The Spectrum of CHM Gene Mutations in Choroideremia and Their Relationship to Clinical Phenotype

Abstract

PurposeWe report the underlying genotype and explore possible genotypic-phenotypic correlations in a large cohort of choroideremia patients.MethodsWe studied prospectively a cohort of 79 patients diagnosed within a tertiary referral service for patients with retinal dystrophies. Phenotypic evaluation consisted of clinical examination, including visual acuity and residual retinal area by fundus autofluorescence (FAF). Genotype was established by sequencing. We also investigated whether particular genotypes were associated with more severe phenotypes by performing analysis of covariance (ANCOVA), with visual acuity and FAF as the dependent variables and age as the covariant.ResultsA total of 74 (94%) of patients in our cohort had causative mutations by sequencing, the majority of which were anticipated to be null. Of these, 35 (47%) had insertions and deletions, 13 (18%) had mutations predicted to affect splicing, and 26 (35%) had single point mutations. In the latter case, 13 of 21 (62%) pedigrees with single point mutations were C to T transitions at C-phosphate-G (CpG) dinucleotides. These mutations were spread across 5 of only 24 CpG dinucleotides in the entire CHM cDNA. Furthermore, these 5 locations are the only sites at which C to T transitions result in a stop codon. No clear evidence was found for genotype–phenotype correlation except in the instance of a patient with a large deletion involving neighbouring sequences.ConclusionsIn patients with a diagnosis of choroideremia made by a specialty service, there is a high likelihood of establishing a genetic diagnosis. The majority of causative mutations appear to be null and, therefore, may benefit from gene replacement therapy. A disproportionate number of single point mutations observed were C to T transitions, consistent with the evolutionary decay of CpG dinucleotides through methylation and subsequent deamination. Hence, the development of choroideremia in such patients may represent the unwanted consequence of human evolution; de novo mutations are predicted to arise at these sites in future generations. (ClinicalTrials.gov number, NCT01461213.)

Novel non‐contiguous exon duplication in choroideremia

“…Detailed assessment of choroideremia patients with missense variants vs those with absent REP1 is not suggestive of phenotypic differences in these cohorts . However, the impact of residual mutant REP1 expression on clinical outcome in the context of gene therapy remains to be assessed, with suggestions that interference could impact success rates .…”

“…The majority of disease‐associated mutations in CHM result in a loss of detectable REP1 and include whole and partial deletions of the gene, and single nucleotide variants leading to premature termination of protein translation through a variety of mechanisms . Mutations maintaining the CHM reading frame are rare; however, missense variants predicted to result in decreased protein stability, as well as variants leading to in‐frame exon skipping have also been reported …”

“…2 The majority of disease-associated mutations in CHM result in a loss of detectable REP1 and include whole and partial deletions of the gene, and single nucleotide variants leading to premature termination of protein translation through a variety of mechanisms. [3][4][5][6] Mutations maintaining the CHM reading frame are rare; however, missense variants predicted to result in decreased protein stability, as well as variants leading to in-frame exon skipping have also been reported. 3,5 Here, we present a novel CHM variant identified in a male patient with typical choroideremia consisting of 2 non-contiguous duplications that has been further characterized at the RNA level by reverse transcription-polymerase chain reaction (RT-PCR).…”

Single-base substitutions in theCHMpromoter as a cause of choroideremia

“…The region implicated amounts to less than 3% of the length of the CHM coding sequence where the large majority of reported causative mutations have been found (Fokkema et al., ). A recent investigation of a large disease cohort (74) found causative mutations in the gene in 94% of the cases previously diagnosed with CHM (Simunovic et al., ). The remaining 6% can be understood to be comprising regulatory mutations, incorrect diagnoses, or deep intronic variant causing cryptic splicing (Carss et al., ).…”

“…The mutation spectrum includes transitions and transversions leading to protein truncation, splice defects, indels, and large deletions ranging from a single exon to the full gene. Missense mutations predicted to alter protein structure or impair function (Esposito et al., ; Sergeev et al., ), transposon insertions (van den Hurk et al., ), partial gene duplications (Chi, MacDonald, & Hume, ; Simunovic et al., ), and other variations are infrequently found, but taken collectively, almost all known pathogenic variants in the CHM gene have been loss‐of‐function mutations that abolish functional REP‐1 (McTaggart et al., ; Simunovic et al., ). Notably, there is no apparent correlation between genotype and phenotype, with the age at onset of symptoms, visual acuity, and visual fields being unrelated to mutation type (Freund, Sergeev, & MacDonald, ; Simunovic et al., ).…”