GNC / VGNC Spring Newsletter

Some of you will be interested in the news and latest advances reported in this issue of the Human Gene Organization (HUGO) Gene Nomenclature Committee (HGNC) Spring Newsletter. 😊

Spring newsletter 2023

HGNC, VGNC, Newsletters · 23 May 2023

Update on genes with the ‘stable’ tag

We now have 3,126 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 busy these 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 metabolizing 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 (peristalsis) of the GI tract.

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

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