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HGNC Newsletter Spring 2010

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There are currently 29060 approved symbols

In this newsletter:  we introduce the EB-eye tool,  three new gene family pages, two new locus types and a new quick and easy way to download Locus Specific Database data.

New gene family pages
We now have gene family pages for two separate protein phosphatase families: the protein phosphatase catalytic subunit (PPP) family, and the protein phosphatase, Mg2+/Mn2+ dependent (PPM) family.  Genes from both families encode proteins that dephosphorylate phosphoserine and phosphothreonine residues but, interestingly, the two families are not related by sequence.  The PPP genes encode catalytic subunits that are often bound by additional regulatory subunits, and are defined by conserved signature motifs within the catalytic phosphatase domain.  The PPM genes encode monomeric enzymes and are defined by a conserved catalytic domain with a dependence on magnesium or manganese ions for their dephosphorylating activity.  For a full description of both families, see “Phosphatase Families Dephosphorylating Serine and Threonine Residues in Proteins” by P.T.W. Cohen, Chapter 85 of the Handbook of Cell Signaling (Second Edition), ISBN: 978-0-12-374145-5.

We also have a new gene family page for the cadherin superfamily. Genes of this superfamily encode calcium-dependent transmembrane proteins and often mediate cell-cell adhesion. All members of the superfamily have at least two cadherin domains with conserved calcium-binding amino acid residues. The cadherin superfamily is subdivided into three defined families: the cadherin major family, the protocadherin family and the cadherin-related family.  The gene family page includes a link to full definitions of the three families, provided by our cadherin specialist advisors.

The EB-eye
The HGNC data has recently been included in the EBI's integrated site search tool, the EB-eye, which is available at the top of all EBI web pages.  HGNC results can be found in the "Genomes" section of the results table.


New RNA locus types
We have recently updated our locus types to include 'RNA, pseudogene' which comprises the 258 pseudogenes of non-protein coding RNA (ncRNA) genes we've named so far,  and 'RNA, cluster' which describes genomic regions containing clusters of ncRNAs, for example the 114 piwi-interacting RNA clusters (PIRCs) which contain clusters of piRNAs.

A link for all Locus Specific Database data
For users who are interested in downloading our complete list of Locus Specific Database links we have created a text file download facility for this dataset, which can be found here.

Gene symbols in the news
Standardisation of gene symbols by the HGNC is not only useful for researchers but also aids scientific communication via the international media.  Here is a selection of some approved symbols that have appeared in the news recently:
In March a possible association was reported between the GPC5 gene and lung cancer in non-smokers.
POLQ appeared in the news in April due to its promise as a cancer therapy target.
Also in April, a mutation of the PTPRQ gene was reported as accounting for some forms of inherited deafness.

Meeting News
Susan will be attending the 3rd Human Variome Project meeting from 10-14 May in Paris.  She will give a presentation entitled "A nomenclature for copy number variant genes?"
Elspeth and Ruth will be attending the 14th Human Genome Meeting from 18-21 May in Montpellier, France.  Ruth will be presenting a poster entitled “ABCA13: the story of a gene symbol”.  The HGNC will also be contactable at the HUGO Information Desk, located at the entrance of the Exhibition area on Level 0 of Le Corum. Please drop by if you have any queries about gene nomenclature.

Bruford E.A.Highlights of the 'gene nomenclature across species' meeting. Hum Genomics. 2010 Feb;4(3):213-7 PMID: 20368143

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