Whole exome sequencing reveals a homozygous splicing mutation in CEP78 as the cause of atypical Usher syndrome in Eastern Jewish patients

Abstract

Purpose : To identify the cause of disease in patients with inherited retinal diseases, and particularly in patients with atypical Usher syndrome, using whole exome sequencing (WES).

Methods : All human studies adhered to the tenets of the Declaration of Helsinki. Patients underwent a comprehensive ophthalmic evaluation, including ophthalmic ancillary tests as well as hearing tests. Whole exome capture was performed using the Nextera Rapid Capture Expanded Exome kit (Illumina, San Diego, CA, USA).

Results : Using WES on the DNA sample of the index case (MOL0679-1 of an Eastern Jewish origin) we identified a homozygous splice-site variant (c.893-1G>A) in the acceptor site of exon 7 of CEP78. The variant was verified by Sanger sequencing and is absent from public variant databases. The affected brother of the index case was also homozygous for the variant. Both patients suffer from a cone-rod dystrophy phenotype with minimal fundus findings accompanied by sensorineural hearing loss involving mainly high frequencies. Mutation analysis in a set of 245 index cases with inherited retinal degenerations revealed another patient of the same origin who had a similar phenotype and was homozygous for this mutation (p=0.0495 by chi square analysis). RT-PCR analysis of CEP78 RNA in blood samples of the patients and controls revealed that the c.893-1G>A mutation causes skipping of exon 7 leading to a frameshift deletion of 65bp followed by a premature stop codon (p.Asp298Valfs*17). The mutation is likely to either be null or produce a short and mutated protein lacking most of the wt protein sequence. The expression level of the mutated transcript was lower than the wt allele, as is expected upon activation of the nonsense mediated mRNA decay mechanism. RT-PCR analysis of 15 human tissues revealed expression in a few tissues (mainly brain and spleen) with the retina showing the most intense PCR amplification.

Conclusions : CEP78 is a centrosomal protein that was reported previously to interact with c-nap2, encoded by the CEP250 gene that we we reported earlier to cause atypical Usher syndrome. Here we show that a mutated CEP78 protein can cause a different, yet another atypical Usher phenotype.

This is an abstract that was submitted for the 2016 ARVO Annual Meeting, held in Seattle, Wash., May 1-5, 2016.