Outcome of ABCA4 Disease-Associated Alleles in Autosomal Recessive Retinal Dystrophies: Retrospective Analysis in 420 Spanish Families

doi:10.1016/j.ophtha.2013.04.002

Ophthalmology

Volume 120, Issue 11, November 2013, Pages 2332-2337

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https://doi.org/10.1016/j.ophtha.2013.04.002 Get rights and content

Objective

To provide a comprehensive overview of all detected mutations in the ABCA4 gene in Spanish families with autosomal recessive retinal disorders, including Stargardt's disease (arSTGD), cone-rod dystrophy (arCRD), and retinitis pigmentosa (arRP), and to assess genotype-phenotype correlation and disease progression in 10 years by considering the type of variants and age at onset.

Design

Case series.

Participants

A total of 420 unrelated Spanish families: 259 arSTGD, 86 arCRD, and 75 arRP.

Methods

Spanish families were analyzed through a combination of ABCR400 genotyping microarray, denaturing high-performance liquid chromatography, and high-resolution melting scanning. Direct sequencing was used as a confirmation technique for the identified variants. Screening by multiple ligation probe analysis was used to detect possible large deletions or insertions in the ABCA4 gene. Selected families were analyzed further by next generation sequencing.

Main Outcome Measures

DNA sequence variants, mutation detection rates, haplotypes, age at onset, central or peripheral vision loss, and night blindness.

Results

Overall, we detected 70.5% and 36.6% of all expected ABCA4 mutations in arSTGD and arCRD patient cohorts, respectively. In the fraction of the cohort where the ABCA4 gene was sequenced completely, the detection rates reached 73.6% for arSTGD and 66.7% for arCRD. However, the frequency of possibly pathogenic ABCA4 alleles in arRP families was only slightly higher than that in the general population. Moreover, in some families, mutations in other known arRP genes segregated with the disease phenotype.

Conclusions

An increasing understanding of causal ABCA4 alleles in arSTGD and arCRD facilitates disease diagnosis and prognosis and also is paramount in selecting patients for emerging clinical trials of therapeutic interventions. Because ABCA4-associated diseases are evolving retinal dystrophies, assessment of age at onset, accurate clinical diagnosis, and genetic testing are crucial. We suggest that ABCA4 mutations may be associated with a retinitis pigmentosa–like phenotype often as a consequence of severe (null) mutations, in cases of long-term, advanced disease, or both. Patients with classical arRP phenotypes, especially from the onset of the disease, should be screened first for mutations in known arRP genes and not ABCA4.

Financial Disclosure(s)

The author(s) have no proprietary or commercial interest in any materials discussed in this article.

Section snippets

Recruitment of Subjects

This study was reviewed and approved by the Ethics Committee of the Fundacion Jimenez Diaz Hospital, and it was performed according to the tenets of the Declaration of Helsinki and further reviews (59th WMA General Assembly, Seoul, Korea, October 2008). The participating subjects signed a written informed consent form after the nature of procedures had been explained fully. The collection of samples belongs to the Biobank of the Fundacion Jimenez Diaz Hospital.

Clinical Evaluation

Diagnoses of arSTGD, arCRD, and

Autosomal Recessive Stargardt's Disease Phenotype

Through the combined methodologic approach, 2 ABCA4 mutant alleles were identified in 159 of 259 families and 1 disease-associated allele was identified in 47 more families, resulting in a mutation detection rate of 70.5%. Haplotype analyses were performed for 133 (51.3%) of the 259 families, showing cosegregation of the disease with the ABCA4 locus in all of them, except for 7 families (1 with 1 mutation and 6 with no mutations). The NGS analysis detected the second mutant allele in 23 (52.3%)

Discussion

Since the ABCA4 gene was identified,² mutations in this gene have been associated with 3 autosomal recessive retinal phenotypes, STGD, CRD, and RP. The role of ABCA4 mutations in arSTGD and arCRD has been analyzed extensively in the Spanish population6, 7, 8 and is well known. The role of mutations in this gene in arRP remains unclear. Therefore, this study was conducted to summarize and review the data and to correlate the outcome of the different ABCA4 disease-associated variants with disease

References (25)

D.S. Papermaster et al.
Biosynthetic and immunochemical characterization of large protein in frog and cattle rod outer segment membranes
Exp Eye Res
(1976)
A. Maugeri et al.
The 2588G→C mutation in the ABCR gene is a mild frequent founder mutation in the Western European population and allows the classification of ABCR mutations in patients with Stargardt disease
Am J Hum Genet
(1999)
R. Allikmets et al.
A photoreceptor cell-specific ATP-binding transporter gene (ABCR) is mutated in recessive Stargardt macular dystrophy
Nat Genet
(1997)
A. Martínez-Mir et al.
Retinitis pigmentosa caused by a homozygous mutation in the Stargardt disease gene ABCR
Nat Genet
(1998)
F.P. Cremers et al.
Autosomal recessive retinitis pigmentosa and cone-rod dystrophy caused by splice site mutations in the Stargardt's disease gene ABCR
Hum Mol Genet
(1998)
D. Valverde et al.
Microarray-based mutation analysis of the ABCA4 gene in Spanish patients with Stargardt disease: evidence of a prevalent mutated allele
Mol Vis [serial online]
(2006)
D. Valverde et al.
Spectrum of the ABCA4 gene mutations implicated in severe retinopathies in Spanish patients
Invest Ophthalmol Vis Sci
(2007)
J. Aguirre-Lamban et al.
Molecular analysis of the ABCA4 gene for reliable detection of allelic variations in Spanish patients: identification of 21 novel variants
Br J Ophthalmol
(2009)
R. Riveiro-Alvarez et al.
Molecular analysis of ABCA4 and CRB1 genes in a Spanish family segregating both Stargardt disease and autosomal recessive retinitis pigmentosa
Mol Vis [serial online]
(2008)
E. Paloma et al.
Analysis of ABCA4 in mixed Spanish families segregating different retinal dystrophies
Hum Mutat
(2002)

R. Riveiro-Alvarez et al.

Frequency of ABCA4 mutations in 278 Spanish controls: an insight into the prevalence of autosomal recessive Stargardt disease

Br J Ophthalmol

(2009)

A.N. Yatsenko et al.

Late-onset Stargardt disease is associated with missense mutations that map outside known functional regions of ABCR (ABCA4)

Hum Genet

(2001)

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Spectrum of Genetic Variants in the Most Common Genes Causing Inherited Retinal Disease in a Large Molecularly Characterized United Kingdom Cohort
2024, Ophthalmology Retina
Inherited retinal disease (IRD) is a leading cause of blindness. Recent advances in gene-directed therapies highlight the importance of understanding the genetic basis of these disorders. This study details the molecular spectrum in a large United Kingdom (UK) IRD patient cohort.
Retrospective study of electronic patient records.
Patients with IRD who attended the Genetics Service at Moorfields Eye Hospital between 2003 and July 2020, in whom a molecular diagnosis was identified.
Genetic testing was undertaken via a combination of single-gene testing, gene panel testing, whole exome sequencing, and more recently, whole genome sequencing. Likely disease-causing variants were identified from entries within the genetics module of the hospital electronic patient record (OpenEyes Electronic Medical Record). Analysis was restricted to only genes listed in the Genomics England PanelApp R32 Retinal Disorders panel (version 3.24), which includes 412 genes associated with IRD. Manual curation ensured consistent variant annotation and included only plausible disease-associated variants.
Detailed analysis was performed for variants in the 5 most frequent genes (ABCA4, USH2A, RPGR, PRPH2, and BEST1), as well as for the most common variants encountered in the IRD study cohort.
We identified 4415 individuals from 3953 families with molecularly diagnosed IRD (variants in 166 genes). Of the families, 42.7% had variants in 1 of the 5 most common IRD genes. Complex disease alleles contributed to disease in 16.9% of affected families with ABCA4-associated retinopathy. USH2A exon 13 variants were identified in 43% of affected individuals with USH2A-associated IRD. Of the RPGR variants, 71% were clustered in the ORF15 region. PRPH2 and BEST1 variants were associated with a range of dominant and recessive IRD phenotypes. Of the 20 most prevalent variants identified, 5 were not in the most common genes; these included founder variants in CNGB3, BBS1, TIMP3, EFEMP1, and RP1.
We describe the most common pathogenic IRD alleles in a large single-center multiethnic UK cohort and the burden of disease, in terms of families affected, attributable to these variants. Our findings will inform IRD diagnoses in future patients and help delineate the cohort of patients eligible for gene-directed therapies under development.
Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
Characterising splicing defects of ABCA4 variants within exons 13–50 in patient-derived fibroblasts
2022, Experimental Eye Research
Citation Excerpt :
In line with a recent report (Schulz et al., 2017), partial skipping of exon 30 due to activation of a cryptic donor splice site was also observed in our study. Another coding variant, c.4919G>A, was associated with STGD1 in both the heterozygous and homozygous states (Riveiro-Alvarez et al., 2013; Simonelli et al., 2000; Briggs et al., 2001). In our study, this variant was homozygous in two siblings.
The ATP-binding cassette subfamily A member 4 gene (ABCA4)-associated retinopathy, Stargardt disease, is the most common monogenic inherited retinal disease. Given the pathogenicity of numerous ABCA4 variants is yet to be examined and a significant proportion (more than 15%) of ABCA4 variants are categorized as splice variants in silico, we therefore established a fibroblast-based splice assay to analyze ABCA4 variants in an Australian Stargardt disease cohort and characterize the pathogenic mechanisms of ABCA4 variants. A cohort of 67 patients clinically diagnosed with Stargardt disease was recruited. Genomic DNA was analysed using a commercial panel for ABCA4 variant detection and the consequences of ABCA4 variants were predicted in silico. Dermal fibroblasts were propagated from skin biopsies, total RNA was extracted and the ABCA4 transcript was amplified by RT-PCR. Our analysis identified a total of 67 unique alleles carrying 74 unique variants. The most prevalent splice-affecting complex allele c.[5461-10T>C; 5603A>T] was carried by 10% of patients in a compound heterozygous state. ABCA4 transcripts from exon 13 to exon 50 were readily detected in fibroblasts. In this region, aberrant splicing was evident in 10 out of 57 variant transcripts (18%), carried by 19 patients (28%). Patient-derived fibroblasts provide a feasible platform for identification of ABCA4 splice variants located within exons 13–50. Experimental evidence of aberrant splicing contributes to the pathogenic classification for ABCA4 variants. Moreover, identification of variants that affect splicing processes provides opportunities for intervention, in particular antisense oligonucleotide-mediated splice correction.
Genotype–Phenotype Correlations in a Spanish Cohort of 506 Families With Biallelic ABCA4 Pathogenic Variants
2020, American Journal of Ophthalmology
Citation Excerpt :
The Spanish variant c.3386G>T should be considered mild, although we previously proposed that it could have a moderately severe effect.20 Severe CRD phenotypes could be diagnosed as RP.7 In this work, all patients with CRD presented with rod disfunction because of ERG findings or symptoms associated with rod degeneration.
To define genotype–phenotype correlations in the largest cohort study worldwide of patients with biallelic ABCA4 variants, including 434 patients with Stargardt disease (STGD1) and 72 with cone-rod dystrophy (CRD).
Cohort study.
We characterized 506 patients with ABCA4 variants using conventional genetic tools and next-generation sequencing technologies. Medical history and ophthalmologic data were obtained from 372 patients. Genotype–phenotype correlation studies were carried out for the following variables: variant type, age at symptom onset (AO), and clinical phenotype.
A total of 228 different pathogenic variants were identified in 506 ABCA4 patients, 50 of which were novel. Genotype–phenotype correlations showed that most of the patients with biallelic truncating variants presented with CRD and that these cases had a significantly earlier AO than patients with STGD1. Three missense variants are associated with CRD for the first time (c.1804C>T; p.[Arg602Trp], c.3056C>T; p.[Thr1019Met], and c.6320G>C; p.[Arg2107Pro]). Analysis of the most prevalent ABCA4 variant in Spain, c.3386G>T; p.(Arg1129Leu), revealed that is correlated to STGD1, later AO, and foveal sparing.
Our study, conducted in the largest ABCA4-associated disease cohort reported to date, updates the genotype–phenotype model established for ABCA4 variants and broadens the mutational spectrum of the gene. According to our observations, patients with ABCA4 presenting with 2 truncating variants may first present features of STGD1 but eventually develop rod dysfunction, and specific missense variants may be associated with a different phenotype, underscoring the importance of an accurate genetic diagnosis. Also, it is a prerequisite for enrollment in clinical trials, and to date, no other treatment has been approved for STGD1.
Clinical spectrum, genetic complexity and therapeutic approaches for retinal disease caused by ABCA4 mutations
2020, Progress in Retinal and Eye Research
The ABCA4 protein (then called a “rim protein”) was first identified in 1978 in the rims and incisures of rod photoreceptors. The corresponding gene, ABCA4, was cloned in 1997, and variants were identified as the cause of autosomal recessive Stargardt disease (STGD1). Over the next two decades, variation in ABCA4 has been attributed to phenotypes other than the classically defined STGD1 or fundus flavimaculatus, ranging from early onset and fast progressing cone-rod dystrophy and retinitis pigmentosa-like phenotypes to very late onset cases of mostly mild disease sometimes resembling, and confused with, age-related macular degeneration. Similarly, analysis of the ABCA4 locus uncovered a trove of genetic information, including >1200 disease-causing mutations of varying severity, and of all types – missense, nonsense, small deletions/insertions, and splicing affecting variants, of which many are located deep-intronic. Altogether, this has greatly expanded our understanding of complexity not only of the diseases caused by ABCA4 mutations, but of all Mendelian diseases in general. This review provides an in depth assessment of the cumulative knowledge of ABCA4-associated retinopathy – clinical manifestations, genetic complexity, pathophysiology as well as current and proposed therapeutic approaches.
Expanding the Clinical and Molecular Heterogeneity of Nonsyndromic Inherited Retinal Dystrophies
2020, Journal of Molecular Diagnostics
Citation Excerpt :
Following the criteria of the ACMG, this variant was reclassified as unknown significance. The ABCA4: p.(Arg1129Leu) allele was the most prevalent allele in the Spanish STGD population (22.4%).19 In this study’s cohort, the allele p.(Arg1129Leu) was found in 10 of the 32 alleles studied in patients with the STGD phenotype.
A cohort of 172 patients diagnosed clinically with nonsyndromic retinal dystrophies, from 110 families underwent full ophthalmologic examination, including retinal imaging, electrophysiology, and optical coherence tomography, when feasible. Molecular analysis was performed using targeted next-generation sequencing (NGS). Variants were filtered and prioritized according to the minimum allele frequency, and finally classified according to the American College of Medical Genetics and Genomics guidelines. Multiplex ligation-dependent probe amplification and array comparative genomic hybridization were performed to validate copy number variations identified by NGS. The diagnostic yield of this study was 62% of studied families. Thirty novel mutations were identified. The study found phenotypic intra- and interfamilial variability in families with mutations in C1QTNF5, CERKL, and PROM1; biallelic mutations in PDE6B in a unilateral retinitis pigmentosa patient; interocular asymmetry RP in 50% of the symptomatic RPGR-mutated females; the first case with possible digenism between CNGA1 and CNGB1; and a ROM1 duplication in two unrelated retinitis pigmentosa families. Ten unrelated cases were reclassified. This study highlights the clinical utility of targeted NGS for nonsyndromic inherited retinal dystrophy cases and the importance of full ophthalmologic examination, which allows new genotype–phenotype associations and expands the knowledge of this group of disorders. Identifying the cause of disease is essential to improve patient management, provide accurate genetic counseling, and take advantage of gene therapy–based treatments.
ABCA4 Variant c.5714+5G>A in Trans With Null Alleles Results in Primary RPE Damage
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: Financial Disclosure(s): The author(s) have no proprietary or commercial interest in any materials discussed in this article.

: Supported by Retics Biobank CIBERER and FIS, ISCIII, Madrid, Spain (grant nos.: RD09-0076-00101, Intra/07/704.1, Intra/09/702.1, PI09/90047, PS09/00459); and Fundaluce 2011, Madrid, Spain; the National Eye Institute, National Institutes of Health, Bethesda, Maryland (grant nos.: EY021163, EY019861, EY019007 [Core Support for Vision Research]); Foundation Fighting Blindness, Owings Mills, Maryland; and Research to Prevent Blindness, New York, New York (unrestricted funds to the Department of Ophthalmology, Columbia University). The Biobank of Fundacion Jimenez Diaz Hospital (RD09/0076/00101) provided the collection of samples of patients and controls.

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Original articleOutcome of ABCA4 Disease-Associated Alleles in Autosomal Recessive Retinal Dystrophies: Retrospective Analysis in 420 Spanish Families

Objective

Design

Participants

Methods

Main Outcome Measures

Results

Conclusions

Financial Disclosure(s)

Section snippets

Recruitment of Subjects

Clinical Evaluation

Autosomal Recessive Stargardt's Disease Phenotype

Discussion

Exp Eye Res

Am J Hum Genet

A photoreceptor cell-specific ATP-binding transporter gene (ABCR) is mutated in recessive Stargardt macular dystrophy

Nat Genet

Retinitis pigmentosa caused by a homozygous mutation in the Stargardt disease gene ABCR

Nat Genet

Autosomal recessive retinitis pigmentosa and cone-rod dystrophy caused by splice site mutations in the Stargardt's disease gene ABCR

Hum Mol Genet

Microarray-based mutation analysis of the ABCA4 gene in Spanish patients with Stargardt disease: evidence of a prevalent mutated allele

Mol Vis [serial online]

Spectrum of the ABCA4 gene mutations implicated in severe retinopathies in Spanish patients

Invest Ophthalmol Vis Sci

Molecular analysis of the ABCA4 gene for reliable detection of allelic variations in Spanish patients: identification of 21 novel variants

Br J Ophthalmol

Molecular analysis of ABCA4 and CRB1 genes in a Spanish family segregating both Stargardt disease and autosomal recessive retinitis pigmentosa

Mol Vis [serial online]

Analysis of ABCA4 in mixed Spanish families segregating different retinal dystrophies

Hum Mutat

Frequency of ABCA4 mutations in 278 Spanish controls: an insight into the prevalence of autosomal recessive Stargardt disease

Br J Ophthalmol

Late-onset Stargardt disease is associated with missense mutations that map outside known functional regions of ABCR (ABCA4)

Hum Genet

Original article
Outcome of ABCA4 Disease-Associated Alleles in Autosomal Recessive Retinal Dystrophies: Retrospective Analysis in 420 Spanish Families