Case#: Case report, 11 year old, female, Korean

CaseHPOs: HP:0007663, HP:0000603, HP:0025010, HP:0000551 (reduced visual acuity, bilateral central scotoma, foveal atrophy, severe color vision deficiency)

CaseHPOsFreeText: Onset at 4 years old. BCVA in both eyes were 20/40, 20/50, and 20/100 at 4, 10, and 11 years, respectively. Cycloplegic refraction showed –0.5 D spherical error with astigmatism of –3.0 D cylindrical error in the right eye, and –1.0 D spherical error with astigmatism of –3.5 D cylindrical error in the left eye. The fundus examination showed slightly atrophic fovea (Figure 1A). Fundus autofluorescence showed hyperfluorescent fovea in both eyes, which may be an artifact (Figure 1A). SD-OCT showed an ellipsoid zone defect in both macular areas with an intact periphery (Figure 1A). Light-adapted 3 ERG and 30 Hz flicker ERG showed almost extinguished wave, while dark-adapted 0.01 ERG and 3 ERG also showed reduced amplitude (Figure 1B). Diagnosis – Cone Rod dystrophy

CasePreviousTesting: As part of this study - No pathogenic variants were identified in the other 97 genes associated with retinal degeneration, including 8 genes known to be associated with AR-CRD (ABCA4, ADAM9, C8orf37, CERKL, EYS, PROM1, RPGRIP1, and TULP1).

CaseMethod1: NGS

CaseGenotypingMethod: NGS of 98 genes known to be associated with inherited retinal degenerations (including cone-rod dystrophy), with confirmation of the identified variant by Sanger sequencing.

Variant: NM_004249.3:c.68C>T (p.Ser23Phe), homozygous

ClinVar: N/A

CAID: CA2860239

gnomAD: The highest population minor allele frequency in gnomAD v2.1.1 is 0.0004158 in the East Asian population; no homozygotes in any population.

VariantEvidence: 3D structures of the wild type and mutated RAB28 proteins, predicted using SWISS-MODEL, showed the p.Ser23Phe variant is located in the GTP binding region. Multiple in silico predictors, including SIFT, PolyPhen, CADD, suggest that the variant is damaging.

CaseAddInfo: Parents are not related. Parents and male sibling had normal vision and fundus findings and all were heterozygous for the RAB28 variant.

FamilyInfo: Family A, German, Pedigree in Fig 1

FamilyHPOs: HP:0007663, HP:0011003, HP:0008001, HP:0030602, HP:0000551, HP:0000603, HP:0000512 (reduced visual acuity, high myopia, foveal hyperpigmentation, hyperfluorescent fovea, color vision defect, central scotoma, abnormal ERG)

FamilyHPOFreeText: All 3 affected family members were diagnosed with CRD in the second decade of life. Optical coherence tomography (OCT) displayed altered photoreceptors in the fovea, whereas the peripheral photoreceptors are intact (Figure 2C, and 2A, 2B). On ERG photopic responses were nondetectable and scotopic responses reduced in all three siblings.

FamilyMethod1: Homozygosity mapping

FamilyMethod2: WES

FamilyGenotypingMethod: Homozygosity mapping, using Affymetrix GeneChip Human Mapping 250K SNP arrays, in 3 affected siblings revealed a shared homozygous region of 4.68 Mb on chromosome 4 containing 15 genes. Subsequently, exome sequencing was performed in 2 of the affected sibling, A-II:1 and A-II:2. No pathogenic variants in the genes known to be mutated in arCRD (ABCA4, ADAM9, C8orf37, CERKL, EYS, RPGRIP1, and TULP1) were observed among the shared variants. RAB28 variant confirmed by Sanger sequencing.

Variant: NM_001017979.2:c.565C>T (p.Glu189Ter), homozygous, (all 3 affected individuals are homozygous, parents not tested)

ClinVar: 60754

gnomAD: Not in gnomAD.

Proband: A-II:1, 14 years at diagnosis, 28 years at last visit, German

CaseHPOsFreeText: Refractive error OD -16D SE, OS -15.5D SE; visual acuity OD 20/320 OS 20/200; hyperpigmented foveal region; autofluorescence showed hyperfluorescent area at foveal region; OCT showed irregular inner and outer segments in fovea, thinning of other retinal layers of fovea; color vision using D-15 Panel showed tritan and defects in scotopic lines; visual field showed concentric reduction to 15–20 degrees (III/4); ERG at age 16 revealed nondetectable cone function and reduced rod responses.

Case#: Patient 5, male, 16 years (at report)

CaseHPOs: HP:0000613, HP:0007663, HP:0000551 (photophobia, reduced visual acuity, color vision defect)

CaseHPOsFreeText: Poor vision and photophobia since the age of 4. BCVA was 0.4 LogMAR in right eye and 0.52 LogMAR in left eye with a refractive error of −5.75 sph −3.00 cyl/15° D in right eye and of −6.00 sph −3.50 cyl/170° D in left eye. Fundus exam showed normal optic disk, a loss of the foveal reflex, and peripheral RPE mottling. Fundus autofluorescence revealed a central hypofluorescence with a mild perifoveal hyperfluorescent area in both eyes while OCT imaging showed a foveal photoreceptor disruption associated with a normal central macular thickness and relative sparing of paracentral retina (Figure 6). Flash full-field ERG recordings showed reduced responses mostly for the photopic component. Visual fields display a central scotoma.

CaseNotHPOs:

CasePreviousTesting: None mentioned but note that, in this study, DNA from all patients was analyzed by CORD NGS panel.

CaseMethod1: NGS panel

CaseGenotypingMethod: CORD NGS panel - ABCA4, ADAM9, AIPL1, C8orf37, CFAP410 (C21orf2), CACNA1F, CACNA2D4, CDHR1, CEP78, CNGA3, CRX, DRAM2, GUCA1A, GUCY2D, UNC119, IFT81, KCNV2, PDE6C, PITPNM3, POC1B, PROM1, PRPH2, RAB28, RAX2, RIMS1, RPGR, RPGRIP1, SEMA4A, TTLL5.

Variant: Variant 1) c.409C>T (p.Arg137Ter)(paternal) Variant 2) c.77C>A (p.Thr26Asn)(maternal)

ClinVar: Variant 1) 60755; Variant 2) N/A

CAID: Variant 1) CA144657; Variant 2) CA356375011

gnomAD: Variant 1) 0.00001764 (European non-Finnish). No homozygotes in any population. Variant 2) Not in gnomAD

VariantEvidence: Variant 1) no nonsense-mediated decay of mRNA was previously reported (Roosing et al, 2013). In the current paper, structural analysis showed that truncation would delete the α4, β6, and α5 structural elements. The lack of β6 and α5 would most likely prevent the correct α/β fold from forming, affecting the guanine nucleotide binding pocket, and resulting in protein degradation. Variant 2) Molecular dynamics simulations of p.Thr26Asn in both its active and inactive states revealed an allosteric structural mechanism that impairs the binding of Mg2+, thus decreasing the affinity for GTP. The impaired GTP-GDP exchange ultimately locks Rab-28 in a GDP-bound inactive state.

CaseAddInfo: Parents and brother are clinically unaffected. The father and brother are heterozygous for the nonsense variant and the mother is heterozygous for the missense variant.

Case#: Patient 4, 64 years (at report), female

CaseHPOs: HP:0000613, HP:0007663, HP:0000551 (photophobia, reduced visual acuity, color vision defect)

CaseHPOsFreeText: Relatively late onset of disease (first symptoms around age 30 years). 1.7 LogMAR in both eyes. Refractive error was −2.00 sph in both eyes. Fundus exam showed a tigroid aspect with vessel thinning, macular atrophy, and optic pallor. Flash full-field ERG recordings showed a non-detectable response for the photopic component and a reduced response for the scotopic response. MfERG response was markedly reduced but still detectable in both eyes, presenting a residual foveal cone function. OCT macular scan showed a marked foveal thinning with advanced photo-receptor layer disruption (Fig 5)

CaseNotHPOs:

CasePreviousTesting: None mentioned but note that, in this study, DNA from all patients was analyzed by CORD NGS panel.

CaseMethod1: NGS panel

CaseGenotypingMethod: CORD NGS panel - ABCA4, ADAM9, AIPL1, C8orf37, CFAP410 (C21orf2), CACNA1F, CACNA2D4, CDHR1, CEP78, CNGA3, CRX, DRAM2, GUCA1A, GUCY2D, UNC119, IFT81, KCNV2, PDE6C, PITPNM3, POC1B, PROM1, PRPH2, RAB28, RAX2, RIMS1, RPGR, RPGRIP1, SEMA4A, TTLL5.

Variant: c.321G>A (p.Trp107Ter), homozygous

ClinVar: N/A

CAID: CA356373812

gnomAD: The variant is absent in gnomAD.

VariantEvidence: Structural analysis of p.Trp107Ter suggested that truncation of the protein sequence after residue W107 would break up helix α3, resulting in the absence of the C-terminal part of α3, β5, α4, β6, and α5. Missing structural elements β5, β6, and α5 would most probably result in failure to fold correctly or bind GTP/GDP causing degradation.

Case#: Patient 2, male, 33 (at report), 6 years old at onset

CaseHPOs: HP:0000613, HP:0007663, HP:0000551 (photophobia, reduced visual acuity, color vision defect)

CaseHPOsFreeText: BCVA LogMAR 1 for both eyes, refractive error −4.25 sph −2.00 cyl/180° D in right eye and −4.00 sph −2.50 cyl/30° D in left eye. The fundus exam showed normal optic disk, signs of foveal atrophy, and “salt and pepper” peripheral retinopathy. Fundus autofluorescence revealed a dark central area due to the absence of the RPE surrounded by an unusual hyperfluorescent perifoveal ring in both eyes while infrared retinography showed foveal atrophy. OCT imaging revealed a marked reduction of the foveal thickness associated with a photoreceptor layer disruption (Figure 3). Goldmann visual field test showed central scotoma with a mild peripheral constriction.

CaseNotHPOs:

CasePreviousTesting: None mentioned but note that, in this study, DNA from all patients was analyzed by CORD NGS panel.

CaseMethod1: NGS panel

CaseGenotypingMethod: CORD NGS panel - ABCA4, ADAM9, AIPL1, C8orf37, CFAP410 (C21orf2), CACNA1F, CACNA2D4, CDHR1, CEP78, CNGA3, CRX, DRAM2, GUCA1A, GUCY2D, UNC119, IFT81, KCNV2, PDE6C, PITPNM3, POC1B, PROM1, PRPH2, RAB28, RAX2, RIMS1, RPGR, RPGRIP1, SEMA4A, TTLL5.

Variant: c.37del (p.Leu13Ter) homozygous

ClinVar: N/A

CAID: CA2860243

gnomAD: The highest MAF in gnomAD v2.1.1 is 0.00003019 in European non-Finnish (no homozygotes in any population)

VariantEvidence: The variant would either result in nonsense-mediated mRNA decay, or retain few of the structural elements required for correct folding, causing degradation.

CaseAddInfo: Patient 3 is the affected sister of Patient 2. She is affected but has a milder phenotype. The father of these individual is unaffected and heterozygous for the variant. No details are provided about the mother.

Case#: MD-0448 proband, female, 18 years old (report), Spain.

CaseHPOs: HP:0007663, HP:0011003, HP:0000651, HP:0007641 (decreased visual acuity, high myopia, diplopia, dyschromatopsia)

CaseHPOsFreeText: Onset at 8 years. BCVA, 0.5 on the Snellen-equivalent decimal scale [Snellen equivalent, 20/40]). Rapid deterioration of vision. BCVA progressed to 0.3 (Snellen equivalent, 20/65) at age 9 years and to 0.2 (Snellen equivalent, 20/100) at 12 years but stable since then. Fundus exam showed a tigroid fundus, bull’s eye maculopathy, thin vessels, peripapillary atrophy, and optic pallor. Peripheral retina appeared normal. Photopic responses were undetectable by ERG, and scotopic responses were residual. Visual-evoked potential recorded pathologic responses, including low amplitude and enlarged latency (implicit time).

CasePreviousTesting: Screened for variants in the ABCA4 gene by ABCA4 genotyping microarray.

CaseMethod1: WES

GenotypingMethod: WES found no pathogenic variants in the genes known to be associated with the arCRD phenotype (ABCA4, ADAM9, C8orf37, CERKL, EYS, RPGRIP1, and TULP1), and no other plausible genetic variant.

Variant: c.651T>G (p.Cys217Trp), homozygous (NM_001017979.3(RAB28):c.574-1238T>G)

ClinVar: 225879

gnomAD: The highest population minor allele frequency in gnomAD is 0.00002904 in the Latino/Admixed American population; no homozygotes in any population.

VariantEvidence: Present only in isoform 2.

CaseAddInfo: The parents and unaffected sibling are all heterozygous for the variant.

CA2860239Allele Registry