Extending the spectrum of CLRN1- and ABCA4-associated inherited retinal dystrophies caused by novel and recurrent variants using exome sequencing

Abstract

Background: Inherited retinal dystrophies (IRDs) are characterized by extreme genetic and clinical heterogeneity. There are many genes that are known to cause IRD which makes the identification of the underlying genetic causes quite challenging. And in view of the emergence of therapeutic options, it is essential to combine molecular and clinical data to correctly diagnose IRD patients. In this study, we aimed to identify the disease-causing variants (DCVs) in four consanguineous Jordanian families with IRDs and describe genotype-phenotype correlations.

Methods: Exome sequencing (ES) was employed on the proband patients of each family, followed by segregation analysis of candidate variants in affected and unaffected family members by Sanger sequencing. Simulation analysis was done on one novel CLRN1 variant to characterize its effect on mRNA processing. Clinical evaluation included history, slit-lamp biomicroscopy, and indirect ophthalmoscopy.

Results: We identified two novel variants in CLRN1 [(c.433+1G>A) and (c.323T>C, p.Leu108Pro)], and two recurrent variants in ABCA4 [(c.1648G>A, p.Gly550Arg) and (c.5460+1G>A)]. Two families with the same DCV were found to have different phenotypes and another family was shown to have sector RP. Moreover, simulation analysis for the CLRN1 splice donor variant (c.433+1G>A) showed that the variant might affect mRNA processing resulting in the formation of an abnormal receptor. Also, a family that was previously diagnosed with nonsyndromic RP was found to have Usher syndrome based on their genetic assessment and audiometry.

Conclusion: Our findings extend the spectrum of CLRN1- and ABCA4-associated IRDs and describe new phenotypes for these genes. We also highlighted the importance of combining molecular and clinical data to correctly diagnose IRDs and the utility of simulation analysis to predict the effect of splice donor variants on protein formation and function.

Keywords: ABCA4; CLRN1; Exome sequencing; Inherited retinal dystrophy.

Figure 1

Pedigrees of the four Jordanian families participating in the study. Squares, circles, and dashes represent males, females, and deceased individuals, respectively. Arrows indicate probands. Solid symbols refer to affected individuals and open symbols to normal or carrier individuals. The two dashed squares in family F1 pedigree divide it into F2‐A and F2‐B. Double horizontal lines indicate consanguinity. M/M, homozygous mutated; M/W, heterozygous mutated; W/W, homozygous wild type. Zygosity for individuals III‐2 and III‐3 in family F1‐A is written in two lines, the above one for CLRN1 (c.433+1G>A), and the lower one for ABCA4 (c.5460+1G>A)

Figure 2

Simulation analysis of the splice donor variant results CLRN1 (c.433+1G>A). (a) Best oriented docked pose of the wild‐type RNA with U1 snRNP. The wild‐type RNA and the U1 snRNP are shown in green and red colors, respectively. The wild‐type polymorphism (Guanine) is shown as G21, it is binding with Cytosine 8 of U1 snRNP, (b) The main noncanonical interacting atoms between Guanine (G21) from wild‐type RNA with Cytosine (C8) from U1 snRNP. (c) Noncanonical interactions became less frequent when G21 is mutated to A. Noncanonical interacting atoms are shown as annotated spheres

Figure 3

Optical coherence tomography (OCT) (a) and (b) fundus photography of probands of all families (OD and OS). White arrows show central atrophic maculopathy with no cystoid macular edema, blue arrow indicates waxy pallor of optic disc, and red arrow indicates attenuation of retinal arterioles. Fundus images also show bone spicules

Figure 4

Electroretinograms (ERGs) of both eyes in all probands including the standard six recordings denoted beside each row