Spring newsletter 2022

HGNC, VGNC, Newsletters  · 

Farewell to Beth

After 9 years of working with us, we have had to say goodbye to Beth Yates, our first developer for the VGNC project. We would like to thank Beth for all of her hard work in setting up the VGNC website, vertebrate.genenames.org, as well as the internal database and curator tools for the VGNC project. We wish Beth all the best for her future.

And welcome to Shradha

We would like to introduce a new member of our team: Shradha Mukherjee, who has joined us as a new full stack developer. Shradha is currently working remotely from Kolkata and we look forward to her joining us in the office later this year.

Look out for our survey

We are planning to have a survey on our website in the coming months and we welcome any suggestions for possible questions or improvements.

Update on genes with the ‘stable’ tag

We now have 2871 gene symbols tagged as ‘stable’ as of May 11th 2022, which is an increase of 50 genes since our Winter newsletter. Examples of genes within the new stable set include a number of clinically relevant zinc finger genes: ZDHHC5, ZDHHC15, ZMYM3, ZMYM5, ZMYND8, ZMYND10, ZMYND11 and ZMYND15.

We also added the stable tag to ANKLE2, a recessive mutation of which causes a form of microcephaly and ANKLE1 which is not listed in current sets of clinically relevant genes but was reviewed at the same time as ANKLE2, due to its shared root symbol.

We also added the stable tag to the most highly published lncRNA genes: H19, HOTAIR, MALAT1, MEG3, NEAT1, PCA3, PVT1, and XIST.

Updates to placeholder symbols

This quarter we have been able to update two C#orf symbols and a KIAA# symbol:

Gene Symbols in the News

This section brings many hopeful stories of links between gene variants and specific conditions, which may help with future treatments.

First, a gene variant and a causative toxic agent have been found which are thought to have caused “Gulf War Syndrome” in combination - the toxic agent is sarin gas, which soldiers were exposed to at sublethal levels, and the variant is of the PON1 gene, which affects the ability of the body to break down toxic chemicals. This finding will hopefully lead to adequate care being offered for those suffering from the condition, the existence of which has previously been controversial.

A mutation in the TLR7 gene has been shown to cause a form of lupus, and engineering this variant into mice causes the creatures to develop lupus-like symptoms. Although this gene is not causative for the majority of lupus cases, many lupus patients show an overactive TLR7 pathway, so this may be a target for wider future therapies for the autoimmune disease.

There is hope that niacin may be used to help treat patients with Alzheimer disease in the future. Studies in mouse models demonstrate that the vitamin activates the HCAR2 receptor in microglia, reducing the formation of plaques and neuronal pathology in the mouse brains.

There is hope that the association of two different variants of the GDF15 gene with hyperemesis gravidarum, an extreme form of sickness during pregnancy, may lead to quicker diagnoses and possible treatments in the future.

There is at least a possible silver lining for women who suffer from endometriosis, polycystic ovary syndrome (PCOS) and preeclampsia linked to the expression of a common IGF1R gene variant - a study has shown that this variant may also protect them from heart disease.

Finally, we like to end this section with news for a gene from one of our VGNC species whenever possible. This time, we bring news of the successful gene therapy treatment of dogs with congenital stationary night blindness - a single injection of LRIT3 gene therapy results in expression of the correct LRIT3 protein in the dog retinas and the ability of the dogs to successfully complete a maze in dim light.

Meeting News

Elspeth attended the virtual NLM curation at scale workshop from March 28th-March 30th and the (still virtual) NC-IUPHAR symposium on 29th April.

Liora and Bryony attended the first ISB UK-local biocuration conference from 5th-6th May at the Wellcome Genome Campus in Hinxton where they enjoyed meeting curators from outside of the HGNC/VGNC project.

Liora and Susan are looking forward to attending the 25th Human Genome Meeting HGM 2022 in tel Aviv, Israel in June where Susan will be giving a talk on our gene symbol stabilisation work and Liora will be presenting a poster on the same subject.

Publications

DiStefano MT, Goehringer S, Babb L, Alkuraya FS, Amberger J, Amin M, Austin-Tse C, Balzotti M, Berg JS, Birney E, Bocchini C, Bruford EA, Coffey AJ, Collins H, Cunningham F, Daugherty LC, Einhorn Y, Firth HV, Fitzpatrick DR, Foulger RE, Goldstein J, Hamosh A, Hurles MR, Leigh SE, Leong IUS, Maddirevula S, Martin CL, McDonagh EM, Olry A, Puzriakova A, Radtke K, Ramos EM, Rath A, Riggs ER, Roberts AM, Rodwell C, Snow C, Stark Z, Tahiliani J, Tweedie S, Ware JS, Weller P, Williams E, Wright CF, Yates TM, Rehm HL. The Gene Curation Coalition: A global effort to harmonize gene-disease evidence resources. Genet Med. 2022 May 4:S1098-3600(22)00746-8. doi: 10.1016/j.gim.2022.04.017. PMID: 35507016

Shmerling M, Chalik M, Smorodinsky NI, Meeker A, Roy S, Sagi-Assif O, Meshel T, Danilevsky A, Shomron N, Levinger S, Nishry B, Baruchi D, Shargorodsky A, Ziv R, Sarusi-Portuguez A, Lahav M, Ehrlich M, Braschi B, Bruford E, Witz IP, Wreschner DH. LY6S, a New IFN-Inducible Human Member of the Ly6a Subfamily Expressed by Spleen Cells and Associated with Inflammation and Viral Resistance. Immunohorizons. 2022 Apr 19;6(4):253-272. doi: 10.4049/immunohorizons.2200018. PMID: 35440514