An A-71C substitution in a green gene at the second position in the red/green visual-pigment gene array is associated with deutan color-vision deficiency

Prevalence of Congenital Color Vision Deficiency in Southern Taiwan and Detection of Female Carriers by Visual Pigment Gene Analysis

This study aimed to investigate the prevalence of color vision deficiencies (CVDs) and determine whether carriers could be detected by analyzing the visual pigment genes. Materials and Methods: The data of students who underwent routine CVD screening using the Ishihara color test in Kaohsiung, Southern Taiwan were analyzed. Furthermore, the DNA samples of 80 randomly selected females and four obligate carriers were analyzed. The most upstream genes, downstream genes, and the most downstream genes in the red/green pigment gene arrays were amplified separately using polymerase chain reaction (PCR), and exon 5 of each gene was analyzed. The prevalence of congenital red-green CVD in this study was 3.46% in males and 0.14% in females. The PCR analysis of the first gene, downstream gene, and last gene revealed normal patterns in 73 normal cases. Seven unusual patterns were detected in two proton carriers and five deutan carriers. Among the randomly selected females, 8.8% (7/80) were CVD carriers. The prevalence of CVD among male Taiwanese students in this study was 3.46%. Female carriers of congenital CVD can be identified by molecular analysis of the visual pigment genes. The proportion of CVD carriers among the randomly selected females was 8.8%, which was slightly higher than expected and further studies are warranted.

Next-Generation Sequencing Applications for Inherited Retinal Diseases

Inherited retinal diseases (IRDs) represent a collection of phenotypically and genetically diverse conditions. IRDs phenotype(s) can be isolated to the eye or can involve multiple tissues. These conditions are associated with diverse forms of inheritance, and variants within the same gene often can be associated with multiple distinct phenotypes. Such aspects of the IRDs highlight the difficulty met when establishing a genetic diagnosis in patients. Here we provide an overview of cutting-edge next-generation sequencing techniques and strategies currently in use to maximise the effectivity of IRD gene screening. These techniques have helped researchers globally to find elusive causes of IRDs, including copy number variants, structural variants, new IRD genes and deep intronic variants, among others. Resolving a genetic diagnosis with thorough testing enables a more accurate diagnosis and more informed prognosis and should also provide information on inheritance patterns which may be of particular interest to patients of a child-bearing age. Given that IRDs are heritable conditions, genetic counselling may be offered to help inform family planning, carrier testing and prenatal screening. Additionally, a verified genetic diagnosis may enable access to appropriate clinical trials or approved medications that may be available for the condition.

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

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.

Acquired color vision deficiency

Acquired color vision deficiency occurs as the result of ocular, neurologic, or systemic disease. A wide array of conditions may affect color vision, ranging from diseases of the ocular media through to pathology of the visual cortex. Traditionally, acquired color vision deficiency is considered a separate entity from congenital color vision deficiency, although emerging clinical and molecular genetic data would suggest a degree of overlap. We review the pathophysiology of acquired color vision deficiency, the data on its prevalence, theories for the preponderance of acquired S-mechanism (or tritan) deficiency, and discuss tests of color vision. We also briefly review the types of color vision deficiencies encountered in ocular disease, with an emphasis placed on larger or more detailed clinical investigations.

A new subset of deutan colour vision defect associated with an L/M visual pigment gene array of normal order and -71C substitution in the Japanese population

In 524 Japanese individuals with deutan colour vision defect, 76 had a normal-order pigment gene array, where the L gene is at the first position and the M gene(s) is located downstream. Of these 76 individuals, 69 had a -71A>C substitution in the M gene without any other mutation. Because the expression of L/M genes is up-regulated by thyroid hormone (T3) in human retinoblastoma WERI cells, we examined the effects of T3 on promoter activity; T3 increased the activity of the -71A promoter 2-fold, but it had no effect on the -71C promoter. Similarly, the -71C promoter was much less activated by T3 than the -71A promoter in HEK293 cells expressing thyroid hormone receptor isoform β2. Such a weak response of the -71C promoter to T3 may cause a decrease in the number of M cones and/or the density of M pigment during the differentiation of M cones. The average Rayleigh match midpoint was 18.9 ± 4.1 in 162 ordinary deuteranomaly individuals, but was 37.3 ± 9.1 in 63 deuteranomaly individuals with -71C. The -71A>C substitution was found to be specific to eastern Asia. These results suggest that there may be a new subset of deuteranomaly associated with -71C in the Japanese (and probably eastern Asian) population(s).

X-linked cone dystrophy and colour vision deficiency arising from a missense mutation in a hybrid L/M cone opsin gene

In this report, we describe a male subject who presents with a complex phenotype of myopia associated with cone dysfunction and a protan vision deficiency. Retinal imaging demonstrates extensive cone disruption, including the presence of non-waveguiding cones, an overall thinning of the retina, and an irregular mottled appearance of the hyper-reflective band associated with the inner segment ellipsoid portion of the photoreceptor. Mutation screening revealed a novel p.Glu41Lys missense mutation in a hybrid L/M opsin gene. Spectral analysis shows that the mutant opsin fails to form a pigment in vitro and fails to be trafficked to the cell membrane in transfected Neuro2a cells. Extensive sequence and quantitative PCR analysis identifies this mutant gene as the only gene present in the affected subject's L/M opsin gene array, yet the presence of protanopia indicates that the mutant opsin must retain some activity in vivo. To account for this apparent contradiction, we propose that a limited amount of functional pigment is formed within the normal cellular environment of the intact photoreceptor, and that this requires the presence of chaperone proteins that promote stability and normal folding of the mutant protein.

Worldwide prevalence of red-green color deficiency

Literature that describes the prevalence of inherited red-green color deficiency in different populations is reviewed. Large random population surveys show that the prevalence of deficiency in European Caucasians is about 8% in men and about 0.4% in women and between 4% and 6.5% in men of Chinese and Japanese ethnicity. However, the male: female prevalence ratio is markedly different in Europeans and Asians. Recent surveys suggest that the prevalence is rising in men of African ethnicity and in geographic areas that have been settled by incoming migrants. It is proposed that founder events and genetic drift, rather than natural selection, are the cause of these differences.

Spectral domain optical coherence tomography and adaptive optics: imaging photoreceptor layer morphology to interpret preclinical phenotypes

Recent years have seen the emergence of advances in imaging technology that enable in vivo evaluation of the living retina. Two of the more promising techniques, spectral domain optical coherence tomography (SD-OCT) and adaptive optics (AO) fundus imaging provide complementary views of the retinal tissue. SD-OCT devices have high axial resolution, allowing assessment of retinal lamination, while the high lateral resolution of AO allows visualization of individual cells. The potential exists to use one modality to interpret results from the other. As a proof of concept, we examined the retina of a 32 year-old male, previously diagnosed with a red-green color vision defect. Previous AO imaging revealed numerous gaps throughout his cone mosaic, indicating that the structure of a subset of cones had been compromised. Whether the affected cells had completely degenerated or were simply morphologically deviant was not clear. Here an AO fundus camera was used to re-examine the retina (~6 years after initial exam) and SD-OCT to examine retinal lamination. The static nature of the cone mosaic disruption combined with the normal lamination on SD-OCT suggests that the affected cones are likely still present.

Cone photoreceptor mosaic disruption associated with Cys203Arg mutation in the M-cone opsin

Missense mutations in the cone opsins have been identified as a relatively common cause of red/green color vision defects, with the most frequent mutation being the substitution of arginine for cysteine at position 203 (C203R). When the corresponding cysteine is mutated in rhodopsin, it disrupts proper folding of the pigment, causing severe, early onset retinitis pigmentosa. While the C203R mutation has been associated with loss of cone function in color vision deficiency, it is not known what happens to cones expressing this mutant opsin. Here, we used high-resolution retinal imaging to examine the cone mosaic in two individuals with genes encoding a middle-wavelength sensitive (M) pigment with the C203R mutation. We found a significant reduction in cone density compared to normal and color-deficient controls, accompanying disruption in the cone mosaic in both individuals, and thinning of the outer nuclear layer. The C203R mosaics were different from that produced by another mutation (LIAVA) previously shown to disrupt the cone mosaic. Comparison of these mosaics provides insight into the timing and degree of cone disruption and has implications for the prospects for restoration of vision loss associated with various cone opsin mutations.

Colour vision deficiency

Colour vision deficiency is one of the commonest disorders of vision and can be divided into congenital and acquired forms. Congenital colour vision deficiency affects as many as 8% of males and 0.5% of females--the difference in prevalence reflects the fact that the commonest forms of congenital colour vision deficiency are inherited in an X-linked recessive manner. Until relatively recently, our understanding of the pathophysiological basis of colour vision deficiency largely rested on behavioural data; however, modern molecular genetic techniques have helped to elucidate its mechanisms. The current management of congenital colour vision deficiency lies chiefly in appropriate counselling (including career counselling). Although visual aids may be of benefit to those with colour vision deficiency when performing certain tasks, the evidence suggests that they do not enable wearers to obtain normal colour discrimination. In the future, gene therapy remains a possibility, with animal models demonstrating amelioration following treatment.

Protan color vision deficiency with a unique order of green-red as the first two genes of a visual pigment array

Normal visual pigment gene arrays on the human X chromosome have a red gene at the first and a green gene at the second positions. More than half of the arrays have additional green genes downstream, but only the first two genes of the array are likely to be expressed in the retina. An array consisting of four genes in two Japanese participants, A121 and A447, was detected either by pulsed field gel electrophoresis and subsequent Southern hybridization or by single nucleotide primer extension reaction. In both participants, the first gene of the array was green, downstream genes were red and green, and the fourth gene was green. The red gene was determined to be at the second position by comparison of polymorphic sites among the intergenic regions that had been amplified by long-range PCR. Such an array with a reverse normal order of pigment genes, green-red as the first two, has never been reported before. They were expected to have normal color vision but showed protan deficiency (protanomaly), a phenotype lacking the red pigment. The red gene had no mutations in the exons and exon/intron boundaries, but had an A-71C substitution in the promoter in both participants.

[Inherited colour vision deficiencies--from Dalton to molecular genetics]

In recent years, great advances have been made in our understanding of the molecular basis of colour vision defects, as well as of the patterns of genetic variation in individuals with normal colour vision. Molecular genetic analyses have explained the diversity of types and degrees of severity in colour vision anomalies, their frequencies, pronounced individual variations in test results, etc. New techniques have even enabled the determination of John Dalton's real colour vision defect, 150 years after his death. Inherited colour vision deficiencies most often result from the mutations of genes that encode cone opsins. Cone opsin genes are linked to chromosomes 7 (the S or "blue" gene) and X (the L or "red" gene and the M or "green" gene). The L and M genes are located on the q arm of the X chromosome in a head-to-tail array, composed of 2 to 6 (typically 3) genes--a single L is followed by one or more M genes. Only the first two genes of the array are expressed and contribute to the colour vision phenotype. The high degree of homology (96%) between the L and M genes predisposes them to unequal recombination, leading to gene deletion or the formation of hybrid genes (comprising portions of both the L and M genes), explaining the majority of the common red-green colour vision deficiencies. The severity of any deficiency is influenced by the difference in spectral sensitivity between the opsins encoded by the first two genes of the array. A rare defect, S monochromacy, is caused either by the deletion of the regulatory region of the array or by mutations that inactivate the L and M genes. Most recent research concerns the molecular basis of complete achromatopsia, a rare disorder that involves the complete loss of all cone function. This is not caused by mutations in opsin genes, but in other genes that encode cone-specific proteins, e.g. channel proteins and transducin.

Genetics of variation in human color vision and the retinal cone mosaic

Variation in human color vision is mainly caused by one common polymorphism (Ser180Ala) in the L pigment, and to the frequent presence of hybrid genes that encode pigments with various spectral properties. Both recombination and gene conversion between the highly homologous L and M pigment genes have generated wide variation in genotype and color vision phenotype. The S, M and L cones are distributed randomly in the central retina. Unlike S cones, M and L cones vary widely in number within the central retina. Determining the number of the three classes of cone and their special distribution in the living retina has significantly advanced the ability to correlate the cone mosaic in normal and color-defective subjects with the color vision phenotype. The transcription factors NR2E3, TRbeta2 and RXRgamma play crucial roles in establishment of the retinal cone mosaic during eye development.

The molecular basis of variation in human color vision

Common variation in red-green color vision exists among both normal and color-deficient subjects. Differences at amino acids involved in tuning the spectra of the red and green cone pigments account for the majority of this variation. One source of variation is the very common Ser180Ala polymorphism that accounts for two spectrally different red pigments and that plays an important role in variation in normal color vision as well as in determining the severity of defective color vision. This polymorphism most likely resulted from gene conversion by the green-pigment gene. Another common source of variation is the existence of several types of red/green pigment chimeras with different spectral properties. The red and green-pigment genes are arranged in a head-to-tail tandem array on the X-chromosome with one red-pigment gene followed by one or more green-pigment genes. The high homology between these genes has predisposed the locus to relatively common unequal recombination events that give rise to red/green hybrid genes and to deletion of the green-pigment genes. Such events constitute the most common cause of red-green color vision defects. Only the first two pigment genes of the red/green array are expressed in the retina and therefore contribute to the color vision phenotype. The severity of red-green color vision defects is inversely proportional to the difference between the wavelengths of maximal absorption of the photopigments encoded by the first two genes of the array. Women who are heterozygous for red and green pigment genes that encode three spectrally distinct photopigments have the potential for enhanced color vision.

Molecular genetics of color-vision deficiencies

The normal X-chromosome-linked color-vision gene array is composed of a single long-wave-sensitive (L-) pigment gene followed by one or more middle-wave-sensitive (M-) pigment genes. The expression of these genes to form L- or M-cones is controlled by the proximal promoter and by the locus control region. The high degree of homology between the L- and M-pigment genes predisposed them to unequal recombination, leading to gene deletion or the formation of L/M hybrid genes that explain the majority of the common red-green color-vision deficiencies. Hybrid genes encode a variety of L-like or M-like pigments. Analysis of the gene order in arrays of normal and deutan subjects indicates that only the two most proximal genes of the array contribute to the color-vision phenotype. This is supported by the observation that only the first two genes of the array are expressed in the human retina. The severity of the color-vision defect is roughly related to the difference in absorption maxima (lambda(max)) between the photopigments encoded by the first two genes of the array. A single amino acid polymorphism (Ser180Ala) in the L pigment accounts for the subtle difference in normal color vision and influences the severity of red-green color-vision deficiency. Blue-cone monochromacy is a rare disorder that involves absence of L- and M-cone function. It is caused either by deletion of a critical region that regulates expression of the L/M gene array, or by mutations that inactivate the L- and M-pigment genes. Total color blindness is another rare disease that involves complete absence of all cone function. A number of mutants in the genes encoding the cone-specific alpha- and beta-subunits of the cGMP-gated cation channel as well as in the alpha-subunit of transducin have been implicated in this disorder.

Variety of genotypes in males diagnosed as dichromatic on a conventional clinical anomaloscope

The hypothesis that dichromatic behavior on a clinical anomaloscope can be explained by the complement and arrangement of the long- (L) and middle-wavelength (M) pigment genes was tested. It was predicted that dichromacy is associated with an X-chromosome pigment gene array capable of producing only a single functional pigment type. The simplest case of this is when deletion has left only a single X-chromosome pigment gene. The production of a single L or M pigment type can also result from rearrangements in which multiple genes remain. Often, only the two genes at the 5' end of the array are expressed; thus, dichromacy is also predicted to occur if one of these is defective or encodes a defective pigment, or if both of them encode pigments with identical spectral sensitivities. Subjects were 128 males who accepted the full range of admixtures of the two primary lights as matching the comparison light on a Neitz or Nagel anomaloscope. Strikingly, examination of the L and M pigment genes revealed a potential cause for a color-vision defect in all 128 dichromats. This indicates that the major component of color-vision deficiency could be attributed to alterations of the pigment genes or their regulatory regions in all cases, and the variety of gene arrangements associated with dichromacy is cataloged here. However, a fraction of the dichromats (17 out of 128; 13%) had genes predicted to encode pigments that would result in two populations of cones with different spectral sensitivities. Nine of the 17 were predicted to have two pigments with slightly different spectral peaks (usually < or = 2.5 nm) and eight had genes which specified pigments identical in peak absorption, but different in amino acid positions previously associated with optical density differences. In other subjects, reported previously, the same small spectral differences were associated with anomalous trichromacy rather than dichromacy. It appears that when the spectral difference specified by the genes is very small, the amount of residual red-green color vision measured varies; some individuals test as dichromats, others test as anomalous trichromats. The discrepancy is probably partly attributable to testing method differences and partly to a difference in performance not perception, but it seems there must also be cases in which other factors, for example, cone ratio, contribute to a person's ability to extract a color signal from a small spectral difference.

Modeling color percepts of dichromats

Protanopes and deuteranopes, despite lacking a chromatic dimension at the receptor level, use the color terms "red" and "green", together with "blue" and "yellow", to describe their color percepts. Color vision models proposed so far fail to account for these findings in dichromats. We confirmed, by the method of hue scaling, the consistent use of these color terms, as well as their dependence on intensity, in subjects shown to have only a single X-chromosomal opsin gene each. We present a model for the processing of photoreceptor signals which, under physiologically plausible assumptions, achieves a trichromat-like representation of dichromatic receptor signals. Key feature of the dichromat model is the processing of the photoreceptor signals in parallel channels with different gains and nonlinearities. In this way, the two-dimensional receptor signals are represented on a manifold in a higher-dimensional space, supporting categorization for efficient image segmentation. Introducing a third cone opsin yields a model that explains normal, trichromat hue scaling.

An insertion/deletion TEX28 polymorphism and its application to analysis of red/green visual pigment gene arrays

TEX28 gene (fTEX) is present immediately downstream of the red/green visual pigment gene array on the human X chromosome. Its pseudogene (pTEX) that lacks exon 1 is present within the array between pigment genes. We found that both fTEX and pTEX genes had a 697 bp insertion/deletion polymorphism in their introns 3. In color-normal male subjects, the frequency of the 697 bp region was 43% (40/94) in pTEX and 97% (91/94) in fTEX in the array of Red-pTEX-Green-fTEX and 10% (9/94) in pTEX and 87% (41/47) in fTEX in the array of Red-pTEX-Green-pTEX-Green-fTEX. These results suggest that normal arrays with multiple green genes may have arisen through gene duplication rather than unequal homologous crossover. In color-vision-deficient male subjects with a single-gene array, the frequency of the 697 bp region was 83% (25/30) in the array of Green-fTEX and 66% (74/112) in the array of Red-fTEX. In color-vision-deficient male subjects with a 2-gene array, the frequency of the region was 44% (16/36) in pTEX and 97% (35/36) in fTEX in the array of Green-pTEX-Green-fTEX and 75% (18/24) in pTEX and 92% (22/24) in fTEX in the array of Red-pTEX-Red-fTEX. These results suggest that 2-green-gene arrays have arisen through unequal homologous crossover between a normal 2-gene array and a single-green-gene array. With data from a long-range PCR method using the insertion/deletion polymorphism, we proposed a structure of the second gene of 3-gene arrays, Green-pTEX-Green-pTEX-Green-fTEX and Red-pTEX-Red-pTEX-Red-fTEX, in color-vision-deficient subjects.

Analysis of L-cone/M-cone visual pigment gene arrays in Japanese males with protan color-vision deficiency

The L-cone/M-cone visual pigment gene arrays were analyzed in 125 Japanese males with protan color-vision deficiency. Arrays were successfully determined in 62/65 subjects with protanopia and 57/60 protanomaly subjects. Among the 62 protanopia subjects, 48 (77%) had an array consisting of a single 5' L-M hybrid gene (PS-array) or a 5' L-M hybrid gene followed by an M gene(s) that was structurally identical to the hybrid gene (PI-array). In the remaining 14 subjects, 11 had an array consisting of a 5' L-M hybrid gene followed by an M gene(s) that was structurally different from the hybrid gene (PD-array) and 3 subjects had an apparently normal array consisting of a single L gene followed by an M gene(s) (PN-array). In the 11 subjects with the PD-array, subject A67 had an 11 bp-deletion in exon 3 of the downstream genes and 6 had an A-71C substitution in the second gene of the array. In the 3 subjects with the PN-array, subject A289 had a missense mutation (Pro231Leu) in exon 4 of the L gene. When the function of the missense mutation was studied by in vitro reconstitution of visual pigments, it was found to be deleterious to both cone opsin and rhodopsin. Among the 57 protanomaly subjects, 49 (86%) had the PD-array, but 25 subjects had a difference only in exon 2 between the first and downstream genes that suggested a contribution of exon 2-encoded difference in the M pigment to color-discrimination. In the remaining 8 subjects, 2 had the PS-array, 2 had the PI-array and the other 4, including subject A89 with a missense mutation (Glu338Gly) in the L gene, had the PN-array. Genotype-phenotype relationships in protan color-vision deficiency are discussed.

Functional photoreceptor loss revealed with adaptive optics: an alternate cause of color blindness

There is enormous variation in the X-linked L/M (long/middle wavelength sensitive) gene array underlying "normal" color vision in humans. This variability has been shown to underlie individual variation in color matching behavior. Recently, red-green color blindness has also been shown to be associated with distinctly different genotypes. This has opened the possibility that there may be important phenotypic differences within classically defined groups of color blind individuals. Here, adaptive optics retinal imaging has revealed a mechanism for producing dichromatic color vision in which the expression of a mutant cone photopigment gene leads to the loss of the entire corresponding class of cone photoreceptor cells. Previously, the theory that common forms of inherited color blindness could be caused by the loss of photoreceptor cells had been discounted. We confirm that remarkably, this loss of one-third of the cones does not impair any aspect of vision other than color.