EFCAB4B (CRACR2A) genetic variants associated with COVID-19 fatality

  1. Dapeng Wang
  2. Sabina D Wiktor
  3. Chew W Cheng
  4. Katie J Simmons
  5. Ashley Money
  6. Lucia Pedicini
  7. Asya Carlton
  8. Alexander L Breeze
  9. Lynn McKeown

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Abstract

The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has resulted in more than 235 million cases worldwide and 4.8 million deaths (October 2021). Severe COVID-19 is characterised in part by vascular thrombosis and a cytokine storm due to increased plasma concentrations of factors secreted from endothelial and T-cells. Here, using patient data recorded in the UK Biobank, we demonstrate the importance of variations in Rab46 (CRACR2A) with clinical outcomes. Using logistic regression analysis, we determined that three single nucleotide polymorphisms (SNPs) in the gene EFCAB4B cause missense mutations in Rab46, which are associated with COVID-19 fatality independently of risk factors. All three SNPs cause changes in amino acid residues that are highly conserved across species, indicating their importance in protein structure and function. Two SNPs, rs17836273 (A98T) and rs36030417 (H212Q), cause amino acid substitutions in important functional domains: the EF-hand and coiled-coil domain respectively. By using molecular modelling, we suggest that the substitution of threonine at position 98 causes structural changes in the EF-hand calcium binding domain. Since Rab46 is a Rab GTPase that regulates both endothelial cell secretion and T-cell signalling, these missense variations may play a role in the molecular mechanisms underlying the thrombotic and inflammatory characteristics observed in patients with severe COVID-19 outcomes.

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    SciScore for 10.1101/2022.01.17.22269412: (What is this?)

    Please note, not all rigor criteria are appropriate for all manuscripts.

    Table 1: Rigor

    Ethicsnot detected.
    Sex as a biological variablenot detected.
    Randomizationnot detected.
    Blindingnot detected.
    Power Analysisnot detected.

    Table 2: Resources

    Software and Algorithms
    SentencesResources
    The genotype data were mainly handled with the PLINK 2.0 analytical framework [26].
    PLINK
    suggested: (PLINK, RRID:SCR_001757)
    Ensembl Variant Effect Predictor (VEP) was used to predict and annotate the effect and impact of the variant on the gene functions from the human genome (GRCh37).
    Ensembl Variant Effect Predictor
    suggested: None
    Variant
    suggested: (VARIANT, RRID:SCR_005194)
    Conservation of Rab46 protein sequence across different species: Rab46 sequence conservation diagram was generated using Basic Local Alignment Search Tool (BLAST; https://blast.ncbi.nlm.nih.gov/Blast.cgi) and WebLogo 3 (
    https://blast.ncbi.nlm.nih.gov/Blast.cgi
    suggested: (TBLASTX, RRID:SCR_011823)
    WebLogo
    suggested: (WEBLOGO, RRID:SCR_010236)
    Amino acid sequence of Rab46 (NP_001138430.1) was searched against protein sequence database in BLAST (BLASTP) and aligned with the identified 100 similar protein sequences (percent sequence identity > 80 %) from 66 different species using COBALT multiple alignment tool.
    BLAST
    suggested: (BLASTX, RRID:SCR_001653)
    BLASTP
    suggested: (BLASTP, RRID:SCR_001010)
    Rab46 structural analysis: The predicted AlphaFold [29, 30] structure of full-length human Rab46 (https://alphafold.ebi.ac.uk/entry/Q9BSW2) and the crystal structure of EF-hand domain (PDB: 6PSD) were pre-processed and energy-minimised using the Protein Preparation Wizard (Maestro software, Release 2020-1, Glide, Schrödinger, LLC, New York, NY, 2020).
    Maestro
    suggested: (Maestro, RRID:SCR_016748)
    Alignment of the wild type and mutant EF-hand domain structures was visualised using PyMOL (The PyMOL Molecular Graphics System, Version 2.0 Schrödinger, LLC.) and changes to the structure visualised using Pymol and the Maestro graphical user interface.
    PyMOL
    suggested: (PyMOL, RRID:SCR_000305)

    Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).

    Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:
    However, we also need to be aware of the limitations of the study because the reported data are from a relatively small sample size in an aged population prior to the rollout of a vaccination programme in the UK. In addition, we do not have a defined list of all the comorbidities that are associated with COVID-19 susceptibility. Here, we have also focussed on the variations that culminate in missense mutations, however, many of the intronic variations identified as being significantly associated with COVID-19 fatality could be of interest especially if they cause changes in expression levels or isoform splicing.

    Results from TrialIdentifier: No clinical trial numbers were referenced.

    Results from Barzooka: We did not find any issues relating to the usage of bar graphs.

    Results from JetFighter: We did not find any issues relating to colormaps.

    Results from rtransparent:
    • Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
    • Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
    • No protocol registration statement was detected.

    Results from scite Reference Check: We found no unreliable references.

    About SciScore

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  2. Version published to 10.1101/2022.01.17.22269412v2 on medRxiv
  3. Version published to 10.1101/2022.01.17.22269412v1 on medRxiv