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1 From the Ocular Molecular Genetics Institute, Massachusetts Eye and Ear Infirmary, Boston; the 2 Bascom Palmer Eye Institute, University of Miami School of Medicine, Florida; 3 Schepens Retina Associates, Boston, Massachusetts; and the 4 Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts.
| Abstract |
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METHODS. One hundred eighteen unrelated patients with recessive Stargardt macular degeneration and eight with recessive CRD were screened for mutations in ABCR (ABCA4) by single-strand conformation polymorphism analysis. Variants were characterized by direct genomic sequencing. Segregation analysis was performed on the families of 20 patients in whom at least two or more likely pathogenic sequence changes were identified.
RESULTS. The authors found 77 sequence changes likely to be pathogenic: 21 null mutations (15 novel), 55 missense changes (26 novel), and one deletion of a consensus glycosylation site (also novel). Fifty-two patients with Stargardt macular degeneration (44% of those screened) and five with CRD each had two of these sequence changes or were homozygous for one of them. Segregation analyses in the families of 19 of these patients were informative and revealed that the index cases and all available affected siblings were compound heterozygotes or homozygotes. The authors found one instance of an apparently de novo mutation, Ile824Thr, in a patient. Thirty-seven (31%) of the 118 patients with Stargardt disease and one with CRD had only one likely pathogenic sequence change. Twenty-nine patients with Stargardt disease (25%) and two with CRD had no identified sequence changes.
CONCLUSIONS. This report of 42 novel mutations brings the growing number of identified likely pathogenic sequence changes in ABCR to approximately 250.
| Introduction |
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Recessive mutations in ABCR have been found in patients with Stargardt macular degeneration, fundus flavimaculatus, conerod degeneration (CRD; a panretinal photoreceptor degeneration with predominant loss of cone function that affects the macula early in its course) and retinitis pigmentosa (a panretinal photoreceptor degeneration usually associated with intraretinal pigmentary deposits).5 15 16 17 18 19 20 21 22 23 To date, approximately 200 mutations in ABCR have been found in patients with these diseases.
We report the results from an analysis of ABCR in 118 patients with juvenile macular degeneration and 8 with CRD.
| Materials and Methods |
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We also included eight patients with CRD in this mutation screen (five
from the Berman-Gund Laboratory, two from the Bascom Palmer Eye
Institute, and one from Schepens Retina Associates). Patients with CRD
had unaffected parents. Ophthalmoscopy revealed panretinal degeneration
affecting the macula more severely. Patients had severely reduced
full-field cone ERG amplitudes (reduced 90% or more), moderately
reduced conerod ERG amplitudes (reduced approximately 50% or more),
and markedly delayed cone implicit times (
40 msec; normal,
32
msec). Mixed conerod responses were typically 30 times larger than
cone-isolated responses in young patients with this condition.
Venous blood samples were obtained from participating patients and some of their relatives after informed consent was received. Leukocyte DNA was purified according to standard methods.
Detection of Sequence Changes
DNA samples were screened with the single-strand conformation
polymorphism (SSCP) technique for sequence changes in the 50 exons of
ABCR (primer sequences are available at a Web site provided
by the Massachusetts Eye and Ear Infirmary
http://eyegene.meei.harvard.edu/OMGI/ABCR/primers.html). Each
exon and 6 to 100 bp of flanking intron sequence were amplified from 20
ng of leukocyte DNA in 20 µl of a solution containing 20 µM dATP,
dTTP, and dGTP; 2 µM dCTP, including 0.6 µCi
[-32P]-dCTP (3000 Ci/mmol); 20 mM tris
hydrochloride (pH 8.4 or 8.6); 0.25 to 5.0 mM
MgCl2; 50 mM KCl; 0.1 mg/ml bovine serum albumin;
20 pmol of each primer; 0.25 U Taq polymerase; and 0% or
10% dimethyl sulfoxide (DMSO). Conditions for the amplification of
each exon were optimized for [MgCl2], 0% or
10% DMSO, annealing temperature, and pH. In some cases, primer sets
for two amplicons with a difference in size of at least 50 bp were
combined in the same amplification reaction mixture. Samples were
heated to 95°C for 4.5 minutes and incubated for 22 to 27 cycles of
the following temperature sequence: 30 seconds at 94°C, 30 seconds at
52°C to 60°C, and 40 seconds at 72°C. Samples underwent a final
incubation at 72°C for 5 minutes. After amplification, samples were
diluted 1:1 with a solution of 40% formamide, 5 mM EDTA, 0.05% SDS,
0.25% bromphenol blue, 0.25% xylene cyanol, and 0.5x TBE (45 mM
Tris-base, 45 mM boric acid, 1 mM disodium EDTA, pH 8.3). The
amplified DNA was heat denatured (95°C for 3 minutes), and the
resultant single-stranded fragments were separated by gel
electrophoresis through 6% polyacrylamide TBE gels, with or without
10% glycerol or through a 5% polyacrylamide gel with TME (30 mM tris,
35 mM 2-[N-morpholino]ethanesulfonic acid, and 1 mM
EDTA)24
at 8 to 16 W for 8 to 16 hours. Gels were
transferred to Whatman paper (Whatman, Inc., Clifton, NJ), dried, and
analyzed by autoradiography. DNA fragments that migrated at rates
different from wild-type fragments were evaluated by direct genomic
sequencing, according to standard methods.
Individuals without a history of retinal degeneration or blood relatives without retinal degeneration were used as control subjects. Normal control subjects were screened for every likely pathogenic sequence change found in at least 6 of the 126 patients screened.
Neutral and intron sequence changes not affecting the canonical splice-acceptor or splice-donor sites were analyzed for their likelihood of creating or destroying splice sites, by using the neural network software that is available at a Web site provided by the Berkeley Drosophila Genome Project, University of California, Berkeley (www.fruitfly.org/seq_tools/splice.html).25
| Results |
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C as a likely null mutation, although
it may only reduce splice donor function because the dinucleotide GC is
occasionally found as a splice donor in some genes.
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A rarely encountered missense change, Ala1637Thr, was interpreted as nonpathogenic because it was found in a patient (032-066) who also had two obviously null mutations determined to be allelic by segregation analysis, Lys356Ter and Gln1513(insC). Another change, Ala1038Val, was found in two patients (032-023 and 034-035), and in both cases segregation analysis showed that it was in cis with Leu541Pro, a combination also reported by Rivera et al.23 We interpreted Leu541Pro as pathogenic because it was found without the Ala1038Val change more frequently in patients than in control subjects. However, Sun et al.26 have shown abnormal ABCR function associated with either Ala1038Val or Leu541Pro, and it is therefore possible that both these changes are pathogenic in isolation. The remaining 49 missense changes were each found in five or fewer patients with Stargardt-CRD and were categorized as likely to be pathogenic. In all, 26 of the 55 likely pathogenic missense changes were novel.
We detected 35 isocoding substitutions and intron changes. These were all interpreted as nonpathogenic. Only one of these, Val2244Val, was predicted to possibly change a splice site. This sequence change affects the first codon of exon 49. Splice-site prediction software identifies the expected splice-acceptor site at the end of intron 48 in the wild-type sequence (probability score 0.98). This changes to a predicted splice-donor site in the mutant sequence (probability score 0.70). Despite this computer-based prediction of an effect on intron splicing, the Val2244Val change was interpreted as nonpathogenic because one of the two patients who were heterozygous for this change (032-066) also had two obvious null mutations determined to be allelic by segregation analysis.
Likely Pathogenic Sequence Changes Found in 95 of 126 Patients
Forty-nine patients with Stargardt and three with CRD had at least
two likely pathogenic sequence changes. An additional three with
Stargardt and two with CRD were homozygotes for a likely pathogenic
sequence change (Leu244Pro, Pro1380Leu, Arg1640Gln, Cys2150Tyr, or
Val1973[delG]). We conducted segregation analyses in 20 of these 57
patients families, and the results showed that the identified
sequence changes segregated as expected for pathogenic alleles (Fig. 2)
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Thirty-seven patients with Stargardt disease and one with CRD each had only one detectable sequence change that we categorized as likely to be pathogenic. There were a total of 24 unique sequence changes among these 38 patients. Five were null mutations, one was an in-frame deletion, and 18 were missense changes. Eight of the missense changes were found in at least one other index patient who was a compound heterozygote with another likely pathogenic sequence change. Of the remaining 10 missense changes, 8 affect amino acid residues that are identical in the mouse abc129 and human ABCR proteins (Table 2) . Four of these missense changes also occur in consensus sequences for functional motifs (Table 2) .
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Nucleotide 2588G
C (Gly863Ala) and Nucleotide 2828G
A
(Arg943Gln)
One likely pathogenic missense change, Gly863Ala, was frequently
associated with a presumed nonpathogenic missense change, Arg943Gln. In
fact, all 9 patients who were heterozygous carriers of Gly863Ala also
carried Arg943Gln. Maugeri et al.21
also found an
association between the Gly863Ala and Arg943Gln changes, but they were
unable to determine whether Gly863Ala by itself was pathogenic. In our
study, the Arg943Gln change was present in five other patients without
Gly863Ala, and it was present without Gly863Ala in 9 of 190 control
alleles. In addition, a recently reported evaluation of the Gly863Ala
mutant protein has shown that it has abnormal function in
vitro.26
Taken together, these results indicate that
Gly863Ala by itself is likely to be pathogenic and Arg943Gln by itself
is not.
Seven of the nine patients with Stargardt disease who were carrying Gly863Ala heterozygously also carried another missense change. Segregation analysis was conducted in the families of four of these 7 patients and the results in all four indicated that the two changes were allelic. Two patients who were heterozygous for the Gly863Ala allele had no other detectable changes likely to be pathogenic.
Nullizygosity Associated with Panretinal Degeneration
We found putative null mutations (e.g., frameshifts, nonsense
mutations, or intron splice-site alterations) in 26 (10%) of the 252
alleles screened in this study. Eleven of these patients were compound
heterozygotes with one null mutation and a second missense mutation.
All had Stargardt macular degeneration. Only four had two allelic null
mutations and all four of these patients had the diagnosis of CRD. The
ERGs recorded from three of these patients (007-014, 035-002, and
032-066 at ages 24, 21, and 19 years, respectively) showed severely
reduced cone amplitudes in response to 30-Hz flickering light (0.2,
0.4, and 6.8 µV, respectively; normal,
50 µV) and showed
moderately reduced rod-dominated amplitudes in response to single
flashes of light (129, 170, and 180 µV, respectively; normal,
350
µV). The fourth patient (032-081) declined evaluation with an ERG.
This is in contrast to patients with Stargardt disease who typically
have full-field rod and cone ERG amplitudes in the normal or
near-normal range at comparable ages.
| Discussion |
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The absence of detected mutations in 29 patients with Stargardt in our survey is not strong evidence for a second recessive Stargardt disease macular degeneration gene besides ABCR. It is more likely that we missed mutations that lie outside the regions of the gene that were screened (e.g., intron sequence far from flanking exons, the promoter region and the 5' and 3' untranslated regions) or that the SSCP mutation screening technique failed to detect some mutations, especially large deletions or insertions that encompass one or both primer sites used for a PCR amplification. Furthermore, we conducted a search for examples of Stargardt macular degeneration not linked to the ABCR locus. Of the 29 index patients with no detected ABCR mutations, only one (032-070) had both an affected sibling who was willing to participate in our research and an informative polymorphism in the ABCR gene. The index patient and the affected sibling had identical ABCR alleles (data not shown). Thus, even in this multiplex family with Stargardt macular degeneration and no identified ABCR mutations, segregation analysis was consistent with ABCR being the disease locus.
The criteria we and others used to classify sequence variants as "likely" to be pathogenic are not perfect. It is possible that some of the likely pathogenic mutations, especially the missense changes, are nonpathogenic. In addition, because segregation analysis was not always possible or was not always informative, some of the patients with two likely pathogenic changes may not be compound heterozygotes but rather may have a complex allele with both changes in cis. Some of the missense mutants previously associated with Stargardt macular degeneration are reported to have abnormal adenosine triphosphatase (ATPase) activity stimulated by all-trans retinal in vitro.26 It is not yet clear whether this assay reliably distinguishes pathogenic missense variants from those that are nonpathogenic.
Of the eight patients carrying Gly863Ala reported by Maugeri et al.,21 five were compound heterozygotes with a null mutation affecting the other allele. This led to speculation that the Gly863Ala sequence change is only pathogenic when present in compound heterozygotes who also carried a null allele. However, none of our patients with this change had a detected null allele. Rather, seven had another missense change and two had no other detectable changes likely to be pathogenic.
ABCR mutations have been reported to cause a spectrum of vision disorders including Stargardt macular degeneration, CRD, and atypical retinitis pigmentosa.15 16 17 18 19 20 21 27 Maugeri et al.21 and others have proposed a model in which two ABCR alleles with severe (null) mutations result in a visual disorder with features that are more severe than typical Stargardt macular degeneration and that they have called atypical retinitis pigmentosa. According to this model, compound heterozygosity for a severe (null) and a moderately severe mutation causes CRD, whereas two moderately severe mutations or a mild and a severe allele together cause Stargardt macular degeneration. Our findings support this model because all four patients with allelic null mutations (035-002, 032-066, 032-081, and 007-014) whom we encountered had CRD, a panretinal degeneration much more severe than typical Stargardt macular degeneration. A fifth patient with CRD (032-030) was homozygous for the missense change Arg1640Gln and a sixth patient (007-009) had the missense change Gly2146Asp and no other sequence changes that we were able to detect. (The two remaining patients with CRD had no detected ABCR mutations.) Although we have determined that all six of these patients have CRD, the late stages of CRD can have fundus features and extinguished ERGs that are indistinguishable from the late stages of retinitis pigmentosa. Therefore, it may be clearer to consider together in one category both CRD and atypical retinitis pigmentosa caused by severe or null ABCR mutations.
| Acknowledgements |
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| Footnotes |
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Submitted for publication January 3, 2001; revised April 25, 2001; accepted May 25, 2001.
Commercial relationships policy: N.
The publication costs of this article were defrayed in part by page
charge payment. This article must therefore be marked
"advertisement" in accordance with 18 U.S.C.
1734
solely to indicate this fact.
Corresponding author: Thaddeus P. Dryja, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114. dryja{at}helix.mgh.harvard.edu
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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 64,1024-1035[Medline][Order article via Infotrieve]
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