Autumn newsletter 2025

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Thanks to our SAB

We would like to thank the members of our Scientific Advisory Board for attending our annual meeting; this time the meeting was virtual but we are looking forward to an in person meeting here in Cambridge next year.

We were pleased to welcome two new board members: Emily Clark is a Genome Analysis Team Leader at the European Bioinformatics Institute (EMBL-EBI), UK who brings expertise in farm animal genomics. Pascale Gaudet is Senior Project Manager at the SwissProt project at the Swiss Institute of Bioinformatics, Switzerland and brings a protein-level perspective to our project.

We had a really productive meeting with useful input during discussions with the SAB. We would particularly like to thank our outgoing chair, Terence Murphy of the National Center for Biotechnology Information, for all of his work on our SAB since he took on the role in 2017.

Stable DOIs for HGNC and PGNC code

The HGNC has recently deposited our code onto the Zenodo open-access research data repository website in order to create permanent, citable DOIs for our available code. The following code for the HGNC project is available:

All PGNC external stack code is available at https://doi.org/10.5281/zenodo

We are pleased to support this effort to standardise the citation of code.

HGNC gene group news

In our previous newsletter we described our new collaboration with Elsevier/SciBite, which is funding Susan for one day a week to concentrate on expanding our gene group resource. This collaboration is off to a flying start with more than 55 new kinase gene groups already added, such as the CDC42 binding protein kinase family and Rho associated coiled-coil containing protein kinase family, which are both subgroups of the DMPK kinase family, which in turn is a subgroup of the pre-existing AGC family kinases group.

Over 40 non-kinase gene groups have also been added, such as the Epsin family and the hierarchical gene group Transaminases, which has the subgroups, Glutamic-oxaloacetic transaminase family, Branched chain amino acid transaminase family, Glutamine–fructose-6-phosphate transaminase family, and Glutamic–pyruvic transaminase family.

Update on genes with the ‘stable’ tag and placeholder symbols

We continue our aim of adding a stable tag to the gene reports of clinically relevant genes - our grand total of genes with this tag now stands at 3588. In the last quarter of 2025 we have added this tag to the following members of the ATPase family: ATP8B1, ATP8B2, ATP8B3, ATP8A1, ATP8A2, ATP8B4, ATP9A, ATP9B, ATP10A, ATP10B, ATP10D, ATP11C. No symbol changes were made to these genes and just two minor gene name updates were made to remove the term “putative” from the gene names of ATP9A and ATP9B as these two genes have recently been shown to encode active phospholipid transporting ATPases (PMID: 40876594 and PMID: 40234049. The following genes were stabilised with no changes to either symbol or gene name: C3, C4A, C4B, C7, DHDDS, NUS1, CCDC40, CCDC39.

Genes encoding coat protein complex I subunits were stabilised (COPA, COPB1, COPB2, COPG1, COPG2, COPZ1, COPZ2, ARCN1) with a slight change to each gene name for simplification with the term “COPI coat complex subunit” updated to “coat protein complex I”. For the stabilised PPFIA# and PPFIB# genes (PPFIA1, PPFIA2, PPFIA3, PPFIA4), the gene names were simplified to include either “PPFIA scaffold protein” or “PPFIB scaffold protein”.

The gene name of EYS was updated from “eyes shut homolog” to “EGF-like photoreceptor maintenance factor” to add functional information and to remove a term that could be viewed as offensive, especially considering that a variant of this gene in causative for the autosomal recessive retinitis pigmentosa phenotype. The gene name of MAX was updated from “MYC associated factor X” to “MYC associated transcriptional regulator X” to be more informative; likewise the gene name of CCDC8 was updated from “coiled-coil domain containing 8” to the more informative “coiled-coil domain containing 8 subunit of 3M complex”. No gene symbols were changed for any of the stabilised genes reported in this newsletter.

Placeholder symbols since June:

The gene symbol of HGNC:30204 was updated from the placeholder symbol C11orf54 to BKGD with the descriptive gene name “beta-keto-L-gulonate decarboxylase” based on the study “C11orf54 catalyzes L-xylulose formation in human metabolism” (PMID: 40737316).

The gene symbol of HGNC:29898 was updated from the placeholder symbol C15orf48 to COXFA4L3 for “cytochrome c oxidase associated subunit FA4L3”. This rename was done alongside HGNC:7687 (COXFA4, gene name “cytochrome c oxidase associated subunit FA4” which was renamed from NDUFA4, “NDUFA4 mitochondrial complex associated”) and HGNC:29836 (COXFA4L2, gene name “cytochrome c oxidase hypoxia associated subunit FA4L2” which was renamed from NDUFA4L2, NDUFA4 mitochondrial complex associated like 2). HGNC:7687 was originally named as NDUFA4 and considered to encode a mitochondrial complex I (NADH:ubiquinone oxidoreductase) subunit. Subsequent research over several years (e.g. PMID: 22902835, PMID: 23746447 and PMID: 30030519) showed that this gene does not encode a core complex I subunit but instead is part of complex IV, resulting in the published proposal of the COXFA4 symbol, although it took some time for the research community to fully endorse this rename. The COXFA4L2 and COXFA4L3 symbols had also already been published for the COXFA4 paralogs in a few papers (PMID: 32045714, PMID: 33671025, PMID: 39478730, and it was the publication of a paper this year (PMID: 41027500), which showed that like COXFA4L3 and COXFA4L2 can replace COXFA4 in the mitochondrial electron transport chain, which provided extra support for the nomenclature update of all three genes.

Gene Symbols in the News

We begin this section with news about genes that have been associated with geographical human adaptation. A variant of the MUC19 gene, believed to be inherited from Denisovans, has been identified in modern Latin Americans with indigenous ancestry and from indigenous archaeological sites across the Americas. A study on the Turkana people of northern Kenya found that overlapping regions near the STC1 gene, which is involved in the response of the kidneys to dehydration, may have enabled the Turkana to adapt to the dry desert conditions in which they live.

In disease-association news, two different classes of FOXA1 mutation have been associated with prostate cancer - class 1 mutations are associated with primary prostate cancer while class mutations are associated with resistance to hormone therapy in metastatic prostate cancer. A study of patients with chronic fatigue syndrome has found that variants in the T cell function associated BTN2A2 and chronic pain associated CA10 genes are more common in patients with the condition.

In sequencing news, regions of the human genome that were previously too difficult to sequence have been decoded; this includes the repetitive region containing the SMN1 and SMN2 genes and the neurodevelopment-associated NBPF8 gene.

A study of transcription factors found that two zinc finger genes are involved in cell cycle regulation. ZNF519, found only in primates, binds to the DNA of and represses key cell cycle genes while ZNF274, found across mammals, affects cell cycle expression and replication timing of specific chunks of the genome.

As is tradition, we end with a story about one of our VGNC species - this time, cat takes the stage and we are delighted to feature a photo of Bryony’s new cats, Ash (black) and Willow (torbie tabby), at the top of this newsletter. Variants of the feline AR gene have been associated with aggression and levels of vocalisation; the longer, less active variant is more common in pedigree cats and is associated with quieter, more docile behaviour while cats with the shorter variant are more likely to meow to be fed or let out and are more aggressive towards strangers.

Meeting News

Elspeth attended ISBT Milan 2025 where she took part in an educational session promoting use of standards in genomics.

Elspeth also recently attended ASHG 2025 from October 14th-18th in Boston, USA, where she presented a poster about HGNC gene groups.

Publications

Liu Y, He S, Pyo K, Zheng S, Chen M, Braschi B, Cheloufi S, Slavov N, Marzluff WF, Murn J. Composition and RNA binding specificity of metazoan RNase MRP. Nucleic Acids Res. 2025 Aug 27;53(16):gkaf829. DOI: 10.1093/nar/gkaf829. PMCID: PMC12390755. PMID: 40867056