|Molecular Vision 2007;
Received 26 June 2006 | Accepted 28 March 2007 | Published 5 April 2007
Low prevalence of LRAT mutations in patients with Leber congenital amaurosis and autosomal recessive retinitis pigmentosa
Meredith O. Sweeney, Terri L. McGee, Eliot L. Berson,
Thaddeus P. Dryja
Ocular Molecular Genetics Institute and the Berman-Gund Laboratory for the Study of Retinal Degenerations, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, MA
Correspondence to: Thaddeus P. Dryja, Massachusetts Eye and Ear Infirmary, 243 Charles Street, Boston, MA 02114; Phone: (617) 573-3319; FAX: (617) 573-3168; email: email@example.com
Purpose: To determine the the prevalence of pathogenic mutations in the gene encoding lecithin retinol acyltransferase (LRAT) in patients from North America with either Leber congenital amaurosis (LCA) or autosomal recessive retinitis pigmentosa (ARRP).
Methods: Exon 1, exon 2, and the coding region of exon 3 of LRAT were PCR-amplified and directly sequenced from the leukocyte DNA of 82 unrelated patients with LCA and 190 unrelated patients with ARRP.
Results: One isocoding change was found in this screen of LRAT (Glu114 GAG>GAA; c.342), and 5 other sequence changes were found in intronic or untranslated regions of the gene. None of these changes were predicted to affect the encoded protein and were therefore deemed non-pathogenic.
Conclusions: LRAT mutations are likely a rare cause of LCA among patients from North America.
Lecithin retinol acyltransferase (LRAT), a 25.3 kDa protein found mainly in the retinal pigment epithelium and liver, catalyzes the formation of retinyl esters from all-trans retinol . In the visual cycle, these retinyl esters are converted to 11-cis retinol by the isomerase activity of RPE65 . The 11-cis retinol is subsequently converted to 11-cis retinaldehyde which is transferred to the photoreceptors where it serves as the chromophore in rod and cone opsins .
Two groups have reported a total of four patients with LRAT mutations. One found a missense mutation, Ser175Arg, in two unrelated homozygote patients with recessive early-onset severe retinal dystrophy . Analysis of the corresponding mutant LRAT protein expressed in vitro showed that it had greatly reduced enzyme activity . The same paper also described an obviously null frameshift mutation (396delAA) in a third patient who was a heterozygote with no mutation discovered in the other allele . The second group found a patient with Leber congenital amaurosis (LCA) posessing a homozygous frameshift mutation (c.217_218delAT), which results in an early stop codon and likely would encode a nonfunctional protein . Support for interpreting these null mutations as the causes of the patients' retinal degeneration comes from the analysis of transgenic mice lacking this gene; these mice have shortened photoreceptor outer segments and early loss of rod and cone photoreceptor function [6,7].
The term "early-onset severe retinal dystrophy" , can refer to either LCA or severe autosomal recessive retinitis pigmentosa (ARRP). Both LCA and ARRP are genetically heterogenous and many of the responsible genes remain unidentified. In order to better determine the proportion of patients with LCA or ARRP having mutations in LRAT, we performed a survey of patients with the clinical diagnosis of LCA and ARRP to find the prevalence of LRAT mutations associated with these two retinal diseases.
This study conformed to the Declaration of Helsinki. We evaluated leukocyte DNA from 82 unrelated patients with LCA and 190 unrelated patients with ARRP. Our patients with LCA typically had nystagmus and visual acuities less than 20/200, while those with ARRP typically had no nystagmus and vision better than 20/200 at the initial visit. Many of these patients had been previously evaluated for mutations in the PDE6A , PDE6B , CRX , RPE65 , ELOVL4 , CNCG1 , USH2A , NRL , RPGRIP , USH3A , RHO , RDS , RDH5 , CRALBP , and RGR  genes; patients with definitely pathogenic mutations in one of those genes were excluded from this study. For each patient, the coding region of LRAT along with flanking intronic sequences, the entire 5' untranslated region (UTR), and 129 bp of the 3' UTR were PCR-amplified using 4 pairs of primers (Table 1). The amplicons were directly sequenced in one direction. Any sequence changes found were confirmed by sequencing in the opposite direction and were evaluated for their likelihood in altering splicing of the LRAT transcript using splice site prediction software found at the web site NNSPLICE 0.9 version .
We found six sequence variants in LRAT in eleven ARRP patients and two LCA patients (Table 2). Most of the changes were in introns or in untranslated regions of the exons. The only change in the coding region was an isocoding change in codon Glu114 (GAG>GAA; c.342) found in two LCA patients (all heterozygotes) and in five ARRP patients (4 heterozygotes and one homozygote), for a rare allele frequency overall of 1.5%. Splice site prediction software indicated that none of these changes were likely to alter RNA splicing (the splicing index was changed less than or equal to 0.01 compared to the normal sequence).
Of the 6 sequence changes we found in LRAT, only one was found in the coding region, and that was the isocoding change in Glu114. Another group found this change in one ARRP patient, in one patient with macular degeneration, and in one patient with cone-rod dystrophy, all heterozygotes . Furthermore, that same study found Glu114Glu in an unaffected homozygote . Three previous studies by other groups also found the Glu114Glu change [4,5,25]. It was interpreted as a nonpathogenic polymorphism because it was found in 2.5% of alleles in retinal dystrophy patients, 2.7% of alleles in RP and flecked retinal dystrophy patients, and 3% of alleles in LCA patients analyzed; these allele frequencies are similar to the frequency of 1.5% found in our survey [4,5,25]. (Note: in the paper by Perrault et al. , this polymorphism was incorrectly labeled as Ser175Pro (unpublished communication from the authors)). The other changes we found are also unlikely to be pathogenic since they occur in introns away from consensus splice donor and acceptor sites or in the non-coding regions of exons; none is predicted to affect splicing.
Table 3 summarizes the results from 30 published studies (including this one) that describe searches among nine or more patients for mutations in eleven genes known to cause LCA (or early-onset retinal dystrophy which we have grouped together with LCA for this table). The two genes that account for the largest proportions of cases are CEP290 (21% of cases overall) encoding a centrosomal protein and GUCY2D encoding guanylate cyclase (13% of cases). Figure 1 is a pie chart with the estimated proportions of LCA patients caused by each gene based on these 30 studies. It is noteworthy that approximately a quarter of all patients with LCA likely have responsible mutations in genes that remain unidentified.
Table 3 lists three studies that analyzed LRAT in a combined total of 314 LCA patients. No patients with LRAT mutations were found. Nevertheless, there are 4 reported LCA patients with pathogenic LRAT mutations [4,5]. Thompson et al.  reported 3 unrelated LCA patients with LRAT mutations, but this paper is not included in Table 3 because the number of LCA patients evaluated was not provided. Senechal et al.  reported one patient with LCA due to LRAT, but this report was also not included in Table 3 because only one LCA patient was evaluated. Based on these reports and the studies such as ours that found no LCA patients with LRAT mutations, it is clear that LRAT mutations account for a very small percentage of LCA cases. In Figure 1, we have arbitrarily set the percentage at 1%.
Our not finding mutations in a set of 190 unrelated patients with ARRP indicates that LRAT is not a common cause of that disease as well. Furthermore, Ruiz et al. (2001)  found no pathogenic mutations in 91 patients with retinitis pigmentosa, 58 patients with cone-rod dystrophy, or 93 patients with age-related macular degeneration. Senechal et al. (2006)  also found no pathogenic LRAT mutations in 134 patients with simplex or multiplex retinitis pigmentosa or in 82 patients with flecked retinal dystrophy. Based on our large survey together with the surveys in the literature, one may confidently conclude that LRAT-caused retinal degeneration is very rare. This rarity can have implications for the development of therapies for patients with this condition. Efficacy studies for proposed therapies may have to be based on results from only a few patients or based on results from similar therapies developed for patients with other defects in the vitamin A cycle affecting the RPE.
This study was supported by the Foundation for Fighting Blindness and grants EY00169, P30 EY014104, and EY08683. It was presented in part at the 2006 ARVO annual meeting in Fort Lauderdale, Florida.
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