Winter newsletter 2023

HGNC, VGNC, Newsletters · 23 Feb 2023

HGNC is recognised as a Global Core Biodata Resource (GCBR)

We are delighted to announce that we have been included in the list of Global Core Biodata Resources (GCBRs) by the Global Biodata Coalition (GBC). This recognises us as a resource that is “crucial for sustaining the broader biodata infrastructure”. You can read more about how we were selected following our application and which other resources are on the list in our blog post on the subject.

Vertebrate gene naming debate

We hope that many of you have chance to read our recent Nature paper “The case for standardizing gene nomenclature in vertebrates”, (see the Publications section below for a full citation). This paper was written in response to the idea proposed in “Universal nomenclature for oxytocin–vasotocin ligand and receptor families” that a new Universal Vertebrate gene nomenclature group should be created that would revise vertebrate gene nomenclature based on data generated by the Vertebrate Genomes Project (VGP). Our paper explains that there is already a system of collaboration in place to achieve this aim between the HGNC, VGNC, Chicken Gene Nomenclature Committee (CGNC), Mouse Genome Nomenclature Committee (MGNC), Rat Genome Nomenclature Committee (RGNC), Xenopus Gene Nomenclature Committee (XGNC) and Zebrafish Nomenclature Committee (ZNC) groups and describes the factors involved when considering nomenclature changes, including the need for stability of clinically-relevant gene symbols in the era of genomic medicine. All of the established nomenclature committees have representatives as authors on the paper. Furthermore, we explain why we do not support the proposed changes to the nomenclature of the oxytocin and arginine vasopressin ligand and receptor gene families that were suggested in “Universal nomenclature for oxytocin–vasotocin ligand and receptor families”. We have also written an accompanying blog post . As explained at the end of the blog, we hope that the vertebrate gene nomenclature committees and the VGP can collaborate in the future to ensure that the VGP’s findings are reflected within the already well-established vertebrate gene naming systems.

Update on genes with the ‘stable’ tag

We now have 3114 approved gene symbols marked with our stable tag, an increase of 87 symbols since our previous newsletter. Within this batch of 87, no symbols had to be changed prior to stabilisation and only two gene names were changed - the names of CD8A and CD8B were updated from “CD8a molecule” and “CD8b molecule” to “CD8 subunit alpha” and “CD8 subunit beta” to reflect the common usage of referring to the expressed proteins as alpha and beta. The genes encode subunits that form active CD8 cell surface glycoproteins either as a heterodimer of CD8A (alpha) and CD8B (beta) subunits, or as a homodimer of two CD8A (alpha) subunits.

Updates to placeholder symbols

C20orf27 has been updated to ADISSP, adipose secreted signaling protein. This change was agreed pre-publication with the authors of a paper about the mouse ortholog. A brown fat-enriched adipokine Adissp controls adipose thermogenesis and glucose homeostasis PMID:36496438

C9orf64 has been updated to QNG1, Q-nucleotide N-glycosylase 1. This change was also agreed pre-publication with the authors of Structural basis of Qng1-mediated salvage of the micronutrient queuine from queuosine-5’-monophosphate as the biological substrate PMID:36610787.

C1orf112 has been updated to FIRRM, based on a discussion with several groups who have worked on the gene. Some of these groups had deposited pre-prints in bioRxiv and will now be able to use the new approved symbol in their final publications.

The three FAM205 (family with sequence similarity 205) paralogs have all been renamed as SPATA31F subfamily members, part of the larger SPATA31 family, based on sequence similarity and the presence of an IPR039509 domain which is found in all SPATA31-encoded proteins. SPATA31F1 and SPATA31F3 are currently annotated as protein coding, while SPATA31F2P is currently annotated as a pseudogene and therefore has a P at the end of its symbol.

Gene Symbols in the News

In gene therapy news, a little girl has become the first NHS patient to receive treatment to correct her ARSA gene, which will hopefully cure her completely from the devastating metachromatic leucodystrophy disease. Heartbreakingly, this disease has progressed too far in her older sister to allow treatment. This gene therapy has worked well for other children involved in clinical trials who now show no signs of the disease.

Gene therapy to provide middle-aged and older mice with a longevity-associated variant of the BPIFB4 gene resulted in a slower rate in the decline of heart function in middle-aged mice and helped reverse decline in elderly mice PMID:36635236. This variant had previously been identified as being enriched in humans that live extremely long lives (upwards of 95 years). There is hope that a treatment for cardiovascular disease involving the BPIFB4 protein may be developed in the future.

Researchers have found a variant in a non-coding part of the CYP24A1 gene that appears to be causative for infantile hypercalcemia-1 (HCINF1). Causative mutations in CYP24A1 coding exons had already been discovered but this newly identified variant is in the 3’UTR and affects folding of the mRNA. Mutations in CYP24A1 are the reason that fortification of food with vitamin D in the 1930s resulted in intoxication in some individuals.

Meeting News

Tamsin attended PAG30 (30th Plant & Animal Genome Conference) in San Diego, USA from January 12th-17th. She presented a poster entitled “Naming Vertebrate Orthologs of Human Unitary Pseudogenes” and took part in the EMBL-EBI workshop with a talk called “A Coordinated Nomenclature System for Vertebrate Genes: Updates from the Vertebrate Gene Nomenclature Committee”. In the previous newsletter, we referred to San Diego as “sunny” and we are sorry to say that this proved overly optimistic for January 2023! However, the conference was a great opportunity to catch up with collaborators after a few years of cancelled meetings!

Susan will be attending the 16th Annual Biocuration Conference in Padova, Italy in April. She looks forward to meeting as many other biocurators as possible including former colleagues!

Publications

Braschi B, Bruford EA, Cavanagh AT, Neuman SD, Bashirullah A. The bridge-like lipid transfer protein (BLTP) gene group: introducing new nomenclature based on structural homology indicating shared function. Hum Genomics. 2022 Dec 2;16(1):66. DOI: 10.1186/s40246-022-00439-3 PMID: 36461115 PMCID: [PMC9719229]

McCarthy FM, Jones TEM, Kwitek AE, Smith CL, Vize PD, Westerfield M & Bruford EA. The case for standardizing gene nomenclature in vertebrates. Nature 614, E31–E32 (2023). DOI: 10.1038/s41586-022-05633-w PMCID: PMC9931569 PMID: 36792746