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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease
Published on: April 4, 2018
Functional Validation of a Novel Deep Intronic IMPG2 Variant Causing Pseudoexon Activation in Retinitis Pigmentosa
Guobing Zheng1, Chenxia Xu1, Fenghua Xie1
1Prenatal Diagnosis Center, Boai Hospital of Zhongshan, Zhongshan, Guangdong, 528400, People's Republic of China.
Objective:
Retinitis pigmentosa (RP) is a genetically heterogeneous group of inherited retinal dystrophies often accompanied by macular involvement. Variants in IMPG2 are known to cause RP type 56 and vitelliform macular dystrophy type 5, but the pathogenic role of deep intronic variants has rarely been characterized. This study aimed to identify and functionally validate a novel deep intronic IMPG2 variant in a patient with RP.
Methods:
A comprehensive clinical, genetic, and functional assessment was performed. Ophthalmic evaluations included fundus photography, optical coherence tomography (OCT), OCT angiography (OCTA), and multifocal electroretinography (mfERG). Whole-genome sequencing followed by Sanger validation and segregation analysis was conducted. In silico splicing prediction and dual minigene assays (pcMINI and pcMINI-C) in HEK293T and HeLa cells were employed to evaluate the splicing effect of the variant.
Results:
A novel homozygous deep intronic variant in IMPG2 (NM_016247.4:c.909-1659A>G), absent from public databases, was identified. Splice prediction tools suggested creation of a cryptic donor site. Functional assays demonstrated aberrant splicing with retention of a 132 bp pseudoexon, introducing a premature termination codon and thereby likely triggering nonsense-mediated decay rather than generating a stable truncated protein. Segregation analysis confirmed autosomal recessive inheritance. The proband exhibited lifelong night blindness, progressive peripheral visual field constriction, and macular structural and functional impairment, consistent with IMPG2-associated retinopathy.
Conclusion:
This study provides the first functional evidence that a deep intronic IMPG2 variant causes pseudoexon activation leading to a premature termination codon and likely nonsense-mediated decay. These findings expand the IMPG2 mutational spectrum, highlight the pathogenic potential of deep intronic variants, and emphasize the importance of functional assays for reclassifying variants of uncertain significance in inherited retinal diseases.
