Genetic Screening
In this study, probands P01 to P05 were PDE6A variants while P06 to P08 were PDE6B variants, all of them were heterozygous variants ,20 mutations sites were identified in them, including 11 missense mutations, one nonsense mutation, three splicing mutations and one delete mutation. We identified two novel variants in PDE6A,three novel mutations in PDE6B,CA4: c.243G > A;p.(Trp81*) in P01 and RHO: c.688G>A;p.(Val230Ile) in P08 are novel variants and maybe affecting the phenotype. Among them, c.401T >C;p.(Leu134Pro) variant in P06 is non- pathogenic; RHO: c.688G>A;p.(Val230Ile) is conflicting interpretations of pathogenicity;other novel variants are all pathogenic(Table 1).
Table 1 variants identified in this study
Family
|
Gene
|
Nucleotide variant
|
Protein variant
|
Polyphen
|
Mutation Taster
|
SIFT
|
PROVEN
|
VF in gnomAD
|
Previously reported
|
P01
|
PDE6A
|
c.1349T > C
|
p.(Phe450Ser)
|
Benign
|
Disease causing
|
Tolerated
|
Neutral
|
0.016%
|
Yes[11]
|
|
PDE6A
|
c.1246G > A
|
p.(Asp416Asn)
|
Probably damaging
|
Disease causing
|
Deleterious
|
Deleterious
|
NA
|
No
|
|
CA4
|
c.243G > A
|
p.(Trp81*)
|
NA
|
NA
|
NA
|
NA
|
NA
|
No
|
P02
|
PDE6A
|
c.1685G>A
|
p.(Arg562Gln)
|
Possibly damaging
|
Disease causing
|
Deleterious
|
Deleterious
|
0.0028%
|
Yes[12]
|
|
PDE6A
|
c.1407 + I G > C
|
p.?
|
NA
|
NA
|
NA
|
NA
|
0.0080%
|
Yes[13–15]
|
P03
|
PDE6A
|
c.2275 -2A > G
|
p.?
|
NA
|
NA
|
NA
|
NA
|
NA
|
Yes[16]
|
|
PDE6A
|
c.1957C > T
|
p.(Arg653*)
|
NA
|
NA
|
NA
|
NA
|
0.0028%
|
Yes[17]
|
P04
|
PDE6A
|
c.1747T > A
|
p.(Tyr583Asn)
|
Possibly damaging
|
Disease causing
|
Tolerated
|
Deleterious
|
NA
|
No
|
|
PDE6A
|
c.1651A > G
|
p.(Lys551Glu)
|
Benign
|
Disease causing
|
Deleterious
|
Deleterious
|
NA
|
Yes[12]
|
|
OPTN
|
c.1634G > A
|
p .(Arg545Gln)
|
Benign
|
Disease causing
|
Tolerated
|
Neutral
|
0.3103%
|
Yes[18, 19]
|
P05
|
PDE6A
|
c.1651A > G
|
p.(Lys551Glu)
|
Benign
|
Disease causing
|
Deleterious
|
Deleterious
|
NA
|
Yes[12]
|
|
PDE6A
|
c.285C > A
|
p.(Ser95Arg)
|
Possibly damaging
|
Disease causing
|
Deleterious
|
Deleterious
|
NA
|
Yes[12]
|
P06
|
PDE6B
|
c.401T > C
|
p.(Leu134Pro)
|
Probably damaging
|
Disease causing
|
Deleterious
|
Deleterious
|
0.0037%
|
No
|
|
PDE6B
|
c.2293G > C
|
p.(Ala765Pro)
|
Benign
|
Polymorphism
|
Deleterious
|
Neutra
|
0.04182%
|
No
|
P07
|
PDE6B
|
c.385G > A
|
p.(Glu129Lys)
|
Probably damaging
|
Disease causing
|
Deleterious
|
Deleterious
|
0.0014%
|
Yes[20]
|
|
PDE6B
|
c.1610-1612del
|
p. 537-538del
|
NA
|
NA
|
NA
|
NA
|
NA
|
No
|
P08
|
PDE6B
|
c.1467+IG > C
|
p.?
|
NA
|
NA
|
NA
|
NA
|
0.0008%
|
Yes[21]
|
|
PDE6B
|
c.2204T > C
|
p.(Leu735Pro)
|
Probably damaging
|
Disease causing
|
Deleterious
|
Deleterious
|
0.0004%
|
Yes[12]
|
|
RHO
|
c.688G>A
|
p.(Val230Ile)
|
Probably damaging
|
Disease causing
|
Tolerated
|
Neutral
|
0.0039%
|
No
|
|
ADGRA3
|
c.921-IG > A
|
p.?
|
NA
|
NA
|
NA
|
NA
|
NA
|
No
|
VF in gnomAD: the variants frequency in health population in gnomAD; NA: data not available
Novel variants and clinical findings
In P01 (Fig. 1a-d), the proband was a 12-year old man who presented with 0.4 vision in her right eye and 0.5 vision in his left eye. He was found night blindness by his parents when he was 6 years old, then ophthalmic examination revealed poor vision correction. Fundus photographs show relatively mild retinal degeneration, swelling of the nerve fiber layer causes unclear optic disc boundaries and tortuous venous of both eyes (Fig. 1a), macular foveal becomes shallower and central macular thicknesses were 296 microns in the right(Fig. 1b)(OCT date was not available in the left).
Variants of c.1246G > A;p.(Asp416Asn M2) in PDE6A gene and c.243G > A;p.(Trp81*M3) in CA4 have not been reported in RP cases previously, predict the effect of missense changes on protein structure and function (Polyphen, Mutation Taster, SIFT, PROVEN) predicted PDE6A c.1246G>A; p.( Asp416Asn) to be probably damaging, disease causing, deleterious and deleterious. Nonsense mutation in CA4: c.243G > A; p.(Trp81*) leads to a premature termination of protein translation and can causes autosomal dominant hereditary retinitis pigmentosa, it maybe pathogenic and affecting the phenotype of P01. We don’t find the variants frequency in health population of the two variants in Genome Aggregation Database (gnomAD), predicted PDE6A c.1246G>A;p.(Asp416Asn) and CA4 c.243G > A;p.(Trp81*) were the causative variants for this RP family.
In P04 (Fig. 2a-f), the proband was a 36-year old man who presented with 0.6 vision in his right eye and 0.5 vision in his left eye. Ophthalmoscopy showed extensive intraretinal pigment migrations extending from the mid-periphery equatorial region to the arcades in both eyes with extensive arterial attenuation, macular and peripapillary atrophy, only a small central foveal island was sparing(Fig. 2a). OCT images show high-density deposits on the surface of RPE layer in macula, residual intraretinal vacuoles and an entirely disrupted and atrophy of the retina and macular, the outer retinal structures are lost(Fig. 2b). Fluorescein angiographic show “bull’s eye” macular atrophy and bonespicule hyperpigmentation blocks fluorescence in large-scale of the posterior pole and spot strong fluorescence(Fig. 2c). The full-field ERG shows a decrease in rod and cone amplitude in rod response and combined rod-cone response, as well as a delayed implicit time. The 30Hz Flicker cone response also shows a decreased amplitude(Fig. 2e).
The c.1634G > A;p.(Arg545Gln) variant of OPTN has been described before with respect to open angle glaucoma and it was a benign variant[22]. So,it does not associated with the phenotype.Variants of c.1747T > A;p.(Tyr583Asn,M1)in PDE6A gene has not been reported in RP cases previously, predict the effect of missense changes on protein structure and function (Polyphen, Mutation Taster, SIFT, PROVEN) predicted it to be probably damaging, disease causing, tolerated and deleterious. We don’t find the variants frequency in health population of the two variants in Genome Aggregation Database (gnomAD), predicted DE6A c.1747T > A;p.(Tyr583Asn) was the causative variants for P04 RP family.
In P06 (Fig. 3a-e), the proband was a 42-year old woman who presented with 0.02 vision in her right eye and 0.4 vision in her left eye. Anterior segment examination show posterior subcapsular cataracts serious in left than right, so the fundus images are not clear in left eye, ophthalmoscopy showed attenuated vessels, and mid-peripheral bone-spicule pigmentation(Fig. 3a). Significant macular atrophy and exudes in outer plexus layer can been seen in right eye and serious than left, there were macular epiretinal membrane in right eye and extensive epiretinal membranes with thickened hyaloid in left eyes. The outer nuclear layer (ONL) and disruption of the ellipsoid zone (EZ) and external limiting membrane (ELM) can been seen in bilateral eye(Fig. 3b). Fluorescein angiographic show bonespicule hyperpigmentation blocks fluorescence, and the hyperfluorescent spots clearly demarcate the atrophic areas(Fig. 3c). Phenotypic differences between the two eyes illustrate that macular atrophy may significant affect vision than extensive epiretinal membranes.
Variants of c.401T > C;p.(Leu134Pro,M1) and c.2293G > C;p.(Ala765Pro,M2) in PDE6B have not been reported in RP cases previously, predict the effect of missense changes on protein structure and function (Polyphen, Mutation Taster, SIFT, PROVEN) predicted PDE6B c.401T > C;p.(Leu134Pro) to be probably damaging, disease causing, deleterious and deleterious; Missense variants of PDE6B c.2293G > C;p.(Ala765Pro) predicted to be benign, polymorphism, deleterious and neutral, the frequency of the two mutations are 0.0037% and 0.04182%, respectively in health population of the two variants in Genome Aggregation Database (gnomAD), predicted PDE6B c.401T > C;p.(Leu134Pro)were the causative variant for this RP family, but variant of c.2293G > C;p.(Ala765Pro,M2) may has no relationship with phenotype of this family.
In P07(Fig. 4a-d), the proband was a 42-year old man, anterior segment examination show posterior subcapsular cataracts in both eyes,so the fundus images are not clear, attenuated vessels, and mid-peripheral bone-spicule pigmentation(Fig. 4a). OCT images show thinning of the retinal and the ellipsoid zone (EZ) is retained only in macular area(Fig. 4b).
Variants of c.1610-1612del;p.(537-538del,M2) has not been reported in RP cases previously, the deletion causes frameshift mutation, the protein structure and function of PDE6B were changed, we don’t find the variant frequency in health population in Genome Aggregation Database (gnomAD), predicted PDE6B c.1610-1612del;p.(537-538del) was the causative variants for this RP family.
In P08(Fig. 5a-c),the proband was a 47-year old woman, fundus photographs show macular atrophy and peripapillary atrophy, attenuated vessels, and mid-peripheral bone-spicule pigmentation(Fig. 5a).
Variants of c.688G>A;p.(Val230Ile) in RHO gene and c.921-IG > A in ADGRA3
have not been reported in RP cases previously, variant of RHO is associated with autosomal dominant retinitis pigmentosa (adRP), predict the effect of missense changes on protein structure and function (Polyphen, Mutation Taster, SIFT, PROVEN) predicted RHO: c.688G>A;p.(Val230 Ile) to be probably damaging, disease causing, tolerated and neutra. The RHO variant has not been described in the literature, but affects a conserved amino acid residue and might also be relevant for the phenotype.The variants frequency in health population of the variant in Genome Aggregation Database (gnomAD) is 0.0039%, so, the variant is conflicting interpretations of pathogenicity, it maybe affecting the phenotype. The splicing mutation of ADGRA3 just has pathogenicity while exist another mutation at the same time can lead to arRP, so it was not the causative variant for this RP family.
Clinal findings of known variants
In P02 (Fig.6a-d), the proband was a 28-year old man who presented with 0.8 vision in both eyes. He had night blindness since infancy, fundus photographs show moderate retinal degeneration, retinal arteriolar attenuation (Fig.6a). OCT images of P02 show nearly normal thickness of macular and mild macular epiretinal membrane, conserved IS/OS line shorter than normal fundus(Fig.6b). .
In P03 (Fig.7a-f2),the proband was a 34-year old woman who presented with 0.3 best corrected visual acuity in both eyes (OD:-10.50DS/+2.00DC×90°, OS:-9.50DS/+1.25DC×75°). She had night blindness since infancy, the cataract surgery had done for both eyes, because of posterior capsular opacity, the fundus images can’t presented clearly. Fundus photographs show macular atrophy and an entirely disrupted ellipsoid zone in the right eye(Fig.7a), epiretinal membrane, cystoid macular edema, outer retinoschisis,lamellar macular hole in the left eye(Fig.7b), pathological myopia maybe the reason of those phenotype. Visual fields were reduced to a small central(Fig.7c). ERGs to all stimuli were not detectable(Fig.7e).
In P05 (Fig. 8a-e), the proband was a 47-year old man who presented with 0.01 vision in his right eye and HM vision in his left eye. He had night blindness since infancy, fundus photographs show gray retinal with severe chorioretinal atrophy with bone spicule pigmentation in the area from macular to the peripheral retina, compatible with macular atrophy and structure change(Fig. 8a). OCT images show macular epiretinal membrane and vitreomacular traction and an entirely disrupted ellipsoid zone in both eyes, disappearance of the foveal depression of the right eye(Fig. 8b).Fluorescein angiographic bonespicule hyperpigmentation blocks fluorescence, and the hyperfluorescent spots clearly demarcate the atrophic areas(Fig. 8c).