Covid SNP identified as doubling risk of lung failure and death from Covid-19


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Here is the study.

Nature Genetics: Identification of LZTFL1 as a candidate effector gene at a COVID-19 risk locus


The severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2) disease (COVID-19) pandemic has caused millions of deaths worldwide. Genome-wide association studies identified the 3p21.31 region as conferring a twofold increased risk of respiratory failure. Here, using a combined multiomics and machine learning approach, we identify the gain-of-function risk A allele of an SNP, rs17713054G>A, as a probable causative variant. We show with chromosome conformation capture and gene-expression analysis that the rs17713054-affected enhancer upregulates the interacting gene, leucine zipper transcription factor like 1 (LZTFL1). Selective spatial transcriptomic analysis of lung biopsies from patients with COVID-19 shows the presence of signals associated with epithelial–mesenchymal transition (EMT), a viral response pathway that is regulated by LZTFL1. We conclude that pulmonary epithelial cells undergoing EMT, rather than immune cells, are likely responsible for the 3p21.31-associated risk. Since the 3p21.31 effect is conferred by a gain-of-function, LZTFL1 may represent a therapeutic target.

The A variant of rs17713054 is found in about 60% of South Asians and 15% of European descent. It is rare among East Asians and Africans (both around 2%). It was already reported in other studies in 2020 (e.g. here) as a potential variant associated with respiratory traits in Covid patients.

Unfortunately that SNP does not seem to be tested by 23andMe, Living DNA, FTDNA, etc. It's not even in the data from my WGS!

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