin}} |
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{{col-break}} |
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* [[Human Genome Organisation]] (HUGO) |
* [[Human Genome Organisation]] (HUGO) |
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* [[Human Genome Project]] |
* [[Human Genome Project]] |
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* [[Gene]] |
* [[Gene]] |
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* [[Gene nomenclature]] |
* [[Gene nomenclature]] |
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{{col-break}} |
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A complete list of all HGNC-approved gene symbols for protein-coding genes: |
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*[[List of human protein-coding genes 1]] |
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*[[List of human protein-coding genes 2]] |
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*[[List of human protein-coding genes 3]] |
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*[[List of human protein-coding genes 4]] |
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{{col-end}} |
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== References == |
== References == |
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== External links == |
== External links == |
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{{Wikidata property|P353}} |
{{Wikidata property|P353|P354}} |
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{{Wikidata property|P354}} |
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* [https://www.genenames.org/ HGNC homepage] |
* [https://www.genenames.org/ HGNC homepage] |
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* [http://www.hugo-international.org/ HUGO homepage] |
* [http://www.hugo-international.org/ HUGO homepage] |
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{{authority control}} |
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| ⚫ | |||
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[[Category:Human genes]] |
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[[Category:Biological nomenclature]] |
[[Category:Biological nomenclature]] |
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[[Category:Genetics in the United Kingdom]] |
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| ⚫ | |||
[[Category:Science and technology in Cambridgeshire]] |
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[[Category:South Cambridgeshire District]] |
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Latest revision as of 00:44, 5 July 2024
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| Content | |
|---|---|
| Description | HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, RNA genes and pseudogenes, to allow unambiguous scientific communication. |
| Data types captured | Gene nomenclature |
| Organisms | Human |
| Contact | |
| Research center | EMBL-EBI, UK; |
| Primary citation | Braschi et al. (2019)[1] |
| Access | |
| Website | www www |
| Download URL | Statistics & Downloads Custom Downloads HGNC Biomart |
| Web service URL | rest |
| Tools | |
| Web | HGNC Comparison of Orthology Predictions,[2][3] Search |
| Miscellaneous | |
| Curation policy | Yes |
The HUGO Gene Nomenclature Committee (HGNC) is a committee of the Human Genome Organisation (HUGO) that sets the standards for human gene nomenclature. The HGNC approves a unique and meaningful name for every known human gene,[4][5] based on a query of experts. In addition to the name, which is usually 1 to 10 words long, the HGNC also assigns a symbol (a short group of characters) to every gene. As with an SI symbol, a gene symbol is like an abbreviation but is more than that, being a second unique name that can stand on its own just as much as substitute for the longer name. It may not necessarily "stand for" the initials of the name, although many gene symbols do reflect that origin.
Purpose
[edit]Full gene names, and especially gene abbreviations and symbols, are often not specific to a single gene. A marked example is CAP which can refer to any of 6 different genes (BRD4 Archived 2013-10-27 at the Wayback Machine, CAP1 Archived 2013-11-02 at the Wayback Machine, HACD1 Archived 2013-10-07 at the Wayback Machine, LNPEP Archived 2012-09-13 at the Wayback Machine, SERPINB6 Archived 2013-10-08 at the Wayback Machine, and SORBS1 Archived 2012-10-12 at the Wayback Machine).
The HGNC short gene names, or gene symbols, unlike previously used or published symbols, are specifically assigned to one gene only. This can result in less common abbreviations being selected but reduces confusion as to which gene is referred to.
Naming guidelines
[edit]The HGNC published its latest human gene naming guidelines in 2020.[5] These may be summarized as:[6]
- gene symbols must be unique
- symbols should only contain Latin letters and Arabic numerals
- symbols should not contain punctuation or "G" for gene
- symbols do not contain any reference to the species they are encoded in, i.e. "H/h" for human
The HGNC states that "gene nomenclature should evolve with new technology rather than be restrictive, as sometimes occurs when historical and single gene nomenclature systems are applied."[7] The HGNC has also issued guides to specific locus types such as endogenous retroviral loci,[8] structural variants[9] and non-coding RNAs.[10][11][12]
Naming procedure
[edit]When assigning new gene nomenclature the HGNC make efforts to contact authors who have published on the human gene in question by email, and their responses to the proposed nomenclature are requested. HGNC also coordinates with the related Mouse and Rat Genomic Nomenclature Committees, other database curators, and experts for given specific gene families or sets of genes.
Revision
[edit]The gene name revision procedure is similar to the naming procedure, but changing a standardized gene name after establishment of a consensus can create confusion, therefore the merit of this is controversial. For this reason the HGNC aims to change a gene name only if agreement for that change can be reached among a majority of researchers working on that gene.
See also
[edit]|
A complete list of all HGNC-approved gene symbols for protein-coding genes:
|
References
[edit]- ^ Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, et al. (January 2019). "Genenames.org: the HGNC and VGNC resources in 2019". Nucleic Acids Research. 47 (D1): D786 – D792. doi:10.1093/nar/gky930. PMC 6324057. PMID 30304474.
- ^ Wright MW, Eyre TA, Lush MJ, Povey S, Bruford EA (November 2005). "HCOP: the HGNC comparison of orthology predictions search tool". Mammalian Genome. 16 (11): 827–8. doi:10.1007/s00335-005-0103-2. PMID 16284797. S2CID 1091618.
- ^ Eyre TA, Wright MW, Lush MJ, Bruford EA (January 2007). "HCOP: a searchable database of human orthology predictions". Briefings in Bioinformatics. 8 (1): 2–5. doi:10.1093/bib/bbl030. PMID 16951416.
- ^ "About the HGNC | HUGO Gene Nomenclature Committee". Archived from the original on 2023-03-26. Retrieved 2018-03-23.
- ^ a b Bruford, Elspeth A.; Braschi, Bryony; Denny, Paul; Jones, Tamsin E. M.; Seal, Ruth L.; Tweedie, Susan (August 2020). "Guidelines for human gene nomenclature". Nature Genetics. 52 (8): 754–758. doi:10.1038/s41588-020-0669-3. PMC 7494048. PMID 32747822.
- ^ "HGNC Guidelines | HUGO Gene Nomenclature Committee". www.genenames.org. Retrieved 26 April 2021.
- ^ Shows TB, McAlpine PJ, Boucheix C, Collins FS, Conneally PM, Frézal J, et al. (1987). "Guidelines for human gene nomenclature. An international system for human gene nomenclature (ISGN, 1987)". Cytogenetics and Cell Genetics. 46 (1–4): 11–28. doi:10.1159/000132471. PMC 7494048. PMID 3507270.
- ^ Mayer J, Blomberg J, Seal RL (May 2011). "A revised nomenclature for transcribed human endogenous retroviral loci". Mobile DNA. 2 (1): 7. doi:10.1186/1759-8753-2-7. PMC 3113919. PMID 21542922.
- ^ Seal RL, Wright MW, Gray KA, Bruford EA (May 2013). "Vive la différence: naming structural variants in the human reference genome". Human Genomics. 7 (1): 12. doi:10.1186/1479-7364-7-12. PMC 3648363. PMID 23634723.
- ^ Wright MW, Bruford EA (January 2011). "Naming 'junk': human non-protein coding RNA (ncRNA) gene nomenclature". Human Genomics. 5 (2): 90–8. doi:10.1186/1479-7364-5-2-90. PMC 3051107. PMID 21296742.
- ^ Wright MW (April 2014). "A short guide to long non-coding RNA gene nomenclature". Human Genomics. 8 (1): 7. doi:10.1186/1479-7364-8-7. PMC 4021045. PMID 24716852.
- ^ Seal R, Chen L, Griffiths-Jones S, Lowe TM, Mathews MB, O'Reilly D, Pierce AJ, Stadler PF, Ulitsky I, Wolin SL, Bruford EA (Feb 2020). "A guide to naming human non-coding RNA genes". EMBO J. 39 (6): e103777. doi:10.15252/embj.2019103777. PMC 7073466. PMID 32090359.
External links
[edit]
Wikidata has the properties:
HGNC gene symbol (P353) (see uses)- HGNC ID (P354) (see uses)