Splicing mutations in inherited retinal diseases

Weisschuh, Nicole; Buena-Atienza, Elena; Wissinger, Bernd

doi:10.1016/j.preteyeres.2020.100874

Cited by 30 publications

(15 citation statements)

References 199 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Furthermore, the challenge of interpreting splicing variants is not limited to hereditary cancer and has been noted in other disease areas, such as inherited retinal diseases. 38 To avoid negative outcomes, it is essential to consider a variety of types of evidence for variant interpretation and to use appropriate control samples during RNA analysis.…”

Section: Discussionmentioning

confidence: 99%

Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation

Truty

Ouyang

Rojahn

et al. 2021

The American Journal of Human Genetics

View full text Add to dashboard Cite

The complexities of gene expression pose challenges for the clinical interpretation of splicing variants. To better understand splicing variants and their contribution to hereditary disease, we evaluated their prevalence, clinical classifications, and associations with diseases, inheritance, and functional characteristics in a 689,321-person clinical cohort and two large public datasets. In the clinical cohort, splicing variants represented 13% of all variants classified as pathogenic (P), likely pathogenic (LP), or variants of uncertain significance (VUSs). Most splicing variants were outside essential splice sites and were classified as VUSs. Among all individuals tested, 5.4% had a splicing VUS. If RNA analysis were to contribute supporting evidence to variant interpretation, we estimated that splicing VUSs would be reclassified in 1.7% of individuals in our cohort. This would result in a clinically significant result (i.e., P/LP) in 0.1% of individuals overall because most reclassifications would change VUSs to likely benign. In ClinVar, splicing VUSs were 4.8% of reported variants and could benefit from RNA analysis. In the Genome Aggregation Database (gnomAD), splicing variants comprised 9.4% of variants in protein-coding genes; most were rare, precluding unambiguous classification as benign. Splicing variants were depleted in genes associated with dominant inheritance and haploinsufficiency, although some genes had rare variants at essential splice sites or had common splicing variants that were most likely compatible with normal gene function. Overall, we describe the contribution of splicing variants to hereditary disease, the potential utility of RNA analysis for reclassifying splicing VUSs, and how natural variation may confound clinical interpretation of splicing variants.

show abstract

Section: Discussionmentioning

confidence: 99%

Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation

Truty

Ouyang

Rojahn

et al. 2021

The American Journal of Human Genetics

View full text Add to dashboard Cite

show abstract

“…This discrepancy has been previously observed in the literature (including in CDH23) [61][62][63] and is believed to be due to differences in expression of splice factors and splice regulatory factors in different cell types or to the methodologic constraints that limit the minigene construct length to a few exons (1 or 2). [64][65][66] The shorter size of the minigene intron unit within the CNGB3 construct (644 bp) compared with intron 6 of the genomic DNA (12,869 bp) likely prevented the inclusion of the aberrant exon that occurs in vivo. Splicing machinery is influenced by the genomic context where higher fidelity splicing outcomes are more likely with larger genomic DNA.…”

Section: Discussionmentioning

confidence: 99%

Phenotype Driven Analysis of Whole Genome Sequencing Identifies Deep Intronic Variants that Cause Retinal Dystrophies by Aberrant Exonization

Scipio

Tavares

Deshmukh

et al. 2020

Invest. Ophthalmol. Vis. Sci.

View full text Add to dashboard Cite

Purpose To demonstrate the effectiveness of combining retinal phenotyping and focused variant filtering from genome sequencing (GS) in identifying deep intronic disease causing variants in inherited retinal dystrophies. Methods Affected members from three pedigrees with classical enhanced S-cone syndrome (ESCS; Pedigree 1), congenital stationary night blindness (CSNB; Pedigree 2), and achromatopsia (ACHM; Pedigree 3), respectively, underwent detailed ophthalmologic evaluation, optical coherence tomography, and electroretinography. The probands underwent panel-based genetic testing followed by GS analysis. Minigene constructs ( NR2E3 , GPR179 and CNGB3 ) and patient-derived cDNA experiments ( NR2E3 and GPR179 ) were performed to assess the functional effect of the deep intronic variants. Results The electrophysiological findings confirmed the clinical diagnosis of ESCS, CSNB, and ACHM in the respective pedigrees. Panel-based testing revealed heterozygous pathogenic variants in NR2E3 (NM_014249.3; c.119-2A>C; Pedigree 1) and CNGB3 (NM_019098.4; c.1148delC/p.Thr383Ilefs*13; Pedigree 3). The GS revealed heterozygous deep intronic variants in Pedigrees 1 ( NR2E3 ; c.1100+1124G>A) and 3 ( CNGB3 ; c.852+4751A>T), and a homozygous GPR179 variant in Pedigree 2 (NM_001004334.3; c.903+343G>A). The identified variants segregated with the phenotype in all pedigrees. All deep intronic variants were predicted to generate a splice acceptor gain causing aberrant exonization in NR2E3 [89 base pairs (bp)] , GPR179 (197 bp), and CNGB3 (73 bp); splicing defects were validated through patient-derived cDNA experiments and/or minigene constructs and rescued by antisense oligonucleotide treatment. Conclusions Deep intronic mutations contribute to missing heritability in retinal dystrophies. Combining results from phenotype-directed gene panel testing, GS, and in silico splice prediction tools can help identify these difficult-to-detect pathogenic deep intronic variants.

show abstract

“…Direct analysis of native transcripts is ideal, but it is not possible for genes specifically expressed in the retina. In such instances, a minigene assay (also called "exon trapping") has been used for validating the predicted splicing defects associated with VUS [8,9]. Here we use a minigene in vitro assay to functionally test six VUS in the genes OPA1, CNGB1, and CLUAP1 that were predicted to alter spicing mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Functional Evaluation of Splicing for Variants of Uncertain Significance in Patients with Inherited Retinal Diseases

Mauro-Herrera

Chiang²,

Radojevic

et al. 2021

Preprint

View full text Add to dashboard Cite

Inherited retinal diseases (IRD) comprise a heterogeneous set of clinical and genetic disorders that lead to blindness. Given the emerging opportunities in precision medicine and gene thera-py, it has become increasingly important to determine whether DNA variants with uncertain significance (VUS) are responsible for the patients’ IRD. This research was performed to assess the functional consequence of six VUS identified in patients with IRD. Clinical assessments in-cluded an ophthalmic examination, best corrected visual acuity, and kinetic perimetry. Imaging was acquired with the Optos ultra-widefield camera and spectral-domain optical coherence to-mography (SD-OCT). Genetic testing was performed by Molecular Vision Laboratories. VUS that were predicted to alter splicing were analyzed with a minigene assay which revealed that VUS in the genes OPA1, CNGB1, and CLUAP1 altered spicing mechanisms. Due to the emerging gene and cell therapies, these results expand the genotype-phenotype correlations for patients diag-nosed with an IRD.

show abstract

Splicing mutations in inherited retinal diseases

Cited by 30 publications

References 199 publications

Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation

Spectrum of splicing variants in disease genes and the ability of RNA analysis to reduce uncertainty in clinical interpretation

Phenotype Driven Analysis of Whole Genome Sequencing Identifies Deep Intronic Variants that Cause Retinal Dystrophies by Aberrant Exonization

Functional Evaluation of Splicing for Variants of Uncertain Significance in Patients with Inherited Retinal Diseases

Contact Info

Product

Resources

About