Spring newsletter 2023HGNC, VGNC, Newsletters ·
Farewell to Liora
We are sad to say that we had to say farewell to one of our curators, Liora, back in March but we are pleased that she has a new role within EMBL-EBI with the Gene Expression team. We would like to thank Liora for all of her work on stabilising HGNC gene symbols and we already miss her!
Visit from our CGNC (Chicken Gene Nomenclature Committee) colleague
We are delighted to report that we are currently enjoying a sabbatical visit from our chicken nomenclature colleague, Fiona McCarthy. Fiona is visiting us from Tucson, Arizona, for a month and this is providing an excellent opportunity to discuss complex nomenclature issues relating to bird genes. It is also lovely to have her input on HGNC and VGNC naming for a while!
Update on genes with the ‘stable’ tag
We now have 3126 approved gene symbols marked with our stable tag. Examples of genes that have recently been marked with the stable tag include: COMP (cartilage oligomeric matrix protein); CSF3R, (colony stimulating factor 3 receptor); MAT1A and MAT2A, (methionine adenosyltransferase 1A and 2A).
The three genes with the root symbol STAG# (STAG1, STAG2 and STAG3) have all been assigned the stable tag following an update to their gene names. The previous gene names were “stromal antigen 1, 2 and 3” based on the isolation of the first murine family member by an antibody raised against mouse stromal cell extracts (PMID: 9305759). As these names reflected the discovery of the initial family member and not the function of the encoded proteins, we updated the gene names to the more functionally informative “STAG1 cohesin complex component 1, 2 and 3”. The new names also better reflect how these genes and their encoded proteins are described in the literature; for example, “STAG1 stromal antigen” returns just 8 hits on PubMed, while “STAG1 cohesin complex” returns more than 50 hits.
Updates to placeholder symbols
It’s been a busy few months with respect to placeholder renaming. We have updated the nomenclature of a number of genes based on the identification of their encoded proteins as being associated with microtubules.
The following genes that previously had placeholder symbols have recently been shown to encode proteins that are found in the lumen of microtubules.
- C20orf85 -> CIMIP1, ciliary microtubule inner protein 1
- FAM166A -> CIMIP2A, ciliary microtubule inner protein 2A
- FAM166B -> CIMIP2B, ciliary microtubule inner protein 2B
- FAM166C -> CIMIP2C, ciliary microtubule inner protein 2C
Note that the genes GUCA1ANB and TEX33 were updated to CIMIP3 and CIMIP4 as part of adoption of the CIMIP# root symbol.
The following genes have recently been shown to encode proteins that are either found in the lumen of microtubules in sperm (and so share the root symbol SPMIP#), or on the outside of the doublet microtubules (and so share the root symbol SPMAP#) in sperm:
- C17orf98 -> SPMAP1, sperm microtubule associated protein 1
- C4orf45 -> SPMIP3, sperm associated microtubule inner protein 3
- C7orf31 -> SPMIP4, sperm microtubule inner protein 4
- C10orf82 -> SPMIP5, sperm microtubule inner protein 5
- C9orf24 -> SPMIP6, sperm microtubule inner protein 6
Note the following genes were also updated with these two roots:
- THEG -> (SPMAP2), sperm microtubule associated protein 2
- THEGL -> (SPMAP2L), sperm microtubule associated protein 2 like
- ATP6V1FNB -> (SPMIP1), sperm microtubule inner protein 1
- SPATA48 -> (SPMIP7), sperm microtubule inner protein 7
- TEPP -> (SPMIP8), sperm microtubule inner protein 8
- TEX37 -> (SPMIP9), sperm microtubule inner protein 9
- TEX43 -> (SPMIP10), sperm microtubule inner protein 10
- TEX49 -> (SPMIP11) sperm microtubule inner protein 11
We have also updated the following placeholder symbols based on information from publications and discussions with the scientific community:
- C1orf109 -> AIRIM, AFG2 interacting ribosome maturation factor
- C18orf25 -> ARK2N, arkadia (RNF111) N-terminal like PKA signaling regulator 2N
- C3orf14 -> CEP15, centrosomal protein 15
- C4orf47 -> CFAP96, cilia and flagella associated protein 96
- C1orf68 -> KPLCE, KPRP N-terminal and LCE C-terminal like protein
- C17orf97 -> LIAT1, ligand of ATE1
- C12orf29 -> RLIG1, RNA 5’-phosphate and 3’-OH ligase 1
New gene groups
We have recently reordered our solute carrier gene group into individual families - you can read more about this in our recent blog post: Solute Carriers.
Other new gene groups that we have added to our resource include: Teneurin transmembrane protein family; Protein kinase A subunits; YTH domain containing N6-methyladenosine readers; Thrombospondin family; NHERF family PDZ scaffold proteins; Tubulin gamma complex associated protein family and the Glycosylphosphatidylinositol-N-acetylglucosaminyltransferase complex
Gene Symbols in the News
One of the solute carriers has recently been in the news - a recent study provided mechanistic data to explain how a mutation in the SLC7A5 gene that causes a rare form of autism affects the brain. The study showed that the reduction in transport of large amino acids by the encoded SLC7A5 protein leads to neurons switching from metabolising lipids instead of amino acids and higher levels of neuronal cell death.
In dementia news, a variant of the RELN gene has been discovered which appears to offer protection from a form of early onset “autosomal dominant Alzheimer’s disease” (ADAD). The variant was discovered in an individual who did not show any signs of the disease until much later in life than is typical for ADAD sufferers. Cell work showed that the variant resulted in tighter binding between the RELN protein and its receptor, leading to stabilisation of the tau protein. In other dementia news, researchers used machine learning-based algorithms to analyse whole genome sequence data and found new associations between structural gene variants and non-Alzheimer disease; for example, they found a deletion variant of the TPCN1 gene in patients with Lewy body dementia - TPCN1 had previously been associated with Alzheimer disease but not Lewy body dementia.
In other gene variant news, a specific mutation of the BRCA1 gene has been discovered in individuals with ancestry from the Orkney island of Westray. This mutation may be found in as many as 1% of individuals with grandparents from Westray and NHS Scotland is currently offering screening to people on the island who have local grandparents and will consider widening this to all Scottish people with grandparents from Westray.
Recently, one of our long non-coding RNA (lncRNA) symbols has made it into the news: CARMN. This lncRNA gene was previously reported as being present in vascular smooth muscle and reduced in vascular disease. New work shows that CARMN is present in smooth muscle cells in other tissues, including esophagus, stomach and intestines and appears to have a role in the movement of the GI tract.
Elspeth attended the Spring NC-IUPHAR meeting in Paris on 20th and 21st April.
Susan went to the 16th Annual Biocuration Conference from 24th-26th April 24th in Padova, Italy where she presented a poster that discussed whether biomedical resources should label their data fields more consistently.
Tamsin will be attending the 19th World Congress of Basic & Clinical Pharmacology 2023 from 2nd-7th July 2023 where she will present our VGNC dog nomenclature, which is particularly relevant to the field of pharmacology.
Jones TEM, Yates B, Braschi B, Gray K, Tweedie S, Seal RL, Bruford EA. The VGNC: expanding standardized vertebrate gene nomenclature. Genome Biol. 2023 May 12;24(1):115. DOI: 10.1186/s13059-023-02957-2. PMID: 37173739; PMCID: PMC10176861