Genotype determination of the OPN1LW/OPN1MW genes: novel disease-causing mechanisms in Japanese patients with blue cone monochromacy

Abstract

Blue cone monochromacy (BCM) is characterized by loss of function of both OPN1LW (the first) and OPN1MW (the downstream) genes on the X chromosome. The purpose of this study was to investigate the first and downstream genes in the OPN1LW/OPN1MW array in four unrelated Japanese males with BCM. In Case 1, only one gene was present. Abnormalities were found in the promoter, which had a mixed unique profile of first and downstream gene promoters and a −71A > C substitution. As the promoter was active in the reporter assay, the cause of BCM remains unclear. In Case 2, the same novel mutation, M273K, was present in exon 5 of both genes in a two-gene array. The mutant pigments showed no absorbance at any of the wavelengths tested, suggesting that the mutation causes pigment dysfunction. Case 3 had a large deletion including the locus control region and entire first gene. Case 4 also had a large deletion involving exons 2–6 of the first gene. As an intact LCR was present upstream and one apparently normal downstream gene was present, BCM in Case 4 was not ascribed solely to the deletion. The deletions in Cases 3 and 4 were considered to have been caused by non-homologous recombination.

Blue Cone Monochromatism with Foveal Hypoplasia Caused by the Concomitant Effect of Variants in OPN1LW/OPN1MW and GPR143 Genes

“…The high degree of sequence homology made the analysis difficult, especially for the OPN1MW gene. The OPN1LW, OPN1MW, and GPR143 (NM_000273.3) variants were confirmed in the patient and his mother by Sanger sequencing, the formers by a long-range PCR protocol as previously reported by Katagiri et al [19].…”

“…The variant has been classified by American College of Medical Genetics and Genomics (ACMG) guidelines [18], with the help of the online software VarSome (https://varsome.com/ accessed on 4 May 2021) as a variant of unknown significance (VUS) according to these scores: PM2, variant not found in gnomAD exomes; PP3, pathogenic computational verdict based on 9 pathogenic predictions from BayesDel_addAF, DANN, FATHMM-MKL, LIST-S2, M-CAP, MVP, MutationTaster, PrimateAI, and SIFT vs. no benign predictions. The patient also presented the common missense mutation c.607T > C (p.Cys203Arg) in the OPN1MW gene, an already described variant causing deutan color vision deficiency when present in the M gene [19], and the c.768-2_769delAGTT splicing variant in the GPR143 gene, known as being related to ocular albinism type I (OMIM # 300500) and X-linked congenital nystagmus-6 (OMIM # 300814) [20], both in hemizygous status and inherited from the mother.…”

Next-Generation Sequencing Applications for Inherited Retinal Diseases

“…In this condition, a c. −71A>C promoter mutation was initially thought to decrease expression and cause a deutan colour vision deficiency. However, after functional analyses, the mutation was revealed to result in more than double the wild-type expression level of the gene [113]. Other deletions in this area have also been shown to result in BCM phenotypes, suggesting that this gene is sensitive to alterations in both under and overexpression [114,115].…”

Whole Genome Sequencing, Focused Assays and Functional Studies Increasing Understanding in Cryptic Inherited Retinal Dystrophies

“…There are multiple IRD disease genes which are unable to be fully interrogated using targeted capture based sequencing approaches. Significant disease associated loci such as the repetitive GC-rich RPGR ORF15 region and the highly homologous opsin gene array within chromosome Xq28 are currently poorly covered in CES and WES strategies alone, requiring additional separate focused assays for analysis [ 13 , 25 , 26 ]. Moreover, there are other IRD disease genes where a significant proportion of pathogenic alleles lie within intronic or non-coding regions such as ABCA4 [ 27 ] and the PRDM13 associated North Carolina Macular Dystrophy locus [ 28 ].…”