Case#: 47-year-old female, sibling of patient 1.

DiseaseAssertion: Discordant STGD phenotype

FamilyInfo: The mother was found to harbour p.L541V/p.A1038V, and the father carried the p.R811C mutation; both of whom were asymptomatic with normal retinal examination (Fig. 1). ABCA4 screening detected three variants: two variants p.L541V and p.A1038V – commonly co-inherited in a complex allele in STGD (Maugeri et al. 2000) – and a third novel variant p.R881C (Fig. 1). Patient 1 had all three variants

CasePresentingHPOs: HP:0007401, HP:0025010, HP:0011507

CasePhenotypeFreeText: Patient 2 is the 47-year-old sister of patient 1. At initial examination in 1994, she reported a central scotoma. VA was 6/9 in both eyes with bilateral subtle foveal atrophy and perifoveal yellowish-white flecks (Fig. 1). By 2003, foveal atrophy had progressed with more perifoveal flecks (Fig. 1). In 2012, her VA was 6/12 bilaterally, but fundus findings remained stable (Fig. 1). AF imaging demonstrated a mottled signal within the central macula, optical coherence tomography showed outer retinal disruption confined to the central macula

CaseNotHPOs: N/A

CaseNotPhenotypeFreeText: N/A

CasePreviousTesting: The article mentions ABCA4 screen but does not go into detail. However, it does say,”(patient 2) harboured the complex allele (p.L541V/p.A1038V)”

GenotypingMethod: Again only mentioned ABCA4 screening without going into detail.

Variant: NM_000350.3:c.1621C>G and NM_000350.3(ABCA4):c.3113C>T

LegacyVariant: c.1621C>G (p.Leu541Val) and c.3113C>T(p.Ala1038Val)

CAID: CA341280463 and CA119135

gnomeAD: chr1-94063251-G-C and chr1-94043413-G-A

PreviouslyPublished: N/A

AdditionalInfo: Figure 1 provides information about the imaging of patients’ eyes that helps determine phenotype.

Case:RP3,03, male proband with first symptoms as 18 years old. DiseaseAssertion:RP19 FamilyInfo:Proband was born in a consangiuineous family of Moroccan origin. Parents were unaffected. InheritancePattern:AutosomalRecessive CasePresentingHPOs:HP:0007994,HP:0000510,HP:0100014 CaseHPOFreeText:Difficulty with dark adaptation, Fig 4B severe impairment of the entire visual field. Fig 4A Scotopic and photopic ERG traces were altered indicating rod and cone photoreceptor dysfunctions. Macular OCT showed relative preservation of the foveal structure. Epiretinal membrane formation was observed. CaseNOTHPOs:HP:0007667 CaseNOTHPOFreeText:absence of cystic spaces CasePreviousTesting: GenotypingMethod:Whole exome sequencing MultipleGeneVariants: compound heterozygous GeneName:ABCA4 Variant:NM_000350.3(ABCA4):c.5908C>T (p.Leu1970Phe) ClinVarID :7892 gnomAD:0.00362 GeneName:ABCA4 Variant:NM_000350.3(ABCA4):c.6148G>C (p.Val2050Leu) ClinVarID :7884 gnomAD:0.00308

Case#: RP3.03, 23yo, 21yo on set, Moroccan

DiseaseAssertion: Retinitis Pigmentosa (RP19)

FamilyInfo: Born into a consanguineous family, parents are unaffected, has five unaffected siblings

CasePresentingHPOs: HP:0000505, HP:0007675, HP:0001133, HP:0007994, HP:0007843, HP:0000510, HP:0000580, HP:0007703

CaseHPOFreeText: Abnormal epiretinal membrane formation, Altered ERG traces, rod and cone photoreceptor dysfunctions, hyper fuorescence ring surrounding macula and peripheral retina, absence of cystic spaces

CaseNotHPOs: HP:0000551

CaseNotHPOFreeText: Central vision loss

Genotyping Method: Genomic DNA was extracted using QIAamp DND Blood Mini Kit, DNA underwent WES by BGI Tech Solutions, DNA was captured by MGIEasy Exome Capture V4 Probe Set, then Alligned using the Burrows-Wheeler Aligner and HaplotypeCaller of GAWK

PreviouslyPublished: CRB1, PDE6B

Variant: c.5908C>T, c.6148G>C

ClinVar: 7892, 7884

SupplementalData: Clinical data (table 1, figure 5), Genetic analysis (table 2), Patient Pedigree (figure 1.)

Case#:5-year-old girl

DiseaseAssertion: Asymptomatic

FamilyInfo: Mother was diagnosed with STGD1 and She was homozygous for a (severe) splice site mutation, IVS 35+2 T>C, Maternal uncle was diagnosed with STGD1. Father passed down the G1961E variant.

CasePresentingHPOs: HP:0030630, HP:0011504

CaseHPOFreeText: The ELM in the central macula appeared thickened with indistinct borders, particularly along its inner border (Fig. 2C), horizontal diameter for the region of thickened ELM was 1113 μm, FAF revealed Bull’s Eye Maculopathy (BEM) (Fig. 2B),

CaseNotHPOs:

CaseNotHPOFreeText: No retinal, vasculature, pigmentary or optic nerve head abnormalities were detected on clinical examination, no focal abnormality observed in the outer nuclear layer (ONL) or RPE (Fig. 2C), There was no FAF evidence of flecks or GA

Genotyping Method:

PreviouslyPublished: No

Variant:NM_000350.3:c.5882G>,

ClinVar:7888

CAID:CA119132

SupplementalData:

Case#: 43-year old man, German descent, onset within first decade of life

DiseaseAssertion: STGD1

FamilyInfo: Family pedigree shown in Figure 1.

CasePresentingHPOs: HP:0011463, HP:0000533, HP:0000580, HP:0030500, HP:0011507, HP:0000548, HP:0000510, HP:0007703, HP:0007663, HP:0000512, HP:0000610

CaseHPOFreeText: Retinal vessels were visibly attenuated.

CaseNotHPOs: n/a

CaseNotHPOFreeText: Peripapillary region around the optic nerve had no disease related changes.

Genotyping Method: Illumina MiSeq platform, Array-CGH analysis

PreviouslyPublished: n/a

Variant: NM_000350.3(ABCA4):c.161G>A (p.Cys54Tyr), NM_000350.3(ABCA4):c.4539+2028C>T

ClinVar: 99065, 236116

SupplementalData: n/a

MonDO: MOND:08000406

Case: Female, onset 6 years VA 20/200 OU identify 1 ouf 15 Ishiara cards and overlooking symptom. Presumably diagnosed with Batten disease but found to harbor genetic variant for Stargardt disease.

DiseaseAssertion: Stargardt disease

FamilyInfo: No family history of visual loss in childhood.

"CasePresentingHPOs: HP:0007663, HP:0007988, HP:0030584, HP:0008043, HP:0008001, HP:0030609 (Reduced visual acuity, Macular hypopigmentation, Color vision test abnormality, Retinal arteriolar constriction, Foveal hyperpigmentation, Photoreceptor layer loss on macular OCT"

CaseHPOFreeText: bull's eye lesions, prominent overlooking, hyperreflective granular deposits

CaseNOTHPOFreeText: HP:0001336, HP:0001250, HP:0000648, HP:0000707

CasePreviousTesting: (Myoclonus, Seizure, Optic atrophy, Abnormality of the nervous system

GenotypingMethod: Genetic testing was negative for all mutations known to cause neuronal ceroid lipofuscinosis, but whole exome sequencing showed compound heterozygosity for 2 pathogenic variants in the ABCA4 gene

MultipleGeneVariants:

(1) GeneName: ABCA4

(1) Variant: c.3007C>T, p.Q1003X

(1) ClinVarID or CAID: CA119132

(1) gnomAD: 0.003406 total AF in gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-94008251-C-T?dataset=gnomad_r4)

(2) GeneName: ABCA4

(2) Variant: c.768G>T

(2) ClinVarID or CAID: CA227458

(2) gnomAD: 0.00007930 total AF in gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-94098794-C-A?dataset=gnomad_r4)

Case#:patient, 25, male

DiseaseAssertion:Retinitis Pigmentosa

FamilyInfo:Unaffected brother with no variants, parents each heterozygous for one pathogenic variant in ABCA4

CasePresentingHPOs: HP:0000007, HP:0011462, HP:0007703, HP:0000662, HP:0007641

CaseHPOFreeText: Onset 20 year old. Gradual onset of blurred vision OD, dyschromatopsia. BCVA 1/20 OD 20/20 OS. Optic disc pale, retinal arteries and foveal reflex attenuated. Yellow deposits in perofoveal area and mid-peripheral retina, which showed mottled appearance OU. OCT - thinning of outer nuclear layer and disruption of ellipsoid zone with hyper-reflective flecks. Severe bilateral constriction in visual field. Hypofluorescence of optic disc OU

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: whole exome (Sanger segregation test)

PreviouslyPublished: n/a

Variant: NM_000350.3:c.4793C>A; NM_000350.3:c.1769A>G

ClinVar: 99321

CAID: CA341279788

SupplementalData: n/a

Patient 71674: Female, Swiss, 13 years old. bi-allelic variants in ABCA4, diagnosed with Retinal dystrophy DD: Retinitis pigmentosa

Figure 3: Segregation analysis performed on family samples GenotypingMethod: Whole exome sequencing performed on HiSeq2000 and NextSeq500 (252 genes)

Multiple Variants: VPS13B NM_017890.4:c.897 8A>G:p.Asn2993Ser Heterozygous CM041280

PCDH15 NM_001142763.1:c. 4329_4337del:p.Pro 1446_Pro1448del Heterozygous

DHX38 NM_014003.3:c.366 2C>T:p.Thr1221Met Heterozygous

USH1G NM_173477.4:c.310 A>G:p.Met104Val Heterozygous

Case#: Male, Family #1, Patient #1, II:1 in pedigree

DiseaseAssertion: Hypomorphic Stargardt disease

FamilyInfo: Paternal female cousin also has hypomorphic Stargardt disease and both of them carry the complex allele p.[L541P; A1038V] and p.N1868I. Additionally, their paternal aunt was diagnosed with Stargardt disease. This information can be found on Fig.1.

CasePresentingHPOs: HP:0000622, HP:0025010

CaseHPOFreeText: This proband developed blurred vision at age 30. The foveal atrophy affects the left eye. In the first visit at 33.9 years old patient presents with 20/25-3 Snellen VA OD, 20/70-2 Snellen VA OS, 0.16 LogMAR VA OD, 0.58 LogMAR VA OS, and stage 1. In the last visit at age 40.7, the patient had a 20/40-2 Snellen VA OD, a 10/80-1 Snellen VA OS, 0.34 LogMAR VA OD, 0.92 LogMAR VA OS, and was now in stage 2. In a Goldmann Visual Field test, they found central scotomas II4e; mild-moderate constriction II2e.

CaseNotHPOs: N/a

CaseNotHPOFreeText: The proband maintained some relative foveolar sparing in his right eye and had a BCVAs of 20/4022 (test done at 40 years old).

Genotyping Method: Genetic testing was performed at Columbia University. It was not stated which method this proband underwent, so the genetic testing could have been one of the following: "The entire ABCA4 gene locus was sequenced in 17 patients; the ABCA4 gene, including all exons and intron/exon boundaries were sequenced in 4 patients. In the remaining 6 cases representing family members, only targeted testing was performed."

PreviouslyPublished: N/a

**Variant: ** M1) NM_000350.3(ABCA4):c.5603A>T M2) NM_000350.3(ABCA4):c.1622T>C (p.Leu541Pro)

ClinVar: M1) 99390 M2) 99067

CAID: N/a

gnomAD: M1) The highest minor allele frequency was 0.05787 (https://www.ncbi.nlm.nih.gov/clinvar/variation/99390/) M2) The highest minor allele frequency was 0.00017 (https://www.ncbi.nlm.nih.gov/clinvar/variation/99067/)

SupplementalData: Table 1. provided patient information for those with p.N1868I ABCA4 Stargardt disease and the associated ABCA4 mutations. Fig.1. shows the pedigrees of the families. Fig.3. shows Macular SD-OCT line profiles for some of the patients. Table 2. describes the onset/symptoms of the patients with p.N1868I ABCA4 Stargardt Disease. Table 3. shows Visual Acuity and Stage at Baseline and Most Recent Follow-up in Patients With p.N1868I ABCA4 Stargardt Disease. Fig.4. shows BCVA better eye vs Duration since first examination for the patients. Table 4. shows clinical findings in the patients.

Case#: Patient 4, Female, Caucasian, 33yo

DiseaseAssertion: STGD1

FamilyInfo: One of eight siblings; four affected. Disease segregates with ABCA4 variants consistent with autosomal recessive inheritance. Parents are deceased and can't be tested.

CasePresentingHPOs: HP:0007663, HP:0007754, HP:0025147, HP:0007924, HP:0011507

CaseHPOFreeText: gradual decline in visual acuity over 9 years, BCVA 20/300 OU, bilateral beaten-bronze appearance of the macula, numerous perimacular yellow flecks, fluorescein angiography showing hyperfluorescence in the posterior pole and dark choroid in the periphery

CaseNotHPOs: N/A

CaseNotHPOFreeText: absence of central hypofluorescence on fluorescein angiography (present in affected siblings but not this patient)

Genotyping Method: SSCP analysis; Taq Dyedeoxy Terminator Cycle Sequencing kit

PreviouslyPublished: N/A

Variant: NM_000350.3(ABCA4):c.2588G>C (p.Gly863Ala), NM_000350.3(ABCA4):c.161G>A (p.Cys54Tyr)

ClinVar: ClinVarID:7879, ClinVarID:99065

CAID: N/A

SupplementalData: Segregation and sequencing data (Figures 1, 4)

Case#: Female, age 44 years old

DiseaseAssertion: Discordant STGD phenotype

FamilyInfo: Information revolving the sister of this patient is given as well as they both have a discordant STGD phenotype. Additionally, it mentions that the parents each harboured a mutation but were asymptomatic/had normal examination results.

CasePresentingHPOs: HP:0001141, HP:0007401, HP:0030602

CaseHPOFreeText: At 23 central vision was deteriorating and patient had a VA of 6/36 in the right eye and 6/60 in the left. Through fundus photography, bilateral yellow/white flecks were found at the posterior pole. 12 years later, her VA was retested and it was 6/60 in both eyes. After autofluorescnece (AF) imaging was done, there was localized low signal at the macula found with abnromal foci. In 2008 her macular atrophy had enlarged and the flecks were less apparent.

CaseNotHPOs: N/a

CaseNotHPOFreeText: In this article there was not a phenotype presented that was normal.

CasePreviousTesting: It mentioned that there were two previously reported variants on the same allele detected in the siblings and one unique novel variant on the second allele for this patient. However, the testing they used was not listed, it just stated that the variants were found through sequencing. For this patient the variants were p.L541P/p.A1038V and p.R881C.

GenotypingMethod: Just mentioned sequencing and ABCA4 screening to look for two variants p.L541V and p.A1038V and a third novel variant p.R881C.

PreviouslyPublished: N/a

Variant: 1) NM_000350.3(ABCA4):c.1622T>C (p.Leu541Pro) 2) NM_000350.3(ABCA4):c.3113C>T (p.Ala1038Val) 3) N/a

ClinVar ID: 1) 99067 2) 7894 3) N/a

**CAID: ** 3) Because there was not a reference or alternate allele provided in this article I was unable to find a CAID for p.R881C.

gnomAD: 1) Highest minor allele frequency was 0.00017 (https://www.ncbi.nlm.nih.gov/clinvar/variation/99067/) 2) Highest minor allele frequency was 0.00188 (https://www.ncbi.nlm.nih.gov/clinvar/variation/7894/) 3) N/a

SupplementalData: Figure 1 had information regarding imaging and other testing done on the patient that is vital for phenotypic characterization. Also, it mentions a variant known as p.R881C, but was unable to find anything on ClinVar or gnomAD.

Case#: 11 year old female

DiseaseAssertion: Stargardt’s Disease

ParentalTesting: She was the product of an uncomplicated pregnancy born to a healthy Filipino mother and Italian/Irish father with no known family history of ocular disease. The mother and father were asymptomatic but not examined. Segregation analyses showed that both parents are asymptomatic carriers.

CasePresentingHPOs: HP:0007754, HP:0011462, HP:0008035

CasePhenotypeFreeText: The ABCA4 gene, when mutated, results in a spectrum of retinal degeneration, including Stargardt macular dystrophy, fundus flavimaculatus, autosomal recessive retinitis pigmentosa, and cone-rod dystrophy (1). Over 800 disease-associated ABCA4 gene mutations have been reported.

CaseNotHPOs: N/A

CaseNotPhenotypeFreeText: N/A

CasePreviousTesting: The proband underwent a full consultative ophthalmic examination at the Ocular Genetics Clinic at Wills Eye Hospital, including visual acuity, slit-lamp, and dilated fundus examination. Fundus autofluorescence and spectral-domain optical coherence tomography (Spectralis; Heidelberg Engineering), Goldmann visual field (Octopus 900 perimeter; Haag-Streit International), and intravenous fluorescein angiography were obtained. Full-field electroretinogram (Espion; Diagnosys LLC) and multifocal electroretinogram (Veris V.6.4.3; EDI Inc.) were performed in accordance with the International Society of Clinical Electrophysiology and Vision standards. Best-corrected visual acuity was 20/125 in the right eye and 20/200 in the left eye. The patient demonstrated eccentric fixation. Pupillary responses were normal. Slit-lamp examination was normal. Fundus examination revealed healthy optic nerves and retinal blood vessels, bilateral macular geographic pigmentary stippling with subretinal flecks in and around this area, and a blunted internal limiting membrane reflex (Fig. 1). Peripheral retina was normal.

GenotypingMethod: Genotyping microarray chips for ABCA4 can identify >98% of the most common mutations. In this report, we describe 2 novel ABCA4 variants in a patient with Stargardt disease. Bioinformatic and in silico analysis of the functional consequences of these variants provided compelling evidence for pathogenicity.

Variant: c.850_857delATTCAAGA and c.6184_6187delGTCT

CAID: CA10604079 and CA10604078

MultipleGeneVariants: N/A

PreviouslyPublished: N/A

AdditionalInfo: Bioinformatic assessment of the c.850_857delATTCAAGA mutation showed that it resulted in a truncated 317 amino acid polypeptide, devoid of several essential domains of the ABCA4 transporter. The c.6184_6187delGTCT mutation led to a premature stop codon at the C-terminal end of the protein, resulting in a loss of a total of 161 amino acid residues. Although less than 7% of the protein was absent, the important VFVNFA motif, present within the last 30 amino acids of the NBD2 domain, was deleted (Fig. 2). This motif is known to be critical to ABCA4 protein function, is highly conserved among members of the ABCA transporter subfamily, and has also been linked to Tangier disease in the ABCA1 protein (9). Removal of this motif in ABCA4 leads to a loss of retinal stimulated ATPase in vitro and energy transduction of the transporter (9, 10). Protein modeling predicted a loss of an essential β-sheet, which significantly altered its structure. The NBD domains are sites of ATP hydrolysis that provide energy for transport of R-PE through rod outer segment membranes. Enzymatic studies suggest that the NBD2 domain in particular provides energy necessary for translocation of retinal derivatives generated in the visual cycle. The structural changes in NBD2 would affect ABCA4 transporter’s ability to transport retinoids, leading to accumulation of cytotoxic lipofuscin in RPE cells and ultimately photoreceptor cell death.

Case#: single case, 37-year-old male, ethnicity not specified although family originally from the Middle East, examined in the UK

DiseaseAssertion: STGD

FamilyInfo: No history of consanguinity. No history of inherited retinal disease, poor vision or colour vision disturbance. Father had recent diagnosis of chronic central serous retinopathy, not consistent with STGD

CasePresentingHPOs: n/a

CaseHPOFreeText: Late-onset Stargardt disease with slowly progressive phenotype. The patient present with a 3-year history of decreased vision in the right eye that had recently significantly worsened. Visual acuity was 6.24 in right eye and 6/6 in left eye. Fundus examination reveled scattered atrophy and pisiform fundal flecks in both eye, right worse than left. Fluorescein angiography showed a silent choroid and partial bull's eye maculopathy, right worse than left. OCT showed loss of photoreceptors in both eyes and partial central sparing in the left eye. Photopic and scotopic ERG showed reduced amplitude of responses in the right eye and lower range amplitudes in the left eye, normal implicit times in both eyes. Pattern ERG and multifocal ERD showed central retinal dysfunction with preserved peripheral function. No change in vision or retinal appearance over the next 14 months of follow up.

CaseNotHPOs: n/a

CaseNotHPOFreeText: No night vision symptoms. No history of retinotoxic drug exposure.

Genotyping Method: Next-generation sequence analysis with the Oxford Genetics Testing Laboratory Macular Gene Panel.

PreviouslyPublished: Thr829Met missense mutation had been previously reported in an individual with autosomal recessive retinitis pigmentosa, but not previously associated with STGD phenotype.

Variant: ABCA4 NM_000350 c.5882G>A, p.(Gly1961Glu) c.2486C>T, p.(Thr829Met)

ClinVar: n/a

CAID: CA958261, CA119132

SupplementalData: n/a

Case#: Patient female, 48y, ethnicity not reported

DiseaseAssertion: Stargardt disease (STGD1) with unusual phenotype resembling pattern dystrophy

FamilyInfo: autosomal recessive inheritance; segregation analysis confirms each parent carries one variant (heterozygous). Pedigree shown in Figure 3. Proband is compound heterozygous for ABCA4 variants.

CasePresentingHPOs: HP:0007663, HP:0007754, HP:0030636, HP:0000548

CaseHPOFreeText: mild visual impairment (BCVA 20/25 and 20/20), perifoveal yellow fleck-like lesions, hyperautofluorescent lesions with lipofuscin accumulation, foveal sparing, subretinal material accumulation, phenotype resembling pattern dystrophy, bilateral macular involvement, decreased p50 values on pattern ERG

CaseNotHPOs: HP:0000510 (normal ERG responses except pattern ERG component)

CaseNotHPOFreeText: normal full-field ERG (scotopic and photopic responses), normal electrooculography, preserved outer retina structure, minimal photoreceptor disruption at fovea

Genotyping Method: targeted next-generation sequencing (Illumina NextSeq500) with SeqCap EZ enrichment panel; Sanger sequencing used for confirmation and segregation analysis

PreviouslyPublished: n/a

Variant: ABCA4 NM_000350.2: c.428C>T (p.Pro143Leu); c.3113C>T (p.Ala1038Val)

ClinVar: 99273; 7894

CAID: n/a

SupplementalData: clinical imaging and genetic/segregation data in supplemental data (Figures 1–3, Table 1)

Case#: 25-year old female, juvenile onset

DiseaseAssertion: STGD1

FamilyInfo: Figure 1 shows family pedigree. Table 1 shows clinical features of a Chinese pedigree. Cosegregation analysis was done and shown in Figure 1A, C.

CasePresentingHPOs: HP:0007663, HP:0007722, HP:0007401, HP:0030329, HP:0030610, HP:0003621, HP:0011507, HP:0007984

CaseHPOFreeText: The uncorrected visual acuity of each eye was 20/400, which has progressively decreased for 13 years.

CaseNotHPOs: n/a

CaseNotHPOFreeText: The retinal vessels were normal.

Genotyping Method: Whole Exome Sequencing, Sanger Sequencing

PreviouslyPublished: n/a

Variant: NM_000350.3(ABCA4):c.3523-2A>G, NM_000350.3(ABCA4):c.5646G>A (p.Met1882Ile)

ClinVar: 866764, 377407

SupplementalData: n/a

Case#: 1 male, 6 years old, from Taiwanese and Korean decent.

DiseaseAssertion: ABCA4-related retinopathy Stargardt disease

FamilyInfo: Single affected individual. Paternal uncle presented with Stargart disease previously, and Taiwanese and Korean descent underwent genetic testing to identify two pathogenic variants in the ABCA4 gene. One of the variants found was the same ABCA4 variant from the originally affected individual. No additional family information is provided in text.

CasePresentingHPOs: HP:0000529 - progressive visual loss, HP:0025010 - Foveal atrophy, HP:0000603 - Central scotoma, HP:0007663 - Decreased visual acuity, HP:0030602 - Abnormal fundus autofluorescence imaging, HP:0007984 - ERG: Reduced dark-adapted b-wave amplitude, HP:0000512 - Abnormal electroretinogram, HP:0020032 - Hyperreflective retinal dots on OCT

CaseHPOFreeText: peripapillary sparing was observed on fundus autofluorescence imaging.

CaseNotHPOs: HP:0012045 - Retinal flecks

CaseNotHPOFreeText: N/A

Genotyping Method: Genetic testing was used and after sequencing two variants were found on the ABCA4 gene.

PreviouslyPublished: N/A

Variant: NM_000350.3(ABCA4):c.3523-2A>G

Variant: NM_000350.3(ABCA4):c.2249T>C (p.Leu750Pro)

ClinVar: Variation ID: 866764

ClinVar: Variation ID: 417984

CAID: N/A

SupplementalData: N/A

Case#: Patient female, 10y, ethnicity not reported

DiseaseAssertion: Stargardt disease (STGD1), early onset

FamilyInfo: autosomal recessive inheritance; co-segregation of variants in parents (each heterozygous). Pedigree shown in Figure 1A. One unaffected sibling reported.

CasePresentingHPOs: HP:0007663, HP:0007754, HP:0002587, HP:0030636, HP:0000548

CaseHPOFreeText: early-onset visual decline (age 7), symmetric disease in both eyes, hyperautofluorescent ring surrounding macular atrophy, lipofuscin accumulation, photoreceptor degeneration.

CaseNotHPOs: HP:0007707

CaseNotHPOFreeText: normal anterior segment on slit lamp exam; no external ocular abnormalities reported.

Genotyping Method: Sanger sequencing confirmation; variant identification likely via next-generation sequencing (not explicitly stated).

PreviouslyPublished: n/a

Variant: ABCA4 NM_000350.2: c.6817-713A>G; c.3259G>A (p.Glu1087Lys)

ClinVar: n/a

CAID: CA2837995439, CA227097

SupplementalData: phenotype and validation data in Figures 1–5 and Supplemental Figures S1–S5

Case#: Patient 37 yo, F, Eastern Asian, onset at 8yo (early onset), Heterozygous, AR inheritance patterns

DiseaseAssertion:Retinitis Pigmentosa (RP)

FamilyInfo: Two brothers with RP and father with poor vision at 30 yo but no formal diagnosis

CasePresentingHPOs: HP:0003581, HP:0007737, HP:0000510, HP:000133

CaseHPOFreeText: N/A

CaseNotHPOs: HP: 0000007, HP:0007663, HP:0000505, HP:0000662

CaseNotHPOFreeText: N/A

Genotyping Method: N/A

PreviouslyPublished: Panel of genes; RP1L1, RP-GRIP1, ABCA4, and GRM6

Variant: c.5501T>C p.(Met1019Ille)

ClinVar: 1481089

SupplementalData: see tables 1 and 2 for genetic variant panel

Case#: Patient 24, male, Caucasian, onset at 50yo, Germany

DiseaseAssertion: STGD

FamilyInfo: co-segregation of variant in 2 family members (siblings) but they do not appear to be affected based on pedigree

CasePresentingHPOs: HP:0030528, HP:0000505, HP:0012508, HP:0001105, HP:0025148

CaseHPOFreeText: progressive paracentral scotoma OU, progressive visual impairment OU (blurry vision). BCVA: OD-0.1, OS-0.22. Tension: 13mmHg/14mmHg. FAF: bilateral hyperautofluorescent macular and peripapillary spots, few spots of paracentral retinal atrophy (foveal sparing). Autofluorescence and deposits (severity): deposits medium, atrophy low. OCT: hyperreflective spots, partially invading into the outer retina, partly confluent lesions of cRORA, foveal sparing, degenerative intraretinal fluid. Central macular thickness: 328µm/322µm. Macular volume: 9.31mm³/9.00mm³. mfERG: bilateral amplitudes in normal range, slight relative reduction in the paracentral areas. Fluorescein angiography: bilateral dark choroid, mild paracentral dye pooling in the late phase. Color vision: Inconspicuous. Clinical examination: pattern-like distribution of the lesions.

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

GenotypingMethod: WES, in-house RD-associated gene panel including 619 candidates and disease-associated genes

PreviouslyPublished: n/a

Variant: ABCA4 NM_000350.2 c.[6601_6602delAG] (p.Arg2201fs);[=], c.[4253+43G>A] p.Ile1377Hisfs3;[=]

CAID: CA227421; CA227172

SupplementalData: phenotype and segregation info in supplemental data (table s1, figure s1)

Case#: 1 female, 12 years old.

DiseaseAssertion: bilateral stage 2B Coats disease. ABCA4 gene mutations were found upon genetic analysis but Stargardt disease was not diagnosed.

FamilyInfo: Single affected individual. Past medical history and family history was reported as normal. No additional information about family is provided in text.

CasePresentingHPOs: HP:0007663 - Reduced visual acuity, HP:0001147 - Retinal exudate, HP:0007763 - Retinal telangiectasia, HP:0025355 - Retinal arteriolar macroaneurysms, HP:0011505- Cystoid macular edema, HP:0020032 - Hyperreflective retinal dots on OCT, HP:0001045 - Vitiligo

CaseHPOFreeText: bilateral significant capillary nonperfusion noted mostly in the temporal retinal periphery together with light-bulb-like capillary dilations and staining of telangiectatic vessels. Mild intravitreal hemorrhage

CaseNotHPOs: HP:0012045 - Retinal flecks, HP:0025010 - Foveal atrophy, HP:0000603 - Central scotoma, HP:0000556 - Retinal dystrophy, HP:0000512 - Abnormal electroretinogram

CaseNotHPOFreeText: Relatively normal foveal architecture.

Genotyping Method: Genetic analysis was performed using Sanger sequencing for the NDP gene, which revealed no pathogenic variants. Exome sequencing was then used with the Illumina HiSeq 2500 platform, which identified two compound heterozygous variants in the ABCA4 gene. Lastly, no mutations were found in the TINF2 gene.

PreviouslyPublished: N/A

Variant: NM_000350.3(ABCA4):c.1373C>T (p.Arg458Cys), NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)

ClinVar: Variation ID: 7888 ( for p.Arg458Cys variant however I believe this is mislabeled for this variant NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu), no variantion ID found for NM_000350.3(ABCA4):c.1373C>T (p.Arg458Cys)

CAID: N/A

SupplementalData: N/A

Case#:Not assigned

DiseaseAssertion:MPS type I with evidence of cognitive impairment defined as a score of at least 1 SD below mean on IQ testing or in one domain of neuropsychological function; attenuated MPS I

FamilyInfo:No information

CasePresentingHPOs:HP:0100543

CaseHPOFreeText:

CaseNotHPOs:HP:0032557

CaseNotHPOFreeText:Subjects were excluded if they had undergone hematopoietic stem cell transplantation, were unable to comply with study procedures, had significant lumbar pathology precluding access to the intrathecal space via lumbar puncture, or significantly impaired spinal CSF flow as detected on a nuclear medicine flow study as part of screening.

CaseEnzymeAssay:No information

CaseUrineGAGs:No information

CaseERT:Yes

CaseBMT:No (exclusion criterion)

Variant1:L238Q

Variant1ClinVarID:265418

Variant1CAID:

Variant2:W402X

Variant2ClinVarID:

Variant2CAID:

AdditionalVariants:N/A

ParentalGenotype:Not specified

PreviouslyPublished

Case#:Not assigned

DiseaseAssertion:MPS type I with evidence of cognitive impairment defined as a score of at least 1 SD below mean on IQ testing or in one domain of neuropsychological function; attenuated MPS I

FamilyInfo:No information

CasePresentingHPOs:HP:0100543

CaseHPOFreeText:

CaseNotHPOs:HP:0032557

CaseNotHPOFreeText:Subjects were excluded if they had undergone hematopoietic stem cell transplantation, were unable to comply with study procedures, had significant lumbar pathology precluding access to the intrathecal space via lumbar puncture, or significantly impaired spinal CSF flow as detected on a nuclear medicine flow study as part of screening.

CaseEnzymeAssay:No information

CaseUrineGAGs:No information

CaseERT:Yes

CaseBMT:No (exclusion criterion)

Variant1:L238Q

Variant1ClinVarID:265418

Variant1CAID:

Variant2:63delC

Variant2ClinVarID:

Variant2CAID:

AdditionalVariants:N/A

ParentalGenotype:Not specified

PreviouslyPublished

Case#:Not assigned

DiseaseAssertion:MPS type I with evidence of cognitive impairment defined as a score of at least 1 SD below mean on IQ testing or in one domain of neuropsychological function; attenuated MPS I

FamilyInfo:No information

CasePresentingHPOs:HP:0100543

CaseHPOFreeText:

CaseNotHPOs:HP:0032557

CaseNotHPOFreeText:Subjects were excluded if they had undergone hematopoietic stem cell transplantation, were unable to comply with study procedures, had significant lumbar pathology precluding access to the intrathecal space via lumbar puncture, or significantly impaired spinal CSF flow as detected on a nuclear medicine flow study as part of screening.

CaseEnzymeAssay:No information

CaseUrineGAGs:No information

CaseERT:Yes

CaseBMT:No (exclusion criterion)

Variant1:65delC

Variant1ClinVarID:

Variant1CAID:

Variant2:H240R

Variant2ClinVarID:947028

Variant2CAID:

AdditionalVariants:N/A

ParentalGenotype:Not specified

PreviouslyPublished