Case: Lin_FamilyA_II:2

CasePresentingHPOsFreeText: Ophthalmic examination notes were retrospectively reviewed in patients. Best-corrected visual acuity (BCVA), slit-lamp biomicroscopy, fundus examination, spectral-domain optical coherence tomography (SD-OCT) scans through the fovea, and short-wavelength fundus autofluorescence (SW-AF, 488 nm), were obtained in all four affected patients with Spectralis HRA+OCT (Heidelberg Engineering, Heidelberg, Germany). Full-field electroretinogram (ERG) testing was performed according to the International Society for Clinical Electrophysiology of Vision (ISCEV) standards. The patients in this study exhibited chorioretinal phenotypes characteristic of RP (Figure 1). All patients initially presented with night blindness followed by progressive constriction of their visual field. ERG recordings were collected from three patients (A-II:2, B-II:1, and D-II:5) (Figure 3). For A-II:2 at 60 years of age and D-II:5 at age 37 years of age, ERG rod responses of the right eyes were almost undetectable.

CasePreviousTesting: WES

CaseGenotypingMethod: Genetic testing was performed in all four patients in this study, using either whole exome sequencing (WES, A-II:2, B-II:1, and D-II:5)

Variant: c.226C>T (p.Arg76Ter)

ClinVarID: or CAID: CA151548

gnomAD: allele frequency of 0.001173 in the Latino population

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Case: Lin_FamilyC_II:1

CasePresentingHPOsFreeText: Ophthalmic examination notes were retrospectively reviewed in patients. Best-corrected visual acuity (BCVA), slit-lamp biomicroscopy, fundus examination, spectral-domain optical coherence tomography (SD-OCT) scans through the fovea, and short-wavelength fundus autofluorescence (SW-AF, 488 nm), were obtained in all four affected patients with Spectralis HRA+OCT (Heidelberg Engineering, Heidelberg, Germany). Full-field electroretinogram (ERG) testing was performed according to the International Society for Clinical Electrophysiology of Vision (ISCEV) standards. The patients in this study exhibited chorioretinal phenotypes characteristic of RP (Figure 1). All patients initially presented with night blindness followed by progressive constriction of their visual field. ERG recordings were collected from three patients (A-II:2, B-II:1, and D-II:5) (Figure 3). For A-II:2 at 60 years of age and D-II:5 at age 37 years of age, ERG rod responses of the right eyes were almost undetectable.

CasePreviousTesting: Genetic testing was performed in all four patients in this study, using either or targeted capture sequencing of 280 retinal dystrophy-related genes (C-II:1).

CaseGenotypingMethod: Genetic testing was performed in all four patients in this study, using either or targeted capture sequencing of 280 retinal dystrophy-related genes (C-II:1).

Variant: c.226C>T (p.Arg76Ter)

ClinVarID: or CAID: CA151548

gnomAD: allele frequency of 0.001173 in the Latino population

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Case: Lin_FamilyB_II:1

CasePresentingHPOsFreeText: Ophthalmic examination notes were retrospectively reviewed in patients. Best-corrected visual acuity (BCVA), slit-lamp biomicroscopy, fundus examination, spectral-domain optical coherence tomography (SD-OCT) scans through the fovea, and short-wavelength fundus autofluorescence (SW-AF, 488 nm), were obtained in all four affected patients with Spectralis HRA+OCT (Heidelberg Engineering, Heidelberg, Germany). Full-field electroretinogram (ERG) testing was performed according to the International Society for Clinical Electrophysiology of Vision (ISCEV) standards. The patients in this study exhibited chorioretinal phenotypes characteristic of RP (Figure 1). All patients initially presented with night blindness followed by progressive constriction of their visual field. ERG recordings were collected from three patients (A-II:2, B-II:1, and D-II:5) (Figure 3). For A-II:2 at 60 years of age and D-II:5 at age 37 years of age, ERG rod responses of the right eyes were almost undetectable.

CasePreviousTesting: WES

CaseGenotypingMethod: Genetic testing was performed in all four patients in this study, using either whole exome sequencing (WES, A-II:2, B-II:1, and D-II:5)

Variant: c.119_122delAACT (p.Lys40llefsTer14)

ClinVarID: or CAID: CA151553

gnomAD: allele frequency of 0.00009237 in the European (non-Finnish) population

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Case: Lin_FamilyD_II:5

CasePresentingHPOsFreeText: Ophthalmic examination notes were retrospectively reviewed in patients. Best-corrected visual acuity (BCVA), slit-lamp biomicroscopy, fundus examination, spectral-domain optical coherence tomography (SD-OCT) scans through the fovea, and short-wavelength fundus autofluorescence (SW-AF, 488 nm), were obtained in all four affected patients with Spectralis HRA+OCT (Heidelberg Engineering, Heidelberg, Germany). Full-field electroretinogram (ERG) testing was performed according to the International Society for Clinical Electrophysiology of Vision (ISCEV) standards. The patients in this study exhibited chorioretinal phenotypes characteristic of RP (Figure 1). All patients initially presented with night blindness followed by progressive constriction of their visual field. ERG recordings were collected from three patients (A-II:2, B-II:1, and D-II:5) (Figure 3). For A-II:2 at 60 years of age and D-II:5 at age 37 years of age, ERG rod responses of the right eyes were almost undetectable.

CasePreviousTesting: WES

CaseGenotypingMethod: Genetic testing was performed in all four patients in this study, using either whole exome sequencing (WES, A-II:2, B-II:1, and D-II:5)

Variant: c.226C>T (p.Arg76Ter)

ClinVarID: or CAID: CA151548

gnomAD: allele frequency of 0.001173 in the Latino population

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Case: Shamieh_ItalianPatient

CasePresentingHPOsFreeText: RCD

CasePreviousTesting:

CaseGenotypingMethod: The next generation sequencing (NGS) panel was selected from the SureSelect Human All ExonKits Version 4 (Agilent, Massy, France) and covers 198 IRD genes in total. Identified variants in KIZ (NM_018474.4) were validated by direct Sanger sequencing, and co-segregation analyses was performed in the DNA of available family members as previously described [ 9 ]. Similarly, the presence of the two mutations c.52G>T, p.Glu18 and c.119_122del, p.Lys40Ilefs14 in the fibroblast cell line of patient CIC01225 was confirmed by direct Sanger sequencing using genomic primers and conditions as previously described [9]

Variant: c.3G>A (p.M1?) homozygous

ClinVarID: or CAID: CA408488039

gnomAD: 0.00004892 allele frequency in the Latino population

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Case: Shamieh_CIC07875

CasePresentingHPOsFreeText: RCD

CasePreviousTesting:

CaseGenotypingMethod: The next generation sequencing (NGS) panel was selected from the SureSelect Human All ExonKits Version 4 (Agilent, Massy, France) and covers 198 IRD genes in total. Identified variants in KIZ (NM_018474.4) were validated by direct Sanger sequencing, and co-segregation analyses was performed in the DNA of available family members as previously described [ 9 ]. Similarly, the presence of the two mutations c.52G>T, p.Glu18 and c.119_122del, p.Lys40Ilefs14 in the fibroblast cell line of patient CIC01225 was confirmed by direct Sanger sequencing using genomic primers and conditions as previously described [9]

Variant: c.226C>T (p. R76*) homozygous

ClinVarID: or CAID: CA151548

gnomAD: 0.001173 frequecny in the Latino population

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Case: Shamieh_FamilyA_II:2; CIC00173

CasePresentingHPOsFreeText: Rod-cone dystrophy, Each subject underwent an ophthalmic exami- nation with clinical assessment as previously described. The three affected individuals with KIZ variants in this study were all diagnosed with RCD in their late teens on the basis of night blindness followed by changes in mid- peripheral visual fields and undetectable responses in a full-field electroretinogram by approximately 35 years of age.

CasePreviousTesting: At a time when next-generation sequencing (NGS) approaches were not commonly used, index subject CIC00173 II.2 (family A, Figure 1) was excluded upon screening by microarray analysis and direct Sanger sequencing for known mutations in EYS and C2orf71 (a major and a minor gene, respectively, implicated in RCD). 11,12 Because exon ORF15 in RPGR (MIM 312610) is not targeted by existing NGS panels,13 we also analyzed it by Sanger sequencing but found no pathogenic variant. Subsequently, we performed targeted NGS on the index subject’s DNA by using a panel of 120 genes previously found to carry mutations in retinal diseases (this panel was modified and improved since our previous study). This survey did not reveal any pathogenic variant, and we therefore proceeded to WES.

CaseGenotypingMethod: In the present study, we applied whole-exome sequencing (WES) to five members (including one affected by RCD) of a consanguineous family (family A).

Variant: c.226C>T (p.Arg76*); homozygous

ClinVarID: or CAID: CA151548

gnomAD: Variant present at a frequency of 0.006316 in the Ashkenazi Jewish (9658 alleles tested) and 0.001173 in the Latino populations.

AddCaseInfo: consanguineous family. Both parents and the sister of the proband each carried one copy of the variant, but none were affected with RCD. To investigate whether the stop variant represents a founder alteration, we performed haplotype analysis for each of the index subjects (CIC00173 II.2 from family A) and CIC01611 II.1 from family B) by selecting 11 microsat- ellite DNA markers flanking the KIZ locus. 25 These markers were distributed over a physical distance of z7.38 Mb, cor- responding to z10.5 cM (genetic distance according to Marshfield genetic maps). Both subjects were found to share a common haplotype of five polymorphic microsa- tellites (DS20S54, DS20S63, DS20S190, DS20S868, and DS20S180) flanking KIZ and spanning z1.75 cM (1.18 Mb) (Figure 1). This result suggests that c.226C>T (p.Arg76*) is most likely a founder mutation causing autosomal-recessive RCD in the southern European population

VariantEvidence: We detected a homozygous nonsense mutation, c.226C>T (p.Arg76*), in the third exon of KIZ, coding for centrosomal protein kizuna (KIZ)

Case: Shamieh_FamilyB_II:1; CIC01611

CasePresentingHPOsFreeText: Rod-cone dystrophy, Each subject underwent an ophthalmic exami- nation with clinical assessment as previously described. The three affected individuals with KIZ variants in this study were all diagnosed with RCD in their late teens on the basis of night blindness followed by changes in mid- peripheral visual fields and undetectable responses in a full-field electroretinogram by approximately 35 years of age.

CasePreviousTesting: No mention of previous testing

CaseGenotypingMethod: screening of coding and flanking exonic regions of KIZ by direct Sanger sequencing

Variant: c.226C>T (p.Arg76*); homozygous

ClinVarID: or CAID: CA151548

gnomAD: Variant present at a frequency of 0.006316 in the Ashkenazi Jewish (9658 alleles tested) and 0.001173 in the Latino populations.

AddCaseInfo: To investigate whether the stop variant represents a founder alteration, we performed haplotype analysis for each of the index subjects (CIC00173 II.2 from family A) and CIC01611 II.1 from family B) by selecting 11 microsat- ellite DNA markers flanking the KIZ locus. 25 These markers were distributed over a physical distance of z7.38 Mb, cor- responding to z10.5 cM (genetic distance according to Marshfield genetic maps). Both subjects were found to share a common haplotype of five polymorphic microsa- tellites (DS20S54, DS20S63, DS20S190, DS20S868, and DS20S180) flanking KIZ and spanning z1.75 cM (1.18 Mb) (Figure 1). This result suggests that c.226C>T (p.Arg76*) is most likely a founder mutation causing autosomal-recessive RCD in the southern European population

PreviouslyPublished:

VariantEvidence:

Case: Shamieh_FamilyC_II:3; CIC01225

CasePresentingHPOsFreeText: Rod-cone dystrophy, Each subject underwent an ophthalmic exami- nation with clinical assessment as previously described. The three affected individuals with KIZ variants in this study were all diagnosed with RCD in their late teens on the basis of night blindness followed by changes in mid- peripheral visual fields and undetectable responses in a full-field electroretinogram by approximately 35 years of age.

CasePreviousTesting: No mention of previous testing

CaseGenotypingMethod: screening of coding and flanking exonic regions of KIZ by direct Sanger sequencing

Variant: compound heterozygous for the c.52G>T (p.Glu18) and c.119_122delAACT (p.Lys40Ilefs14) variants.

ClinVarID: or CAID: c.52G>T (CA151550) , c.119_122delAACT (CA151553)

gnomAD: allele frequency = 0.00009237 for the c.119_122delAACT variant, c.52G>T variant is absent from gnomAD v2.1.1

AddCaseInfo: Cosegregation analysis revealed that the father was heterozygous for the nonsense mutation and the mother was heterozygous for the frameshift deletion

Case: Gustafson_II:3

CasePresentingHPOsFreeText: Retrospective review of ophthalmic examination notes was performed in three affected family members (II:2, II:4, and II:6). Information about eye examination, including best corrected visual acuity (BCVA) and dilated fundus examination, kinetic perimetry, and spectral-domain optical coherence tomography (SD-OCT) scans through the fovea were obtained in all three affected patients (Spectralis HRA+OCT, Heidelberg Engineering, Heidelberg, Germany and Cirrus HD OCT, Carl Zeiss Meditech Inc., Dublin, CA, USA). Full-field electroretinogram (ERG) testing was performed according to International Society for Clinical Electrophysiology of Vision (ISCEV) standards [ 4 ] in the two sisters (II:2 and II:4) but was not performed in the second cousin (II:6).

CasePreviousTesting: WES

CaseGenotypingMethod: Whole exomes of three affected (II:2, II:4 and II:6) and to unaffected family members (I:6, II:3) were sequenced using Agilent Sure Select V1 probes (Agilent Technologies, Inc., Santa Clara, CA, USA) and Illumina HiSeq 2500 (Illumina, San Diego, CA, USA). Whole genomes of family members II:2, II:3, II:4, II:6, and I:6 were sequenced at more than 30X depth using Illumina HiSeq X (Illumina,). Segregation of substitution mutations and small deletions were tested by dideoxy sequencing

Variant: c.226C>T (p.Arg76*)

ClinVarID: or CAID: CA151548

gnomAD: allele freq. of 0.001173 in the Latino population

AddCaseInfo: Ashkenazi Jewish

PreviouslyPublished:

VariantEvidence:

Case: Gustafson_II:1, female, 60 years old

CasePresentingHPOsFreeText: Retrospective review of ophthalmic examination notes was performed in three affected family members (II:2, II:4, and II:6). Information about eye examination, including best corrected visual acuity (BCVA) and dilated fundus examination, kinetic perimetry, and spectral-domain optical coherence tomography (SD-OCT) scans through the fovea were obtained in all three affected patients (Spectralis HRA+OCT, Heidelberg Engineering, Heidelberg, Germany and Cirrus HD OCT, Carl Zeiss Meditech Inc., Dublin, CA, USA). Full-field electroretinogram (ERG) testing was performed according to International Society for Clinical Electrophysiology of Vision (ISCEV) standards [ 4 ] in the two sisters (II:2 and II:4) but was not performed in the second cousin (II:6)

CasePreviousTesting: WES

CaseGenotypingMethod: Whole exomes of three affected (II:2, II:4 and II:6) and to unaffected family members (I:6, II:3) were sequenced using Agilent Sure Select V1 probes (Agilent Technologies, Inc., Santa Clara, CA, USA) and Illumina HiSeq 2500 (Illumina, San Diego, CA, USA). Whole genomes of family members II:2, II:3, II:4, II:6, and I:6 were sequenced at more than 30X depth using Illumina HiSeq X (Illumina,). Segregation of substitution mutations and small deletions were tested by dideoxy sequencing

Variant: c.226C>T (p.Arg76*)

ClinVarID: or CAID: CA151548

gnomAD: allele freq. of 0.001173 in the Latino population

AddCaseInfo: Ashkenazi Jewish

PreviouslyPublished:

VariantEvidence:

Case: Jauregui_Case3

CasePresentingHPOsFreeText: The data presented in this study, including images and genetic testing results, is not identifiable to individual patients. A retro- spective review of patients with a clinical diagnosis of RP by an inherited retinal disease specialist (SHT) at the Department of Ophthalmology at Columbia University was conducted. The clinical diagnosis was based on pre- senting symptoms, family history, fundus examination, and subsequently supported by clinical imaging, full-field electroretinography (ffERG), and/or genetic testing. Ophthalmic examinations included a slit-lamp and dilated funduscopic examination, best-corrected visual acuity (BCVA), short-wavelength fundus autofluorescence (SW- AF, 488 nm excitation), and spectral domain optical coherence tomography (SD-OCT). The inclusion criteria for this study were the diagnosis of RP and genetic characterization of the disease, while the exclusion criteria precluded monocular patients or those without SD-OCT or SW-AF imaging

CasePreviousTesting: not mentioned

CaseGenotypingMethod: not mentioned

Variant: c.226C>T (p.R76X)

ClinVarID: or CAID: CA151548

gnomAD: allele freq. of 0.001173 in the Latino population

AddCaseInfo: Male. Caucasian, 21 years old

PreviouslyPublished:

VariantEvidence:

Case: Jauregui_Case2

CasePresentingHPOsFreeText: The data presented in this study, including images and genetic testing results, is not identifiable to individual patients. A retro- spective review of patients with a clinical diagnosis of RP by an inherited retinal disease specialist (SHT) at the Department of Ophthalmology at Columbia University was conducted. The clinical diagnosis was based on pre- senting symptoms, family history, fundus examination, and subsequently supported by clinical imaging, full-field electroretinography (ffERG), and/or genetic testing. Ophthalmic examinations included a slit-lamp and dilated funduscopic examination, best-corrected visual acuity (BCVA), short-wavelength fundus autofluorescence (SW- AF, 488 nm excitation), and spectral domain optical coherence tomography (SD-OCT). The inclusion criteria for this study were the diagnosis of RP and genetic characterization of the disease, while the exclusion criteria precluded monocular patients or those without SD-OCT or SW-AF imaging

CasePreviousTesting: not mentioned

CaseGenotypingMethod: not mentioned

Variant: c.226C>T (p.R76X)

ClinVarID: or CAID: CA151548

gnomAD: allele freq. of 0.001173 in the Latino population

AddCaseInfo: Male. Caucasian, 60 years old

PreviouslyPublished:

VariantEvidence:

Case: Jauregui_Case1

CasePresentingHPOsFreeText: The data presented in this study, including images and genetic testing results, is not identifiable to individual patients. A retro- spective review of patients with a clinical diagnosis of RP by an inherited retinal disease specialist (SHT) at the Department of Ophthalmology at Columbia University was conducted. The clinical diagnosis was based on pre- senting symptoms, family history, fundus examination, and subsequently supported by clinical imaging, full-field electroretinography (ffERG), and/or genetic testing. Ophthalmic examinations included a slit-lamp and dilated funduscopic examination, best-corrected visual acuity (BCVA), short-wavelength fundus autofluorescence (SW- AF, 488 nm excitation), and spectral domain optical coherence tomography (SD-OCT). The inclusion criteria for this study were the diagnosis of RP and genetic characterization of the disease, while the exclusion criteria precluded monocular patients or those without SD-OCT or SW-AF imaging

CasePreviousTesting: not mentioned

CaseGenotypingMethod: not mentioned

Variant: c.119_122delAACT (p.K40IfsX14)

ClinVarID: or CAID: CA151553

gnomAD: allele freq. of 0.00009237 in the European (non-finnish) population

AddCaseInfo: Male. Caucasian, 56 years old

PreviouslyPublished:

VariantEvidence: