Autumn newsletter 2024
Newsletters ·
HGNC is funded for another 5 years!
We have had a testing time in the last year, as anyone who follows the HGNC will be aware and have been reliant on bridge funding. We are therefore delighted to announce that we have been awarded funding from the NHGRI that will enable us to continue naming genes for the next five years. We are also now fully settled in our new home on the Addenbrookes Biomedical Campus in Cambridge.
Changes to our download files
All HGNC download files, including the archive files, are now in a publicly accessible Google Storage Bucket. Downloads page links have been updated as a result.
VGNC and HCOP downloads are still currently hosted at the EBI as FTP files, but these will be moving across to the Google Storage Bucket in the future.
The beginning of the Plant Gene Nomenclature Committee (PGNC)
As of March this year, we have branched out from vertebrate gene naming into the wonderful world of plants - specifically that of the tree model organism Populus trichocarpa, also known as black cottonwood, western balsam-poplar or California poplar. This species has a fully sequenced genome, which is already on assembly version 4.1, and is an economically important source of timber. The new project is a collaboration between our group and Dr Stanton Martin and his team in The Centre for Bioenergy Innovation (CBI) at Oak Ridge National Laboratory, with Susan as lead curator.
Please do not inundate us with requests for naming genes in other new species - the big difference with this project was that it came with an offer of financial support! You can read more about it in our recent blog post; note we have now finished the initial period of consultation with the community and have begun entering symbols and names for poplar genes into our new internal plant database.
Update on genes with the ‘stable’ tag and placeholder symbols
We currently have 3520 gene symbols marked with the stable tag, an increase of 66 genes since our last newsletter.
Where possible, we keep the gene symbols of clinically relevant genes stable. We have changed just one gene symbol in 2024 as part of the stabilisation process - we updated the nomenclature of HGNC:1152 from BVES (blood vessel epicardial substance) to POPDC1 (popeye domain cAMP effector 1). The gene symbol POPDC1 was already in use for this gene and its approval is now consistent with the other gene family members, POPDC2 and POPDC3. Additionally, BVES was considered misleading because this gene was originally isolated from the heart but is not specifically expressed in blood vessels.
We have updated the gene names, without changing the gene symbols, for 25 genes that have been given the stable tag this year. These include genes with symbols beginning “SMARC”, whose names have been simplified to better reflect what is known about their current function. We updated the names of genes that previously contained the term “ADP ribosylation factor”, such as ARF3, to remove this term and add the functional information that these genes are GTPases, e.g., the gene name of ARF3 is now “ARF GTPase 3”. The original “ADP ribosylation factor” term referred to the effect of ARFs on a cholera toxin ADP-ribosyltransferase, so did not reflect the normal function of the proteins encoded by these genes.
We continue to reassign the nomenclature of genes with placeholder symbols whenever possible. We were able to rename three “placeholder” gene that previously had the approved symbols C2orf50, C2orf73 and C3orf84 as ciliary microtubule inner proteins with the symbols CIMIP5, CIMIP6, and CIMIP7 based on data from the publication “Uncovering structural themes across cilia microtubule inner proteins with implications for human cilia function”.
We renamed C6orf226 as PEX39, peroxisomal biogenesis factor 39 based on “Peroxisomes : novel findings and future directions”; C1orf131 as FSAF1, 40S small subunit processome assembly factor 1 based on “Nucleolar maturation of the human small subunit processome” ; C17orf49 as BACC1 BPTF associated chromatin complex component 1 based on a combination of a well-used alias that did not meet our guidelines (BAP18 - BPTF associated protein of 18 kDa) and data from recent papers. Additionally, we updated C5orf60 to SPATA31J1, SPATA31 subfamily J member 1 based on its membership within the SPATA31J family.
Gene Symbols in the News
New research has linked the gene UBAP1L to rare forms of inherited retinal disease found in a small number of individuals, most of whom were from regions of the world that have previously been underrepresented in genetic studies. Although the exact function of this gene is yet to be determined, analysis of the identified variants suggest that the phenotype is due to loss of UBAP1L gene function.
A young British girl who was born deaf due to auditory neuropathy caused by a variant of the OTOF gene has become the first in the world to be able to hear, following receiving gene therapy with a functional copy of the OTOF gene in one ear. Although some children with this condition can achieve hearing via a cochlear implant, the success of such implants can vary and implants need replacing over time, while gene therapy has the potential to provide a lifelong cure.
In further gene therapy news, a single dose of CRISPR-Cas9 therapy that targets the KLKB1 gene has been shown to effectively treat hereditary angiodema. In contrast to the OTOF case above, this therapy does not target the causative SERPING1 gene. Instead, by targeting the KLKB1 gene, the therapy reduces the production of prekallikrein and therefore inhibits the kallikrein-kinin cascade, a downstream effect of the disease.
Meeting News
Susan and Elspeth attended the IUFRO Tree Biotech 2024 meeting from August 4th-8th in Annapolis, Maryland, USA where they presented a poster entitled “Standardized Gene Naming in Populus trichocarpa”. They enjoyed meeting members of the tree genomics community.
Elspeth will attend ASHG 2024 in Denver, Colorado, USA from November 5th-9th where she will present a talk entitled “How should we name non-coding elements?” at the featured symposium “How do we describe and ascribe clinical significance to the non-coding genome?”.