# The role of non-coding variants in Usher disease

> **NIH NIH K08** · UNIVERSITY OF WASHINGTON · 2024 · $230,277

## Abstract

PROJECT SUMMARY/ABSTRACT
Primary cilia, or non-motile cilia, are present in almost every mammalian cell. Ciliopathies cause a
spectrum of diseases in multiple organs, including the brain, kidney and liver. The most debilitating,
however, are sensory neuropathies leading to deafness and blindness. Retinal ciliopathies account for
one third of all inherited retinal diseases (IRDs), and are a major cause of visual impairment and
blindness in the pediatric population. Usher syndrome is the most common retinal ciliopathy and
presents a tremendous health burden due to congenital hearing impairment and progressive decline in
vision. Usher type 2 (USH2) is the most common subtype with the USH2A gene accounting for the
majority of cases. USH2 is inherited in an autosomal recessive manner; however, in approximately 20%
of patients with clinical features typical for USH2, only one mutation of USH2A has been identified by
exome sequencing, thereby precluding a definitive diagnosis. The second disease variant may reside in
non-coding regions of the USH2A gene. Whereas the protein coding variants of IRDs have been
studied in human and other model systems, the role of non-protein coding variants contributing to
monoallelic disease is much less understood. Non-coding variants are difficult to classify, especially in
gene products as large and complex as USH2A (spans 800 kilobases and contains 72 exons), and thus
remain under-diagnosed. Genome sequencing of IRD patients can identify pathogenic non-coding
variations in regulatory regions to explain causative changes and is increasingly being used to
genetically diagnose patients suffering from suspected monogenic disease. Phasing genetic variation is
also critical for human disease studies. We hypothesize that genomic sequencing and haplotype
phasing of the USH2A locus and its surrounding regulatory regions will provide a more accurate
detection of pathogenic variants in monoallelic patients. This will be accomplished by combining the
base-level accuracy of Illumina short-read sequencing with the longer read lengths obtained from
Nanopore based amplification-free targeted sequencing. Identification of non-coding variants and their
phase information are essential first steps towards understanding their pathogenic effects in patient-
derived stem cells. The pathogenicity of non-coding variants will be explored using luciferase knock-in
cell culture systems as well as patient-derived induced pluripotent stem cells (iPSCs) differentiated in
vitro to form retinal organoids (ROs). Use of ROs will provide clinically relevant tissue from patients that
can be edited using CRISPR-Cas9 technology to determine variant pathogenicity and mutational
burden. This proposal has tremendous therapeutic potential as non-coding deep-intronic variants have
been the focus of gene targeting and gene editing technologies in various IRDs.

## Key facts

- **NIH application ID:** 10808198
- **Project number:** 5K08EY033789-02
- **Recipient organization:** UNIVERSITY OF WASHINGTON
- **Principal Investigator:** Debarshi Mustafi
- **Activity code:** K08 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2024
- **Award amount:** $230,277
- **Award type:** 5
- **Project period:** 2023-04-01 → 2028-03-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10808198

## Citation

> US National Institutes of Health, RePORTER application 10808198, The role of non-coding variants in Usher disease (5K08EY033789-02). Retrieved via AI Analytics 2026-05-26 from https://api.ai-analytics.org/grant/nih/10808198. Licensed CC0.

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