Dataset Information

A Japanese family with cone-rod dystrophy of delayed onset caused by a compound heterozygous combination of novel CDHR1 frameshift and known missense variants.

ABSTRACT: We analyzed two siblings in a Japanese family with delayed onset cone-rod dystrophy (CRD) using whole-exome sequencing. A novel frameshift c.1106dup (p.H370Afs*17) variant and a known missense c.2027?T?>?A (p.I676N) variant in CDHR1 were identified. Both patients shared the same variants, although they displayed a significant difference in disease severity. A meta-analysis of the relationship between the severity and the variant type was performed using the reported cases in the literature and did not reveal a definitive correlation.

SUBMITTER: Haque MN

PROVIDER: S-EPMC6459921 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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A Japanese family with cone-rod dystrophy of delayed onset caused by a compound heterozygous combination of novel <i>CDHR1</i> frameshift and known missense variants.

Haque Muhammad Nazmul MN Kurata Kentaro K Hosono Katsuhiro K Ohtsubo Masafumi M Ohishi Kentaro K Sato Miho M Minoshima Shinsei S Hotta Yoshihiro Y

Human genome variation 20190412

We analyzed two siblings in a Japanese family with delayed onset cone-rod dystrophy (CRD) using whole-exome sequencing. A novel frameshift c.1106dup (p.H370Afs*17) variant and a known missense c.2027 T > A (p.I676N) variant in <i>CDHR1</i> were identified. Both patients shared the same variants, although they displayed a significant difference in disease severity. A meta-analysis of the relationship between the severity and the variant type was performed using the reported cases in the literatur ...[more]

PMID: 30992995

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Project description:Purpose: ARL3 (ADP-ribosylation factor-like 3) variants cause autosomal dominant retinitis pigmentosa (RP) or autosomal recessive Joubert syndrome. We found a family with rod-cone dystrophy (RCD) and verified it was associated with compound heterozygous variants in ARL3 gene. Methods: Ophthalmic examinations including optical coherence tomography and electroretinogram (ERG) were performed. Targeted next generation sequencing (NGS) was performed for the proband using a custom designed panel. Sanger sequencing and co-segregation were conducted in the family members. Changes of protein structure mediated by the variants were studied in vitro. ARL3 protein stability and its interaction with RP2 protein were assessed by cycloheximide chase assay and co-immunoprecipitation (Co-IP) assay. Results: Visual acuity of the 18-year-old male proband was 0.25 in the right and 0.20 in the left eye, while his non-consanguineous parents and sister was normal. The proband showed signs of RCD, including nyctalopia, peripheral field loss, bone-spicule deposits in the retina, and reduced ERG responses. The father, aged 50 years old, showed visual acuity of 1.0 in both eyes. Unlike the proband, he presented late onset and mild cone-rod dystrophy (CRD), including macular atrophy, central scotomata, moderate reduction in photopic ERG responses. None of all the family members had hearing abnormality, mental dysplasia or gait instability. We identified two novel compound heterozygous variants (c.91A>G, p.T31A; c.353G>T, p.C118F) in ARL3 in the proband, while his father only had variant c.91A>G. Bioinformatics analysis indicated amino acid positions of the two variants are highly conserved among species. The in silico tools predicted the variants to be harmful. Protein structure analysis showed the two variants had potential to alter the protein structure. Based on the ACMG guidelines, the two variants were likely pathogenic. In addition, the ARL3 mutations destabilized ARL3 protein, and the mutation c.353G>T disrupted the interaction between ARL3 and RP2 in HEK293T cells. Conclusions: We showed novel compound heterozygous variants in ARL3 were associated with early onset of autosomal recessive RCD, while c.91A>G along may be associated with a late onset of dominant CRD. The two variants in ARL3 could be causative by destabilizing ARL3 protein and impairing its interaction with RP2 protein.

Project description:UnlabelledMutations in RPGRIP1 are associated with early onset retinal degenerations in humans and dogs. Dogs homozygous for a 44 bp insertion including a polyA(29) tract potentially leading to premature truncation of the protein, show cone rod degeneration. This is rapid and blinding in a colony of dogs in which the mutation was characterised but in dogs with the same mutation in the pet population there is very variable disease severity and rate of progression.ObjectiveWe hypothesized that this variability must be associated with leakiness of the RPGRIP1 mutation, allowing continued RPGRIP1 production. The study was designed to discover mechanisms that might allow such leakiness.MethodsWe analysed alternate start sites and splicing of RPGRIP1 transcripts; variability of polyA(n) length in the insertion and slippage at polyA(n) during transcription/translation.Results and significanceWe observed a low rate of use of alternative start codons having potential to allow forms of transcript not including the insertion, with the possibility of encoding truncated functional RPGRIP1 protein isoforms. Complex alternative splicing was observed, but did not increase this potential. Variable polyA(n) length was confirmed in DNA from different RPGRIP1(-/-) dogs, yet polyA(n) variability did not correspond with the clinical phenotypes and no individual was found that carried a polyA(n) tract capable of encoding an in-frame variant. Remarkably though, in luciferase reporter gene assays, out-of-frame inserts still allowed downstream reporter gene expression at some 40% of the efficiency of in-frame controls. This indicates a major role of transcriptional or translational frameshifting in RPGRIP1 expression. The known slippage of reverse transcriptases as well as RNA polymerases and thermostable DNA polymerases on oligoA homopolymers meant that we could not distinguish whether the majority of slippage was transcriptional or translational. This leakiness at the mutation site may allow escape from severe effects of the mutation for some dogs.

Dataset Information

A Japanese family with cone-rod dystrophy of delayed onset caused by a compound heterozygous combination of novel CDHR1 frameshift and known missense variants.

Publications

A Japanese family with cone-rod dystrophy of delayed onset caused by a compound heterozygous combination of novel <i>CDHR1</i> frameshift and known missense variants.

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