Predicting the pathogenicity of RPE65 mutations

A R Philp; M Jin; S Li; E I Schindler; A Iannaccone; B L Lam; R G Weleber; G A Fishman; S G Jacobson; R F Mullins; Gabriel H Travis; Edwin M Stone

doi:10.1002/humu.21033

Back

Predicting the pathogenicity of RPE65 mutations

Journal article

Open access

Peer reviewed

Predicting the pathogenicity of RPE65 mutations

A R Philp, M Jin, S Li, E I Schindler, A Iannaccone, B L Lam, R G Weleber, G A Fishman, S G Jacobson, R F Mullins, …

Human mutation, Vol.30(8), pp.1183-1188

08/2009

DOI: 10.1002/humu.21033

PMCID: PMC2717180

PMID: 19431183

Files and links (1)

url

https://doi.org/10.1002/humu.21033View

Published (Version of record) Open Access

Abstract

To assist in distinguishing disease-causing mutations from nonpathogenic polymorphisms, we developed an objective algorithm to calculate an "estimate of pathogenic probability" (EPP) based on the prevalence of a specific variation, its segregation within families, and its predicted effects on protein structure. Eleven missense variations in the RPE65 gene were evaluated in patients with Leber congenital amaurosis (LCA) using the EPP algorithm. The accuracy of the EPP algorithm was evaluated using a cell-culture assay of RPE65-isomerase activity The variations were engineered into plasmids containing a human RPE65 cDNA and the retinoid isomerase activity of each variant was determined in cultured cells. The EPP algorithm predicted eight substitution mutations to be disease-causing variants. The isomerase catalytic activities of these RPE65 variants were all less than 6% of wild-type. In contrast, the EPP algorithm predicted the other three substitutions to be non-disease-causing, with isomerase activities of 68%, 127%, and 110% of wild-type, respectively. We observed complete concordance between the predicted pathogenicities of missense variations in the RPE65 gene and retinoid isomerase activities measured in a functional assay. These results suggest that the EPP algorithm may be useful to evaluate the pathogenicity of missense variations in other disease genes where functional assays are not available.

Algorithms

Carrier Proteins - physiology

Amino Acid Sequence

Cell Line

Biocatalysis

Mutagenesis, Site-Directed

Humans

Eye Proteins - chemistry

Molecular Sequence Data

Male

Mutation, Missense

DNA Primers

Reverse Transcriptase Polymerase Chain Reaction

Carrier Proteins - genetics

Pedigree

Base Sequence

Carrier Proteins - chemistry

Female

Eye Proteins - physiology

Eye Proteins - genetics

cis-trans-Isomerases

DNA, Complementary

Details

Title: Subtitle: Predicting the pathogenicity of RPE65 mutations
Creators: A R Philp - Department of Ophthalmology and Visual Sciences, University of Iowa Hospitals and Clinics, Iowa City, Iowa
M Jin
S Li
E I Schindler
A Iannaccone
B L Lam
R G Weleber
G A Fishman
S G Jacobson
R F Mullins
Gabriel H Travis
Edwin M Stone
Resource Type: Journal article
Publication Details: Human mutation, Vol.30(8), pp.1183-1188
DOI: 10.1002/humu.21033
PMID: 19431183
PMCID: PMC2717180
NLM abbreviation: Hum Mutat
ISSN: 1059-7794
eISSN: 1098-1004
Publisher: United States
Grant note: R01 EY016822 / NEI NIH HHS Howard Hughes Medical Institute R01 EY016822-01 / NEI NIH HHS EY-01584 / NEI NIH HHS T32 GM007337 / NIGMS NIH HHS EY-016822 / NEI NIH HHS EY-017451 / NEI NIH HHS R01 EY017451 / NEI NIH HHS R01 EY015844 / NEI NIH HHS R01 EY015844-04 / NEI NIH HHS
Language: English
Date published: 08/2009
Academic Unit: Iowa Neuroscience Institute; Ophthalmology and Visual Sciences
Record Identifier: 9983979950602771

Metrics

21 Record Views

42 Times Cited - Web of Science