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Related Experiment Video

Updated: Jun 23, 2026

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
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Published on: April 4, 2018

Predicting the pathogenicity of RPE65 mutations.

A R Philp1, M Jin, S Li

  • 1Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, Iowa.

Human Mutation
|May 12, 2009
PubMed
Summary
This summary is machine-generated.

An objective algorithm, the estimate of pathogenic probability (EPP), accurately distinguishes disease-causing mutations from benign variants. This tool shows high concordance with functional assays for RPE65 gene variations linked to Leber congenital amaurosis.

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Published on: January 16, 2019

Area of Science:

  • Genetics
  • Molecular Biology
  • Ophthalmology

Background:

  • Distinguishing pathogenic mutations from nonpathogenic polymorphisms is crucial for genetic diagnosis.
  • Leber congenital amaurosis (LCA) is a severe inherited retinal disease often caused by mutations in the RPE65 gene.

Purpose of the Study:

  • To develop and validate an objective algorithm, the estimate of pathogenic probability (EPP), for assessing the pathogenicity of missense variations.
  • To evaluate the EPP algorithm's accuracy using RPE65 gene variations in LCA patients.

Main Methods:

  • Developed an EPP algorithm incorporating variation prevalence, family segregation, and predicted protein structure effects.
  • Assessed eleven missense variations in the RPE65 gene using the EPP algorithm.
  • Validated EPP predictions through a cell-culture assay measuring RPE65-isomerase activity.

Main Results:

  • The EPP algorithm correctly identified eight disease-causing RPE65 variants with <6% wild-type isomerase activity.
  • The algorithm also identified three non-disease-causing variants with isomerase activities ranging from 68% to 127% of wild-type.
  • Complete concordance was observed between EPP predictions and functional assay results.

Conclusions:

  • The EPP algorithm accurately predicts the pathogenicity of missense variations in the RPE65 gene.
  • This objective algorithm shows potential utility for evaluating missense variations in other disease genes, especially when functional assays are unavailable.