Characterization of RP1L1, a highly polymorphic paralog of the retinitis pigmentosa 1 (RP1) gene

Retinitis pigmentosa (RP) is a genetically heterogeneous inherited retinal degeneration which affects approximately 1 of 3,500 people worldwide. Individuals affected with retinitis pigmentosa exhibit night blindness, followed by a progressive reduction of visual field, which usually culminates in legal or complete blindness. Reduced or absent electroretinogram (ERG) and bone spicule-like pigmentary deposits accompany these symptoms Despite the large number of recent disease gene discoveries, much work still remains to completely understand the genetics of retinitis pigmentosa. Mutation analysis of the known disease-associated genes fails to identify mutations in at least 50% of cases and prevelences determined by linkage mapping are often inflated. For instance, despite the relatively large number of families originally mapped to the RP10 locus, mutations in the RP10 gene, IMPDH1, appear to account for less than 5% of adRP cases (unpublished data). The RP11 locus, estimated to be responsible for approximately 20% of adRP cases, also shows less than predicted mutation frequencies One strategy that can be used to find new adRP genes is to identify candidates that have sequence similarity to known adRP genes or that share functional pathways. For instance, three of the recently identified adRP disease-associated genes, HPRP3, PRPF8, and PRPF31, encode pre-mRNA splicing factors that participate in a common pathway. Using this strategy, we decided to characterize the nearest relative of RP1, and to determine if mutations in this newly characterized gene cause adRP. Purpose: To determine the full-length sequence of a gene with similarity to RP1 and to screen for mutations in this newly characterized gene, named retinitis pigmentosa 1-like 1(RP1L1). Since mutations in the RP1 gene cause autosomal dominant retinitis pigmentosa, it is possible that mutations in RP1's most sequence similar relative, RP1L1, may also be a cause of inherited retinal degeneration. Methods: A combination of cDNA clone sequencing, RACE, and database analysis were used to determine the RP1L1 mRNA sequence and its genomic organization. PCR analysis, semi-quantitative RT PCR, and in situ hybridization were used to determine the expression pattern of RP1L1. Single-strand conformational analysis and automated sequencing were used to screen probands from 60 adRP families for potential disease-causing mutations in RP1L1. Results: The human RP1L1 gene is encoded in 4 exons, which span 50 kb on chromosome 8p. The length of the RP1L1 mRNA is large, over 7 kb, but its exact length is variable between individuals due to the presence of several length polymorphisms, including a 48 bp repeat. RP1L1 encodes a protein with a minimal length of 2,400 amino acids and a predicted weight of 252 kDa. Expression of RP1L1 is limited to the retina and appears to be specific to photoreceptors. Mutational analysis of 60 autosomal dominant retinitis pigmentosa probands revealed the presence of 38 sequence substitutions in RP1L1. Over half of these substitutions result in alteration of the RP1L1 protein, but none of these substitutions appear to be pathogenic. Conclusions: The RP1L1 gene encodes a large, highly polymorphic, retinal-specific protein. No RP1L1 disease-causing mutations were identified in any of the samples tested, making it unlikely that mutations in RP1L1 are a frequent cause of autosomal dominant retinitis pigmentosa. Additional experiments will be needed to determine if mutations in RP1L1 cause other forms of inherited retinal degeneration