For those GEITP-ers interested in the continual advances in gene nomenclature — stripped and pasted below is the Human Gene Nomenclature Committee (HGNC; based in London) Newsletter for winter of 2020. Within the https://www.genenames.org/ web site, one can find the correct standardized gene names in the genomes for virtually all living organisms (at least, the ones that have been studied).
Winter newsletter 2020; 28 Feb 2020
Pig genes now in VGNC
We are pleased to announce that one of our first major achievements of 2020 is the addition of domestic pig genes to our VGNC resource! We had long been interested in adding pig due to its medical and economic relevance, but previous genome sequence versions had too many gaps and misplaced contigs to make this possible. Happily, a much improved pig reference genome is now available, and we have gone full steam ahead with naming pig genes. We have already approved gene nomenclature for 12,414 protein-coding pig genes and we will continue this effort throughout 2020!
New links to the Alliance of Genome Resources
We have now added links to the human gene pages within the Alliance of Genome Resources website from our Symbol Reports. This project aims “to develop and maintain sustainable genome information resources that facilitate the use of diverse model organisms in understanding the genetic and genomic basis of human biology, health and disease”. You can find the new link in the Gene Resources section of our Symbol Reports – as shown for the relevant part of the BRAF Symbol Report here: [view only online].
We are pleased that HGNC IDs are being used by the Alliance as the unique identifier in the URLs of their human gene pages. For example, the URL for BRAF is https://www.alliancegenome.org/gene/HGNC:1097. We have also added the cross-reference ID to our Custom downloads tool, the download files found on our Statistic and downloads, and to our REST API. When “fetching” a gene symbol report using our REST service, you will now see a field within the XML or JSON labelled “agr” with an HGNC ID as the value (see our REST help page). Use this ID within the URL template below: https://www.alliancegenome.org/gene/HGNC ID. We plan to add Alliance of Genome Resources cross reference IDs to our BioMart server in the near future.
Progress on replacing placeholder symbols
Renaming genes with placeholder symbols continues to be a priority for HGNC curators. Here are some examples of placeholder symbols that we have renamed in the last few months:
C16orf58 to RUSF1, RUS family member 1
C3orf67 to CFAP20DC, CFAP20-domain containing
FAM92A1 to CIBAR1, CBY1-interacting BAR domain containing 1
FAM92B to CIBAR2, CBY1-interacting BAR domain containing 2
New HGNC gene groups
We have curated several new gene groups for genenames.org within the past few months as part of our ongoing curation work. Highlights include:
Negative elongation factor complex members
Heterogeneous nuclear ribonucleoproteins
Glycosylphosphatidylinositol transamidase complex
CREB3 transcription factor family
The Sec7 family is the top level of a hierarchical structure of related gene groups. This group has the two genes FBXO8 and GBF1 listed at this top level, because they do not belong to any of the Sec7 subgroups. Genes within Sec7 subgroups can be viewed on the Sec7 page by selecting the arrow next to the text ‘Genes contained within subgroups’. You will then be able to view the following table:
(view only online).
It is also possible to view each subgroup on separate pages, as follows:
IQSEC ArfGEF family
Pleckstrin and Sec7 domain containing
Gene Symbols in the News
Gene therapy has been used to successfully prevent blindness in patients with RPE65 mutations both in the UK and in the United Arab Emirates. The therapy prevents a further deterioration of eyesight, so it cannot be used for patients that have already lost their sight.
The BAZ1B gene has been implicated in the development of the ‘finer facial features’ that modern adult human exhibit – compared to Neandertals and other great apes. According to this research, changes in the BAZ1B sequence in modern humans has resulted in a change in neural crest activity during embryogenesis which may explain the facial differences.
A mutation in the VHL gene has recently been associated with a limited ability to exercise, due in part to impaired mitochondrial function. 😊