Summer newsletter 2022

HGNC, VGNC, Newsletters  · 

Globus file transfer

The HGNC now provides a shared Globus endport for HGNC data. Globus is a non-profit service for secure, reliable research data management and transfer. Transferring files via Globus is quick and is not affected by network glitches that may corrupt the transferred file. All of our files on this page can be downloaded from Globus and this is the preferred method for file transfer if you want to download more than one file, as it is far quicker for the user. An additional benefit is that the files at the HGNC endport also contain download files from the VGNC website.

Please complete our survey

Thanks to all who have completed the HGNC/VGNC survey. If you haven’t already done so, we would really appreciate it if you did! This will be helpful to us as we are in the process of applying for renewal of funding. You can find a link to the survey from the homepage of either www.genenames.org or https://vertebrate.genenames.org/.

Update on genes with the ‘stable’ tag

We now have 2946 gene symbols tagged as ‘stable’ as of August 1st 2022, which is an increase of 75 genes since our Spring newsletter. Examples of genes that have recently had the tag added include BMP5, BMP7, CFAP221, CLDN11, CLRN2, DLX4 and PANX1; all of these genes still have the same symbol that they were first approved with!

Although our aim is to keep clinically relevant genes stable wherever possible, in a small proportion of cases we do make changes to symbols of these genes as part of the curational review process. An example of this is the RIGI gene, which was assigned the stable tag following its rename from DDX58, a process which involved an HGNC curator contacting over 100 researchers. The reason for the symbol change was i) the DDX symbol suggested that the encoded protein contained a DEAD-box but it actually contains a DEAH-box and ii) the alias “RIG-I” was used in the scientific literature far more than the approved symbol DDX58 (this in itself is not necessarily sufficient to trigger a symbol change, particularly if the well published alias is not suitable for approval). Hyphens are avoided where possible in HGNC gene symbols, so the new gene symbol has the format RIGI. The alias symbol RIG-I initially stood for “retinoic acid inducible gene I” which is functionally uninformative; after some discussion with interested researchers there was agreement for the gene name “RNA sensor RIG-I”.

Updates to placeholder symbols

In the last quarter we have been able to rename genes from all three of our major placeholder categories (FAM#, KIAA# and C#orf#).

The following genes previously named together as FAMs (family with sequence similarity members) have been renamed based on information from publications:

The following gene KIAA# genes were renamed with the BLTP root symbol:

The following C#orf# symbols were renamed, some of which were due to a change of locus type from protein-coding gene to long non-coding RNA:

Gene Symbols in the News

In this section, we have three news stories about genes being newly linked to specific conditions. In the first, the GRIA1 gene has been discovered as causative for a neurodevelopmental condition that has yet to be named, following discovery of variants of this gene in patients and the creation of Xenopus tadpole models for the disease. The FIBCD1 gene has been associated with a different newly discovered, ​​rare neurodevelopmental disorder. Although the two patients studied had different symptoms compared to one another, fruit fly and mouse knockout models showed neurological defects. Finally, loss-of-function variants of the FOCAD gene have been shown to cause a paediatric form of severe liver disease. The team found that hepatocyte homeostasis is disrupted when FOCAD is knocked out.

Meeting News

Liora and Susan attended the 25th Human Genome Meeting HGM 2022 in Tel Aviv, Israel in June where Susan gave a talk on our gene symbol stabilisation work and Liora presented a poster on the same subject.

Ruth will be attending Genome Informatics 2022 where she will present a poster based on the naming of histone genes across mammalian species.

Publications

Seal RL, Tweedie S, Bruford EA. A standardised nomenclature for long non-coding RNAs. IUBMB Life. 2022 Jul 26. DOI: 10.1002/iub.2663, PMID: 35880706

Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Standardized annotation of translated open reading frames. Nat Biotechnol. 2022 Jul 13. DOI: 10.1038/s41587-022-01369-0 PMID: 35831657

Bruford E, On Behalf Of The HUGO Gene Nomenclature Committee. Comment on Herring et al. The Use of “Retardation” in FRAXA, FMRP, FMR1 and Other Designations. Cells. 2022 Jun 16;11(12):1937. DOI: 10.3390/cells11121937 PMID: 35741066 PMCID: PMC9221639

Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Piližota I, Guijarro-Clarke C; OpenEBench team the Quest for Orthologs Consortium, Iwasaki W, Lecompte O, Sonnhammer E, Roos DS, Gabaldón T, Thybert D, Thomas PD, Hu Y, Emms DM, Bruford E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A. The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 2022 May 12:gkac330 DOI: 10.1093/nar/gkac330 PMID: 35552456