Homozygosity mapping and whole-genome sequencing reveals a deep intronic PROM1 mutation causing cone–rod dystrophy by pseudoexon activation

Mayer, Achim; Rohrschneider, Klaus; Strom, Tim M.; Glöckle, Nicola; Kohl, Susanne; Wissinger, Bernd; Weisschuh, Nicole

doi:10.1038/ejhg.2015.144

Cited by 35 publications

(25 citation statements)

References 19 publications

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“…While this is the first intronic variant outside of the splice site consensus sequences deemed pathogenic in TULP1 , the causality of deep‐intronic variants has also been described in nine other retinal dystrophy genes: ABCA4 , CEP290 , CHM , OA1 , OAT, OFD1 , PROM1 , PRPF31 , and USH2A (Bax et al., ; Braun et al., ; Carss et al., ; den Hollander et al., ; Liquori et al., ; Mayer et al., ; Naruto et al., ; Rio Frio et al., ; Vache et al., ; van den Hurk et al., ; Webb et al., ) (http://www.dbass.soton.ac.uk). Intronic variants are likely to explain a substantial portion of the current genetically unexplained or monoallelic retinal dystrophy cases, and underscore the importance of genetic tests uncovering those regions, such as whole genome sequencing.…”

Section: Discussionmentioning

confidence: 90%

The identification of a RNA splice variant in TULP1 in two siblings with early‐onset photoreceptor dystrophy

Verbakel

Fadaie

Klevering

et al. 2019

Molec Gen & Gen Med

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Background Early‐onset photoreceptor dystrophies are a major cause of irreversible visual impairment in children and young adults. This clinically heterogeneous group of disorders can be caused by mutations in many genes. Nevertheless, to date, 30%–40% of cases remain genetically unexplained. In view of expanding therapeutic options, it is essential to obtain a molecular diagnosis in these patients as well. In this study, we aimed to identify the genetic cause in two siblings with genetically unexplained retinal disease. Methods Whole exome sequencing was performed to identify the causative variants in two siblings in whom a single pathogenic variant in TULP1 was found previously. Patients were clinically evaluated, including assessment of the medical history, slit‐lamp biomicroscopy, and ophthalmoscopy. In addition, a functional analysis of the putative splice variant in TULP1 was performed using a midigene assay. Results Clinical assessment showed a typical early‐onset photoreceptor dystrophy in both the patients. Whole exome sequencing identified two pathogenic variants in TULP1, a c.1445G>A (p.(Arg482Gln)) missense mutation and an intronic c.718+23G>A variant. Segregation analysis confirmed that both siblings were compound heterozygous for the TULP1 c.718+23G>A and c.1445G>A variants, while the unaffected parents were heterozygous. The midigene assay for the c.718+23G>A variant confirmed an elongation of exon 7 leading to a frameshift. Conclusion Here, we report the first near‐exon RNA splice variant that is not present in a consensus splice site sequence in TULP1, which was found in a compound heterozygous manner with a previously described pathogenic TULP1 variant in two patients with an early‐onset photoreceptor dystrophy. We provide proof of pathogenicity for this splice variant by performing an in vitro midigene splice assay, and highlight the importance of analysis of noncoding regions beyond the noncanonical splice sites in patients with inherited retinal diseases.

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Section: Discussionmentioning

confidence: 90%

The identification of a RNA splice variant in TULP1 in two siblings with early‐onset photoreceptor dystrophy

Verbakel

Fadaie

Klevering

et al. 2019

Molec Gen & Gen Med

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“…Previous IRD-associated intronic variants have created new splice acceptor or donor sites that allowed the insertion of a PE. 22,30,[42][43][44][45][46][47][48][49][50] To our knowledge we are the first to report on the insertion of a PE that is not due to this mechanism but possibly because of the creation of new ESE motifs in IRDs. Previously, the loss of an ESE and the creation of a splicing suppressor has been reported in the OPN1LW/OPN1MW gene array due to the coding variant c.532A>G (p.Ile178Val), which is associated with exon 3 exclusion and a congenital color vision defect (MIM: 303800 and 303900).…”

Section: Discussionmentioning

confidence: 99%

Identification and Rescue of Splice Defects Caused by Two Neighboring Deep-Intronic ABCA4 Mutations Underlying Stargardt Disease

Albert

Garanto

Sangermano

et al. 2018

The American Journal of Human Genetics

113

173

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Sequence analysis of the coding regions and splice site sequences in inherited retinal diseases is not able to uncover ∼40% of the causal variants. Whole-genome sequencing can identify most of the non-coding variants, but their interpretation is still very challenging, in particular when the relevant gene is expressed in a tissue-specific manner. Deep-intronic variants in ABCA4 have been associated with autosomal-recessive Stargardt disease (STGD1), but the exact pathogenic mechanism is unknown. By generating photoreceptor precursor cells (PPCs) from fibroblasts obtained from individuals with STGD1, we demonstrated that two neighboring deep-intronic ABCA4 variants (c.4539+2001G>A and c.4539+2028C>T) result in a retina-specific 345-nt pseudoexon insertion (predicted protein change: p.Arg1514Leufs36), likely due to the creation of exonic enhancers. Administration of antisense oligonucleotides (AONs) targeting the 345-nt pseudoexon can significantly rescue the splicing defect observed in PPCs of two individuals with these mutations. Intriguingly, an AON that is complementary to c.4539+2001G>A rescued the splicing defect only in PPCs derived from an individual with STGD1 with this but not the other mutation, demonstrating the high specificity of AONs. In addition, a single AON molecule rescued splicing defects associated with different neighboring mutations, thereby providing new strategies for the treatment of persons with STGD1. As many genes associated with human genetic conditions are expressed in specific tissues and pre-mRNA splicing may also rely on organ-specific factors, our approach to investigate and treat splicing variants using differentiated cells derived from individuals with STGD1 can be applied to any tissue of interest.

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“…The striking observation that 79% of cases with molecular diagnoses are accounted for by mutations in genes discovered between 1995 and 2004 suggests that while the continued addition of new disease-causing genes will of course improve diagnostic services, the comprehensive evaluation of protein-coding and regulatory variants affecting known disease-causing genes may have a greater influence on diagnostic yield. For example, the genomic sequencing of genes known to cause IRD has identified large deletions,14 deeply intronic disease-causing mutations31 and variants in regulatory regions,32 which would elude traditional custom panel NGS analysis.…”

Section: Discussionmentioning

confidence: 99%

Molecular findings from 537 individuals with inherited retinal disease

et al. 2016

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Background Inherited retinal diseases (IRDs) are a clinically and genetically heterogeneous set of disorders, for which diagnostic second-generation sequencing (next-generation sequencing, NGS) services have been developed worldwide. Methods We present the molecular findings of 537 individuals referred to a 105-gene diagnostic NGS test for IRDs. We assess the diagnostic yield, the spectrum of clinical referrals, the variant analysis burden and the genetic heterogeneity of IRD. We retrospectively analyse disease-causing variants, including an assessment of variant frequency in Exome Aggregation Consortium (ExAC). Results Individuals were referred from 10 clinically distinct classifications of IRD. Of the 4542 variants clinically analysed, we have reported 402 mutations as a cause or a potential cause of disease in 62 of the 105 genes surveyed. These variants account or likely account for the clinical diagnosis of IRD in 51% of the 537 referred individuals. 144 potentially disease-causing mutations were identified as novel at the time of clinical analysis, and we further demonstrate the segregation of known disease-causing variants among individuals with IRD. We show that clinically analysed variants indicated as rare in dbSNP and the Exome Variant Server remain rare in ExAC, and that genes discovered as a cause of IRD in the post-NGS era are rare causes of IRD in a population of clinically surveyed individuals. Conclusions Our findings illustrate the continued powerful utility of custom-gene panel diagnostic NGS tests for IRD in the clinic, but suggest clear future avenues for increasing diagnostic yields.

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Homozygosity mapping and whole-genome sequencing reveals a deep intronic PROM1 mutation causing cone–rod dystrophy by pseudoexon activation

Cited by 35 publications

References 19 publications

The identification of a RNA splice variant in TULP1 in two siblings with early‐onset photoreceptor dystrophy

The identification of a RNA splice variant in TULP1 in two siblings with early‐onset photoreceptor dystrophy

Identification and Rescue of Splice Defects Caused by Two Neighboring Deep-Intronic ABCA4 Mutations Underlying Stargardt Disease

Molecular findings from 537 individuals with inherited retinal disease

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