In silico structural and biochemical functional analysis of a novel cyp21a2 pathogenic variant

Michal Cohen, Emanuele Pignatti, Monica Dines, Adi Mory, Nina Ekhilevitch, Rachel Kolodny, Christa E. Flück, Dov Tiosano

Research output: Contribution to journalArticlepeer-review


Classical congenital adrenal hyperplasia (CAH) caused by pathogenic variants in the steroid 21-hydroxylase gene (CYP21A2) is a severe life-threatening condition. We present a detailed investigation of the molecular and functional characteristics of a novel pathogenic variant in this gene. The patient, 46 XX newborn, was diagnosed with classical salt wasting CAH in the neonatal period after initially presenting with ambiguous genitalia. Multiplex ligation-dependent probe analysis demonstrated a full deletion of the paternal CYP21A2 gene, and Sanger sequencing revealed a novel de novo CYP21A2 variant c.694–696del (E232del) in the other allele. This variant resulted in the deletion of a non-conserved single amino acid, and its functional relevance was initially undetermined. We used both in silico and in vitro methods to determine the mechanistic significance of this mutation. Computational analysis relied on the solved structure of the protein (Protein-data-bank ID 4Y8W), structure prediction of the mutated protein, evolutionary analysis, and manual inspection. We predicted impaired stability and functionality of the protein due to a rotatory disposition of amino acids in positions downstream of the deletion. In vitro biochemical evaluation of enzymatic activity supported these predictions, demonstrating reduced protein levels to 22% compared to the wild-type form and decreased hydroxylase activity to 1–4%. This case demonstrates the potential of combining in-silico analysis based on evolutionary information and structure prediction with biochemical studies. This approach can be used to investigate other genetic variants to understand their potential effects.

Original languageEnglish
Article number5857
Pages (from-to)1-11
Number of pages11
JournalInternational Journal of Molecular Sciences
Issue number16
StatePublished - 14 Aug 2020

Bibliographical note

Funding Information:
This research did not receive any specific grant from any funding agency in the public, commercial or not-for-profit sector. RK is partially supported by Israel Science Foundation grant number 450/16.

Publisher Copyright:
© 2020 by the authors. Licensee MDPI, Basel, Switzerland.


  • CYP21A2
  • Congenital adrenal hyperplasia
  • Consurf
  • In silico
  • Protein structure
  • VUS

ASJC Scopus subject areas

  • Catalysis
  • Molecular Biology
  • Spectroscopy
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Inorganic Chemistry


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