Genome scale analysis of pathogenic variants targetable for single base editing

BMC Med Genomics. 2020 Sep 18;13(Suppl 8):80. doi: 10.1186/s12920-020-00735-8.


Background: Single nucleotide variants account for approximately 90% of all known pathogenic variants responsible for human diseases. Recently discovered CRISPR/Cas9 base editors can correct individual nucleotides without cutting DNA and inducing double-stranded breaks. We aimed to find all possible pathogenic variants which can be efficiently targeted by any of the currently described base editors and to present them for further selection and development of targeted therapies.

Methods: ClinVar database (GRCh37_clinvar_20171203) was used to search and select mutations available for current single-base editing systems. We included only pathogenic and likely pathogenic variants for further analysis. For every potentially editable mutation we checked the presence of PAM. If a PAM was found, we analyzed the sequence to find possibility to edit only one nucleotide without changing neighboring nucleotides. The code of the script to search Clinvar database and to analyze the sequences was written in R and is available in the appendix.

Results: We analyzed 21 editing system currently reported in 9 publications. Every system has different working characteristics such as the editing window and PAM sequence. C > T base editors can precisely target 3196 mutations (46% of all pathogenic T > C variants), and A > G editors - 6900 mutations (34% of all pathogenic G > A variants).

Conclusions: Protein engineering helps to develop new enzymes with a narrower window of base editors as well as using new Cas9 enzymes with different PAM sequences. But, even now the list of mutations which can be targeted with currently available systems is huge enough to choose and develop new targeted therapies.

Keywords: ABE; APOBEC; Base editor CRISPR/Cas9; Hereditary diseases; Pathogenic variants; PmCDA1.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • CRISPR-Associated Protein 9
  • CRISPR-Cas Systems*
  • Databases, Nucleic Acid
  • Disease / genetics
  • Gene Editing*
  • Genome, Human
  • Humans
  • Mutation*


  • CRISPR-Associated Protein 9