Case#: Case1, Sex:Male, Age:19

DiseaseAssertion: STGD

FamilyInfo: n/a

CasePresentingHPOs: n/a

CaseHPOFreeText: Clinical Notes: Peripapillary sparing, discrete flecks; nummular atrophy. General notes: Panretinal cone dysfunction with preserved rod function was documented by ERG

CaseNotHPOs:n/a

CaseNotHPOFreeText: n/a

Genotyping Method: Whole exome sequencing data generation. Additional sequencing targeted amplification fo PRPH2 and ELOVL4 using PCR.

PreviouslyPublished: n/a

Variant: Variant 1 given as p.N965S; NM_000350.3(ABCA4):c.2894A>G (p.Asn965Ser). Variant 2 given as p.R2038W; NM_000350.3(ABCA4):c.6112C>T (p.Arg2038Trp)

ClinVar: Variation ID: 236096; Variation ID: 99430

CAID: CA958124; CA227368

SupplementalData: Proband variant information given in Table 1.

PMID: 10612508

Gene: ABCA4

Case#: Patient 1, 40-year-old female

DiseaseAssertion: STGD1

FamilyInfo: One of four affected siblings in a family of eight. Segregation consistent with autosomal recessive inheritance.

CasePresentingHPOs: HP:0000545 — Decreased visual acuity HP:0000612 — Central scotoma HP:0007754 — Macular atrophy HP:0030638 — Retinal flecks HP:0000512 — Abnormal fundus morphology

CaseHPOFreeText: Progressive decline in visual acuity since age 15. Best-corrected visual acuity RE 20/400, LE 20/150. Central scotomas reported. Fundus exam showed bilateral central macular atrophy (worse in right eye), pigment deposits at the level of the retinal pigment epithelium, and numerous yellow flecks in the midperiphery. Fluorescein angiography demonstrated central hypofluorescence corresponding to atrophy with surrounding hyperfluorescence and peripheral dark choroid.

CaseNotHPOs: HP:0000662 — Night blindness (absent)

CaseNotHPOFreeText: Patient denied nyctalopia.

GenotypingMethod: PCR amplification and direct sequencing of all 50 exons of ABCA4 following SSCP screening.

PreviouslyPublished: Yes

Variant: NM_000350.2:c.2588G>C (p.Gly863Ala) NM_000350.2:c.161G>A (p.Cys54Tyr)

ClinVar: Not reported

CAID: Not reported

SupplementalData: Segregation demonstrated in pedigree (Figure 1); mutation confirmation by sequencing (Figure 4)

Case#: Patient 10, female, Lithuanian, onset at 6yo

DiseaseAssertion: STGD

FamilyInfo:Both parents and older brother healthy; no clinical signs in grandparents or extended family; inheritance most likely autosomal recessive

CasePresentingHPOs: HP:0000505, HP:0012508, HP:0001105, HP:0025148, HP:0000662

CaseHPOFreeText: progressive central vision loss from age 6; visual acuity dropped from OD=0.3, OS=0.3 to OD=0.08, OS=0.1 over 4 years; fundus examination: yellow pisciform flecks at the maculae; OCT: thin atrophic neurosensory retina in foveal region, altered photoreceptor reflectivity, thinner RPE; ERG: loss of scotopic b-waves, attenuated scotopic a-wave, missing oscillatory potentials, loss of photopic a- and b-waves; “bull’s eye” maculopathy noted

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: RetChip v1.0 STGD-module array and confirmation by Sanger sequencing

PreviouslyPublished: n/a

Variant: ABCA4 NM_000350.2 c.1622T>C p.(L541P), NM_000350.2 c.3113C>T p.(A1038V)

CAID: CA226911, CA119135

SupplementalData: clinical images, OCT, ERG, and pedigree information included in supplemental data (Figs. 1–5)

Case Annotation Template

Case#: Patient 2, female, age 62

DiseaseAssertion: STGD

FamilyInfo: diagnosis of autosomal recessive STGD based on the pedigree and clinical phenotype of fleck deposits with or without genetic testing

CasePresentingHPOs: HP:0000608, HP:0000007, HP:0030610, HP:0030500

CaseHPOFreeText: Macular degeneration. autosomal recessive, Photoreceptor outer segment loss on macular OCT, Yellow/white lesions of the macula

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: n/a

PreviouslyPublished: n/a

Variant: ENST00000370225.4:c.1222C>T

ClinVar: NM_000350.3(ABCA4):c.1222C>T (p.Arg408Ter)

CAID: CA179692

SupplementalData: composite mask analysis shown in figure 3 for patient 2, "Both patient 2 and 14 show foveal preservation of IS/OS and RPE," "Patients 2, 19, and 11 show large areas of matched degeneration and isolated IS/OS loss, "

Case#: Patient 10, female, age 19

DiseaseAssertion: STGD

FamilyInfo: diagnosis of autosomal recessive STGD based on the pedigree and clinical phenotype of fleck deposits with or without genetic testing

CasePresentingHPOs: HP:0000608, HP:0000007, HP:0030610, HP:0030500

CaseHPOFreeText: Macular degeneration. autosomal recessive, Photoreceptor outer segment loss on macular OCT, Yellow/white lesions of the macula

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: n/a

PreviouslyPublished: n/a

Variant: Allele 1: NM_000350.3:c.2588G>C Allele 2: NM_000350.3:c.1222C>T

ClinVar: Allele 1: NM_000350.3(ABCA4):c.2588G>C (p.Gly863Ala) Allele 2: NM_000350.3(ABCA4):c.1222C>T (p.Arg408Ter)

CAID: Allele 1: CA119128 Allele 2: CA179692

SupplementalData: composite mask analysis shown in figure 3 for patient 10

MonDO: MONDO:0019353

Case: Family SG-04 Patient II:1. Indian Male, 26 years old diagnosed with Stargardt's disease DiseaseAssertion: Stargardt disease

FamilyInfo: Only child of nonconsanguineous parents. Proband's unaffected mother (I:1) harbored only one heterozygous variant (p.Gly1961Glu) in ABCA4. His father (I:2) was clinically normal and was not included for genetic testing.

CasePresentingHPOs: HP:0001129, HP:0007401 (Large central visual field defect, Macular atrophy)

CaseHPOFreeText: atrophic macular lesions

CaseNOTHPOs: HP:0011507 (macular flecks)

CasePreviousTesting: Five clinically confirmed unrelated patients with Stargardt disease and their available family members were enrolled for genetic analysis. Study subjects underwent a complete ophthalmic examination including measurement of visual acuity, intraocular pressure, slit lamp biomicroscopy, detailed fundus examination, fundus photography, fundus autofluorescence (FAF), spectral domain optical coherence tomography (SD-OCT), and full field electroretinography (ERG). Fifty normal controls without any history of eye diseases were included.

GenotypingMethod: NGS panel testing targeting 184 genes with previously known pathogenic variations associated with multiple eye disorders. Peripheral blood samples were obtained from all subjects.

MultipleGeneVariants:

(1) GeneName: ABCA4

(1) Variant: p.Gly1961Glu

(1) CAID: CA119132

(1) gnomAD: The total minor allele frequency in gnomAD v4.1.0 is 0.003406 (5498/1614012 alleles).

(2) GeneName: ABCA4

(2) Variant: p.Tyr872X

(2) CAID: CA341276149

(2) gnomAD: Not found in gnomad v. 4.1

Case#: 32-year old woman, onset in early twenties

DiseaseAssertion: STGD1

FamilyInfo: n/a

CasePresentingHPOs: HP:0011462, HP:0011507, HP:0000505, HP:0007722, HP:0030500, HP:0030329, HP:0030610, HP:0000575, HP:0030602

CaseHPOFreeText: Patient’s best-corrected visual acuity was OD: 20/200 and OS: 20/40. Refractive error was OD: −5.25/−0.75 × 4° and OS: −5.75/−0.50 × 133°. Flecks in macular area extended anterior to the vascular arcades and the optic disc in both eyes. Atrophic lesion in the macula with flecks observed across the posterior pole. IS/OS junction loss central macular area bilaterally. Absolute scotoma in left eye (ie total deviation −20 dB). Defect in the RPE/Bruch membrane complex was observed on SD-OCT in both eyes in the central macula. The defects in the RPE-Bruch membrane complex measured OD: 332 um and OS: 266 um in maximum horizontal diameter. Herniation of the retina through these defects into the sub-RPE/choroidal space. Abnormal thickening of the RPE in the parafoveal region. Normal amplitudes and implicit times in both rod and cone photoreceptor systems were detected by ERG.

CaseNotHPOs: HP:0000510, HP:0007984

CaseNotHPOFreeText: Normal amplitudes and implicit times in both rod and cone photoreceptor systems were detected by ERG. There was no evidence of sub-RPE choroidal neovascularization (CNV), pigment epithelial defects (PED) or subretinal fluid.

Genotyping Method: ABCR 600 micro-array chip

PreviouslyPublished: n/a

Variant: NM_000350.3(ABCA4):c.5714+5G>A

ClinVar: 99403

SupplementalData: n/a

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#: Female, 69yo, Puerto Rican

DiseaseAssertion: STDG1

FamilyInfo: Parents were first cousins (consanguinity), no other family history reported

CasePresentingHPOs: HP:0030603, HP:0007754, HP:0000512, HP:0008020, HP:0000603

CaseHPOFreeText: progressive vision loss, severe reduction in visual acuity (counting fingers at 5’ and 3’), bilateral central scotoma, extensive central macular atrophy, retinal pigment epithelium atrophy and pigment hyperplasia, multifocal retinal atrophy, central hypoautofluorescence with peripheral expansion, reduced macular thickness and volume on OCT, abnormal visual field (marked mean deviation)

CaseNotHPOs: HP:0000510

CaseNotHPOFreeText: normal rod response on full-field electroretinogram

Genotyping Method: Next-generation sequencing (Invitae Corporation, San Francisco, California)

PreviouslyPublished: N/A

Variant: NM_000350.3(ABCA4):c.5714+5G>A

ClinVar: ClinVarID:99403

CAID: N/A

SupplementalData: N/A

Case#: Male, mid-40s

DiseaseAssertion: STGD1

FamilyInfo: Retinal disease reported in sibling and material grandfather. Mother exhibited decreased visual acuity, BEM in right eye, and tapetal reflex in both eyes.

CasePresentingHPOs: HP:0000622, HP:0000613, HP:0000662, HP:0011504, HP:0007663, HP:0011463

CaseHPOFreeText: n/a

CaseNotHPOs: HP:0007843, HP:0011507

CaseNotHPOFreeText: Autofluorescence(qAF): 381.5. The Case's qAF was noted to be in the range observed in healthy eyes, and also lower than many other STGD1 patients with the same age. There were no flecks, intraretinal pigment migration, retinal vessel attenuation, or optic nerve pallor (Figure 1).

Genotyping Method: Sanger Sequencing

PreviouslyPublished: n/a

Variant: NM_000350.3(ABCA4):c.1411G>A (p.Glu471Lys), NM_001034853.2(RPGR):c.3070G>T (p.Glu1024Ter)

ClinVar: 99052, 1275798

SupplementalData: n/a

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#: patient, 11, Somali, onset 8yo

DiseaseAssertion: STGD

FamilyInfo: parents and four siblings did not report visual issues

CasePresentingHPOs: HP:0000007, HP:0011504, HP:0000608

CaseHPOFreeText: BCVA 20/70 OD, 20/80 OS. Bull's eye maculopathy. Outer retinal and RPE atrophy. Slight opacity at level of RPE; loss of outer retinal structures in central area. Normal peripheral retina.

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: whole genome

PreviouslyPublished: PMID:28559085

Variant: NM_000350.3:c.5882G>A p.(Gly1961Glu) ; NM_000350.3:c.634C>T p.(Arg212Cys)

ClinVar:7888; 7898

CAID:n/a

SupplementalData:n/a

Case Annotation Template

Case#: Patient 40, female, Caucasian, onset at 2-3yo, Spain

DiseaseAssertion: STGD

FamilyInfo: Brother and Sister not affected showed heterozygous patterns of (p.His423Arg (c.1268A>G), IVS33+48 C>T) mutations. R1129L mutation heterozygous in the unaffected father; mutation not found in the unaffected mother. Patient has 4yo asymptomatic female child

CasePresentingHPOs: HP:0000505, HP: 0011463, HP:0030786, HP:0007641, HP:0007663, HP: 0000610, HP: 0007814, HP:0000007

CaseHPOFreeText: Macular yellow flecks, macular dystrophy

CaseNotHPOs: N/A

CaseNotHPOFreeText: Normal biomicroscopy

Genotyping Method: Conventional mutational screening on 77 STGD families and screened on the ABCR400 Microarray. Haplotype analyses, HR karyotypes, and MLPA were also performed.

PreviouslyPublished: N/A

Variant: p.Arg1129Leu (c.3386G>T)

CAID: CA227116

SupplementalData:N/A

Case#: Male, 60

DiseaseAssertion: Stargardt disease

FamilyInfo: Possible macular degeneration in father

CasePresentingHPOs: HP:0007401, HP:0025010

CaseHPOFreeText: Vision was 20/40 in the right eye and 20/20 in the left eye. Dilated examination revealed scattered subretinal yellow flecks and macular atrophy bilaterally. The flecks were hyperautofluorescent. Fluorescein angiography showed obscuration of background choroidal fluorescence and window defects associated with the atrophy. Optical coherence tomography showed foveal atrophy and hyperreflective deposits at the level of the retinal pigment epithelium.

CaseNotHPOs: N/A

CaseNotHPOFreeText: Anterior segment examination was unremarkable. Normal cone and rod responses.

CasePreviousTesting: Target enrichment and next-generation sequencing were performed.

GenotypingMethod: N/A

PreviouslyPublished: N/A

Variant: Variant 1: NM_000350.3:c.5461-10T>C Variant 2: NM_000350.3:c.5603A>T

ClinVar: Variant 1: 92870 Variant 2: 99390

gnomAD: N/A

SupplementalData: Figure 1 shows fundus photographs (A and B), fundus autofluorescence (C and D), fluorescein angiography (E and F), near-infrared reflectance imaging (G), and an optical coherence tomography scan (H).

Case #: Male, 60 years old

DiseaseAssertion: He was diagnosed with late-onset Stargardts disease.

FamilyInfo: Has a family history with his father possibly having macular degeneration.

CasePresentingHPOs: HP:0007401, HP:0025010, HP:0012045 (sub-retinal/yellow), HP:0030602

CaseHPOFreeText: Proband presents with blurry vision (right eye) from over the past two years, with the right eye having 20/40 vision, while the left was 20/20. In addition to this, through dilation scattered subretinal yellow flecks and macular atrophy bilaterally, were revealed. The flecks were hyperautofluorescent. Obscuration of background choroidal fluorescence and window defects were also found. As well as foveal atrophy and hyperreflective deposits (RPE).

CaseNotHPOs: None found

CaseNotHPOFreeText: No abnormalities in the anterior segment examination. Through a full-field electroretinogram, normal rod and cone responses were found.

Genotyping Method: The genotyping was done through the use of target enrichment and next-generation sequencing.

PreviouslyPublished: N/a

Variant: 1) NM_000350.3(ABCA4):c.5461-10T>C 2) NM_000350.3(ABCA4):c.5603A>T (p.Asn1868Ile)

ClinVar: 1) 92870 2) 99390

CAID: N/a

gnomAD: 1) Highest minor allele frequency was 0.00031 (https://www.ncbi.nlm.nih.gov/clinvar/variation/92870/) 2) Highest minor allele frequency was 0.05787 (https://www.ncbi.nlm.nih.gov/clinvar/variation/99390/)

SupplementalData: I was able to find a variant (NM_000350.3(ABCA4):c.[5461-10T>C;5603A>T]) that addresses both of the variants. Also, Fig.1 shows the phenotype of the proband through tests.

Case#: a 46-year-old male

DiseaseAssertion: Pseudoxanthoma elasticum (PXE)

FamilyInfo: NR

CasePresentingHPOs: HP:0200034, HP:0011506, HP:0001102, HP:0025533, HP:0007401, HP:0200056, HP:0007754, HP:0031526, HP:0007663

CaseHPOFreeText: skin papules, CNV in right eye, angioid steaks, peau d'orange, peripheral comet lesions and macular atrophy at the poseterior pole (more severe in left eye). Juxtafoveal pigmented scar in right eye and fibrotic tissue at the interpapillomacular region in left eye. Pattern dystrophy-like changes were evident at posterior pole. OCT scan showed subretinal fluid with ellipsoid zone abnormalities at the fovea with juxtafoveal hyperreflective alteration corresponding to the fundus scar in the right eye. At the interpapillomacular region, the atrophy of the outer retinal layer and RPE was evident (hypertransmission phenomenon). In left eye, OCT scan showed widespread RPE atrophy with atrophy of the outer retinal layers. 6/10 visual acuity in right eye and 1/20 in left eye.

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

Genotyping Method: Whole exome sequencing analysis focusing on 340 genes associated with the calcification process or inherited retinal diseases

PreviouslyPublished: NR

Variant: c.6647C>T, p.Ala2216Val, NM_000350.3

ClinVar: 236149

CAID: CA10602405

SupplementalData: NR

Case#: Patient 66yo, M, Japan, Symptoms in teens

DiseaseAssertion: Stargardt (STGD) Heterozygous, Autosomal recessive

FamilyInfo: No family with similar symptoms

CasePresentingHPOs: HP:0008002, HP:0007722, HP:0000610, HP:0000602

CaseHPOFreeText: Ring shaped paracentral scotoma

CaseNotHPOs: HP: 0030329, HP:0000608, HP:0000493

CaseNotHPOFreeText: Well preserved foveal function, well preserved retinal, and normal thickness RPE

Genotyping Method: N/A

PreviouslyPublished: 4 other polymorphisms

Variant: c.839T>C p.Met280Thr Heterozygous

ClinVar: 1349490

SupplementalData: see tables 1 for gene variant and found polymorphisms

Case#: a 56-year-old female

DiseaseAssertion: Pseudoxanthoma elasticum (PXE)

FamilyInfo: NR

CasePresentingHPOs: HP:0200034, HP:0001102, HP:0025533, HP:0011506, HP:0500087

CaseHPOFreeText: Papules on neck and axillae, marked skin laxity and redundance in neck, axillae, periumbilican area, groyne, and inner thighs, angioid streaks, peau d'orange. In right eye, a CNV, a large peripapillary atrophy, a small iuxafoveal scar, and RPE-Bruch's membrane complex normalities nasally to the fovea.

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

Genotyping Method: Next generation sequencing focusing on 362 genes associated with calcification-related diseases and inherited retinal diseases

PreviouslyPublished: NR

Variant: c.1928T>G, p.Val643Gly, NM_000350.3

ClinVar: 99102

CAID: CA226958

SupplementalData: This variant has been reported likely pathogenic in VarSome and literature.

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

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

Case#: patient, 12, Somali, onset 5yo

DiseaseAssertion: STGD

FamilyInfo: parents and 5 siblings did not report visual issues

CasePresentingHPOs: HP:0000007, HP:0011504, HP:0000608

CaseHPOFreeText: BCVA 20/135 OD; 20/100 OS. Red-green color deficit. Bull's eye maculopathy, but no pallor of optic disc. Normal peripheral retina. Loss of macular photoreceptor layer; severely reduced cone function.

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: whole exome sequencing

PreviouslyPublished: n/a

Variant: NM_000350.3:c.5882G>A p.(Gly1961Glu) ; NM_000350.3:c.634C>T p.(Arg212Cys)

ClinVar: 7888; 7898

CAID: n/a

SupplementalData: n/a

Case#: Case 3, male, onset at 24yo, Italy

DiseaseAssertion: STGD1

FamilyInfo: third-degree consanguineous parents; both parents healthy heterozygous carriers of the ABCA4 variant

CasePresentingHPOs: HP:0000529, HP:0007754, HP:0000518

CaseHPOFreeText: progressive deterioration of vision at age 24. Bilateral macular dystrophy and diffuse lens opacities on ophthalmologic examination. OCT, ERG, and VEP consistent with Stargardt maculopathy.

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: NGS (custom enrichment panel), Illumina NextSeq550; variant confirmed by Sanger sequencing.

PreviouslyPublished: n/a

Variant: NM_000350.3(ABCA4):c.2828G>A (p.Arg943Gln), homozygous; rs1801581

ClinVar: Variation ID: 7913

CAID: n/a

SupplementalData: n/a

Case#: a 29-year-old man

DiseaseAssertion: Stargardt Disease

FamilyInfo: NR

CasePresentingHPOs: HP:0007663

CaseHPOFreeText: 20/70 visual acuity in both eyes

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

Genotyping Method: ABCA4 microarray (ABCR5000 chip)

PreviouslyPublished: NR

Variant: NM_000350.3:c.5882G>A, p.G1961E and c.5018+2C>T (rare splice variant)

ClinVar: 7888, NR

CAID: CA119132, NR

SupplementalData: No CAID or ClinVar ID were found for the rare splice variant c.5018+2C>T

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#: Patient 11, male, age 53

DiseaseAssertion: STGD

FamilyInfo: diagnosis of autosomal recessive STGD based on the pedigree and clinical phenotype of fleck deposits with or without genetic testing

CasePresentingHPOs: HP:0000608, HP:0000007, HP:0030610, HP:0030500

CaseHPOFreeText: Macular degeneration. autosomal recessive, Photoreceptor outer segment loss on macular OCT, Yellow/white lesions of the macula

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: n/a

PreviouslyPublished: n/a

Variant: NM_000350.3:c.5461-10T>C

ClinVar: NM_000350.3(ABCA4):c.5461-10T>C

CAID: CA220687

SupplementalData: composite mask analysis shown in figure 3 for patient 11, show large areas of matched degeneration and isolated IS/OS loss

Case#: Patient 14, female, age 42

DiseaseAssertion: STGD

FamilyInfo: diagnosis of autosomal recessive STGD based on the pedigree and clinical phenotype of fleck deposits with or without genetic testing

CasePresentingHPOs: HP:0000608, HP:0000007, HP:0030610, HP:0030500

CaseHPOFreeText: Macular degeneration. autosomal recessive, Photoreceptor outer segment loss on macular OCT, Yellow/white lesions of the macula

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: n/a

PreviouslyPublished: n/a

Variant: Allele 1: NM_000350.3:c.4222T>C Allele 2: NM_000350.3:c.4918C>T

ClinVar:Allele 1: NM_000350.3(ABCA4):c.4222T>C (p.Trp1408Arg) Allele 2: NM_000350.3(ABCA4):c.4918C>T (p.Arg1640Trp)

CAID:Allele 1: CA227166 Allele 2: CA227253

SupplementalData: composite mask analysis shown in figure 3 for patient 14, show diffusely intact IS/OS and RPE with central area of mixed types of degeneration. Both patient 2 and 14 show foveal preservation of IS/OS and RPE

Case#: 1 male, 24 years old, from consanguineous parents, Somali ancestry.

DiseaseAssertion: ABCA4-related retinopathy Stargardt disease

FamilyInfo: Single affected individual consanguineous parents, Somali ancestry. No additional information about family is provided in text.

CasePresentingHPOs: HP:0000572- reduced central vision, HP:0001102- Angioid streaks, HP:0007980- retinal pigment epithelium atrophy, HP:0007401- Macular atrophy, HP:0000630- Abnormal retinal arterial/arteriolar morphology

CaseHPOFreeText: Presents with reduced central vision, Fundus autofluorescence (FAF) showed angioid streaks, reduced signal in the central macula indicative of retinal pigment epithelium atrophy. Electrophysiological testing showed severe macular dysfunction with generalized retinal involvement.

CaseNotHPOs: HP:0200070- Peripheral retinal atrophy

CaseNotHPOFreeText: Peripheral retina appears unaffected after ultra-widefield FAF imaging

Genotyping Method: PCR-amplification and Sanger sequencing of ABCA4 on Exon 42, Stargardt/Macular dystrophy SmartPanel v5; Molecular Vision Laboratory, Hillsboro, Oregon tested DNA for mutations which confirmed findings of ABCA4, with no additional pathogenic mutations found.

PreviouslyPublished: PMID: 22261738, 1 male, 24 years old, from consanguineous parents, Somali ancestry presenting with reduced vision.

Variant: NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)

ClinVar: Variation ID: 7888

CAID: N/A

SupplementalData: N/A

Case#: Case 6, Sex:Female, Age:34

DiseaseAssertion: STGD

FamilyInfo: n/a

CasePresentingHPOs: n/a

CaseHPOFreeText: Clinical Notes: Classic Stargardt. General notes: participant had classic features of STGD and field ERG showed abnormal cone responses with preserved rod function.

CaseNotHPOs:n/a

CaseNotHPOFreeText: n/a

Genotyping Method: Exome sequencing data generation. Additional sequencing targeted amplification fo PRPH2 and ELOVL4 using PCR.

PreviouslyPublished: n/a

Variant: ABCA4, NM_000350.3(ABCA4):c.2966T>C (p.Val989Ala)

ClinVar: Variation ID: 99180

SupplementalData: Proband variant information given in Table 1.

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#: a 45-year-old man from Sardinia, Italy

DiseaseAssertion: Cone rod dystrophy

FamilyInfo: Five members, this patient is the only one affected by CRD

CasePresentingHPOs: HP:0000505, HP:0007663, HP:0000603, HP:0001123, HP:0000608, HP:0007401, HP:0011504, HP:0000548, HP:0030329, HP:0000543

CaseHPOFreeText: 1998: Subacute central vision loss in both eyes, choroidal and RPE atrophy surrounding left fovea and small white patches of atrophy around right fovea. Pale appearance of optic disc in both eyes. Punctate retinal pigment epitheliopathy observed bilaterally in midperipheral retina, hyperfluorescent macular regions suggesting bull's eye maculopathy. Paracentral ring scotoma, surrounded by a relative annular scotoma, early and predominant involvement of photopic over scotopic responses; 2018: BCVA was bilateral light perception with visual field extinction. FAF showed a central round area of decreased autofluorescence corresponding to area of macular atrophy, surrounded by an area of relatively increased autofluorescence. Several roundish areas of reduced autofluorescence in midperipheral retina. Severe macular atrophy surrounded by a ring of preserved RPE in both eyes. Sparse pigmentary deposits in midperipheral retina of both eyes. Severe bilateral retinal thinning with disappearance of external retinal layers. Outer retina tubulations

CaseNotHPOs: HP:0025148

CaseNotHPOFreeText: No pigment deposits on optic disc, no dark choroid

Genotyping Method: Candidate gene approach on ABCA4 followed by whole exome sequencing

PreviouslyPublished: NR

Variant: NM_000350, c.4535C>G, p.P1512R

ClinVar: 99291

CAID: CA227203

SupplementalData: Patient's healthy brother showed the same molecular condition for ABCA4. Patient also has 2 novel frameshift mutations in C2orf71.

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#: a 12-year-old female admitted to the B Department Hédi Raies institut of Ophtalmology in Tunis, Tunisia

DiseaseAssertion: Cone rod dystrophy

FamilyInfo: No parental consanguinity nor pathological or opthalmological history in the family

CasePresentingHPOs: HP:0000529, HP:0000662, HP:0001141, HP:0000543,HP:0007737, HP:0030602

CaseHPOFreeText: progressive visual loss, poor night vision, 1/20 visual acuity in both eyes, pallor of the optic disk, attenuated retinal vessels, paravascular bone spiculed pigmentations and an epimacular membrane, paravascular and macular heterogeneous hypoautofluorescence, diffuse alteration of ellipsoid zone, decreased photopic and scotopic responses.

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

Genotyping Method: Whole exome sequencing, Sanger sequencing

PreviouslyPublished: NR

Variant: c.885delC, NM_000350.3

ClinVar: 438109

CAID: CA958684

SupplementalData: Karyotyping showed monosomy 45,X in the patient

Case#: Patient 9, female, Mexican, symptoms onset 6 yrs. ago, Mexico City

DiseaseAssertion: IRD

FamilyInfo: parents are non-sanguineous and asymptomatic, they also denied any history related to ocular diseases. Information disclosed that the mother had one stillbirth and three miscarriages, but denied any related diseases/health issues to this child.

CasePresentingHPOs: HP:00305, HP:00080, HP:0000493, HP:0025586, HP:0030329, HP:0012713

CaseHPOFreeText: Proband presented with light sensitivity as well as adaptation difficulties when going from dark-to-light. Right eye was 20/200 and left eye was 20/160 from the visual acuity test. Macular bull's eye appearance. Subnormal rod and cone responses. Peripapillary sparing retina.

CaseNotHPOs: HP:0007737, HP:0000750, HP:0000510

CaseNotHPOFreeText: No afferent pupillary defect. No anomalies in anterior segment.

Genotyping Method: QIAamp DNA Blood Kit was used to extract gDNA and quantification/purity of the sample was found using a NanoDrop 2000 spectrophotometer. 293 genes were sequenced. gDNA was sequenced via Illumina technology. Following, certain sequences were additionally analyzed against a reference genome in order to identify changes and interpret.

PreviouslyPublished: n/a

Variant: NM_000350.3(ABCA4):c.4926C>G (p.Ser1642Arg), NM_000350.3(ABCA4):c.5044_5058del (p.Val1682_Val1686del)

ClinVar: 99332, 99340

CAID: n/a

SupplementalData: Phenotype data in results section as well as figures 1, 2, and 3 showing phenotypic testing results.

Case#: Patient 66yo, M, Japan, Symptoms in teens

DiseaseAssertion: Stargardt (STGD) Heterozygous, Autosomal recessive

FamilyInfo: No family with similar symptoms

CasePresentingHPOs: HP:0008002, HP:0007722, HP:0000610, HP:0000602

CaseHPOFreeText: Ring shaped paracentral scotoma

CaseNotHPOs: HP: 0030329, HP:0000608, HP:0000493

CaseNotHPOFreeText: Well preserved foveal function, well preserved retinal, and normal thickness RPE

Genotyping Method: N/A

PreviouslyPublished: 4 other polymorphisms

Variant: c.839T>C p.Met280Thr Heterozygous

ClinVar: 1349490

SupplementalData: see tables 1 for gene variant and found polymorphisms

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 19, female, age 16

DiseaseAssertion: STGD

FamilyInfo: diagnosis of autosomal recessive STGD based on the pedigree and clinical phenotype of fleck deposits with or without genetic testing

CasePresentingHPOs: HP:0000608, HP:0000007, HP:0030610, HP:0030500

CaseHPOFreeText: Macular degeneration. autosomal recessive, Photoreceptor outer segment loss on macular OCT, Yellow/white lesions of the macula

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: n/a

PreviouslyPublished: n/a

Variant: Allele 1: NM_000350.3:c.5714+5G>A Allele 2: NM_000350.3:c.4469G>A

ClinVar: Allele 1: NM_000350.3(ABCA4):c.5714+5G>A Allele 2: NM_000350.3(ABCA4):c.4469G>A (p.Cys1490Tyr)

CAID: Allele 1: CA227338 Allele 2: CA227198

SupplementalData: composite mask analysis shown in figure 3 for patient 19, show large areas of matched degeneration and isolated IS/OS loss

Case#: 14-year-old, female, asian (Chinese) patient

DiseaseAssertion: ABCA-4 associated retinal dystrophy

FamilyInfo: The effect of the deep intronic variant on splicing was validated by a minigene assay in our previous study (Tian et al., 2022). Co-segregation analysis result exhibited that the variant c.1222C>T p.(Arg408Ter) came from the female parent, and the deep intronic variant c.2919-884G>T p.[Phe973LeufsTer3,=] from the male parent

ParentalTesting: Co-segregation analysis result exhibited that the variant c.1222C>T p.(Arg408Ter) came from the female parent, and the deep intronic variant c.2919-884G>T p.[Phe973LeufsTer3,=] from the male parent

CasePresentingHPOs: HP:0000556

CasePhenotypeFreeText: ABCA4-associated retinal dystrophy

CaseNotHPOs: NR

CaseNotPhenotypeFreeText: NR

CasePreviousTesting:NR

GenotypingMethod:

In the present study, we recruited a 14-year-old female patient diagnosed with ABCA4-RD. Biallelic variants were found in this patient, including the nonsense variant c.1222C>T p.(Arg408Ter) detected by Sanger sequencing and the deep intronic variant c.2919-884G>T p.[Phe973LeufsTer3,=] identified by next-generation sequencing.

We isolated peripheral blood mononuclear cells (PBMCs) from the patient’s peripheral venous blood and introduced three episomal plasmids containing transcription factors OCT4, SOX2, NANOG, LIN28, c-MYC, KLF4, and SV40LT into PBMCs. The reprogramming iPSC line, named BIOi003-A, showed stabilized morphology (Fig. 1A) and a normal karyotype in culture (Fig. 1B). Then, the endogenous expression of two pluripotent biomarkers, POU5F1 and NANOG, was detected (Table 2). The expression levels were compared with human embryonic stem cell line H1(hESC-H1) and mesenchymal stem cell line P3 (MSC-P3) by qRT-PCR (Fig. 1C). Surface markers SSEA4 and TRA-1–81 were analyzed by flow cytometry (Fig. 1D). the ABCA4 compound heterozygous variants c.(1222C>T;2919-884G>T) p.[Arg408Ter;Phe973LeufsTer3,=] were verified by Sanger sequencing (Fig. 1E). Furthermore, the teratoma assay exhibited the differentiation capacity of this iPSC line in vivo (Fig. 1F). Short tandem repeats (STR) analysis exhibited that the PBMCs and the iPSC line came from the same patient. PCR proved negative for mycoplasma contamination

Variant: NM_000350.3(ABCA4):c.1222C>T (p.Arg408Ter) and NM_000350.3(ABCA4):c.2919G>T (p.Leu973Phe)

LegacyVariant: c.1222C>T (p.Arg408Ter) and c.2919G>T (p.Leu973Phe)

ClinVar: 99035 and NR

CAID: CA179692 and CA341275270

gnomeAD: 1:94544895 G / A and NR

MultipleGeneVariants: No

PreviouslyPublished:No

AdditionalInfo: One patient was homozygous at the ABCA-4 gene, so there is information about both variants in one annotation because there is only one patient.

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#:48-year old man, onset at 13-years old

DiseaseAssertion: STGD1

FamilyInfo: n/a

CasePresentingHPOs: HP:0003621, HP:0025147, HP:0011507, HP:0030329, HP:0030610, HP:0007722, HP:0007703, HP:0007663

CaseHPOFreeText: BCVA was 20/200 bilaterally and refractive error was OD: −1.50/+0.50 × 149° and OS: −1.50/+0.25 × 161°. Hyperautofluorescent transitional zone in each eye more pronounced in right eye. The left eye showed a complete defect of the RPE-Bruch membrane complex with herniation of the outer retina. Maximum horizontal diameter of this RPE-Bruch membrane complex defect was 266um.

CaseNotHPOs: HP:0000510, HP:0000548, HP:0007984

CaseNotHPOFreeText: No defect observed in the RPE and Bruch membrane in right eye. Patient had normal cone and rod responses on ERG

Genotyping Method: ABCR 600 micro-array chip

PreviouslyPublished: n/a

Variant: NM_000350.3(ABCA4):c.4216C>T (p.His1406Tyr), NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu)

ClinVar: 99259, 7888

SupplementalData: n/a

Case#: Case2, Sex:Female, Age:15

DiseaseAssertion: STGD

FamilyInfo: n/a

CasePresentingHPOs: n/a

CaseHPOFreeText: Clinical Notes: Few yellowish Flecks without autofluorescence. General notes: participant presented with atypical macular degeneration.

CaseNotHPOs:n/a

CaseNotHPOFreeText: n/a

Genotyping Method: Exome sequencing data generation. Additional sequencing targeted amplification fo PRPH2 and ELOVL4 using PCR.

PreviouslyPublished: n/a

Variant: Variant 1 given as p.G1961E; NM_000350.3:c.5882G>A p.(Gly1961Glu) . Variant 2 given as p.Q636X; NM_000350.3(ABCA4):c.1906C>T (p.Gln636Ter).

ClinVar: Variation ID: 7888 ; Variation ID: 265012

CAID: ; CA10588302

SupplementalData: Proband variant information given in Table 1.

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

PMID:39398711

Gene: ABCA4

HGNC ID: 34

Case Annotation Template

Case#: 19-year-old male

DiseaseAssertion: Stargardt disease 1 (STGD1)

FamilyInfo: No family history of eye disease reported. Autosomal recessive inheritance consistent with STGD1. Homozygous ABCA4 variant identified.

CasePresentingHPOs: DecreasedCentralVA, MacularAtrophy, MacularFlecks, PeripapillarySparing, OpticNervePallor

CaseHPOFreeText: Five-year history of progressive bilateral central vision loss, worse at near. Alternating exotropia measuring 16 prism diopters in all gazes OU. Best corrected visual acuity 20/200 OU. Fundus examination revealed pigment deposition and macular mottling. Fundus autofluorescence showed central decreased autofluorescence surrounded by increased autofluorescence. Fluorescein angiography demonstrated dark choroid. OCT showed loss of the central ellipsoid zone with hyperreflective deposits. Multifocal ERG demonstrated significant functional loss.

CaseNotHPOs: NightBlindness

CaseNotHPOFreeText: Patient denied nyctalopia, photophobia, or flashes. Color vision normal on Ishihara testing.

Genotyping Method: Genotyping Method: Next-generation sequencing (NGS) with deletion/duplication analysis (Invitae Corporation).

PreviouslyPublished: N/A

Variant: ABCA4 c.52C>T (p.Arg18Trp)

ClinVar: ClinVarID:7899

CAID: N/A

SupplementalData: N/A

Case#: IV-1, male, 11 y.o, Pakistani

DiseaseAssertion: Limb-girdle muscular dystrophy (LGMD2F), sarcoglycanopathy

FamilyInfo: Consanguineous parents, both described as healthy and showing no abnormality. Three unaffected siblings were also reported: IV-2 (male, 10 y.o), IV-4 (male, 7 y.o), and IV-5 (female, 1.5 y.o). A deceased sister is included on the pedigree, but no details about this individual were reported. See Figure 1.

CasePresentingHPOs: HP:0001288, HP:0002650, HP:0003547, HP:0003749, HP:0001655

CaseHPOFreeText: Reduced weight gain noted at 3-4 y.o. Mild cardiac hypertrophy observed on cardiac review (additional echocardiography results reported in "Echocardiography" section). Additional phenotypic information reported in Supplementary Table 1.

CaseNotHPOs: HP:0009077, HP:0000703, HP:0001382, HP:0000365, HP:0001510, HP:0001249, HP:0000478, HP:0030148, HP:0011675

CaseNotHPOFreeText: Extensor muscles of the wrist, toes flexors, and hip abductors noted to be relatively normal. Additional phenotypic information reported in Supplementary Table 1.

MotorAchievement: Sat without assistance at 8 months of age, walked at 15 months of age, ran at 1.5 months of age. Never jumped or hopped. Frequent falls noted, as well as difficulty in walking and climbing stairs since 3 y.o.

CreatineKinase: 18SU (normal: 20SU for children, 10SU for adults) (see Supplementary Table 1). No assertion was made by the authors regarding whether this represents a normal or decreased CK level.

PreviousTesting: Thyroid stimulating hormone: 2.3mU/L (normal: <0.6mU/L); Serum VZV IgG: 286mlU/ml (normal: >150mlU/ml); IGF-1:186 ng/μl (normal: 102-520 ng/μl for males, 14 y.o); PRL: 202 ng/dl (normal: 42.5-414 ng/dl for males); Vitamin D: 47nmol/L (normal: 25-50 nmol/L); Free T4: 17.0 pmol/L (normal:10.8-19.0 pmol/L) (see Supplementary Table 1)

GenotypingMethod: (1) Targeted next generation sequencing of 31 genes associated with LGMD from proband genomic DNA extracted from peripheral blood sample; (2) Sanger sequencing of genomic DNA extracted from peripheral blood samples to confirm SGCD variant of interest in proband and three family members (III-3, III-4, IV-4). Variant was identified in homozygosity in the proband, in heterozygosity in each of the parents, and was not present in the unaffected sibling (IV-4).

Variant: NM_000337.5:c.289C>T (p.Arg97Ter)

CAID: CA3530549

gnomAD: Not reported