Case#: Male, Family #2, patient #4, onset at 48y.o

DiseaseAssertion: STGD

FamilyInfo: proband sister(#3) identical ABCA4 allele to proband, developed central vision issues. Proband son has complex allele w/ early onset cone-rod dystrophy. Proband daughter(#6) has complex allele mutation, central vision issues developed at 17. retinal exam showed atrophic macular lesions. Proband second daughter(patient #5, asymptomatic)

CasePresentingHPOs: HP:0012508, HP:0030500

CaseHPOFreeText:Proband presented with bull's eye macular lesions with no fundus flecks. Normal rod-mediated amplitudes, normal single-flash response, reduces 32-Hz flicker amplitude.

CaseNotHPOs: n/a

CaseNotHPOFreeText: maintained foveal sparing in both eyes 20/25+2 R.E, 20/25+1 L.E.

Genotyping Method: Genotyping performed at Columbia University, sequencing technology used is not disclosed.

PreviouslyPublished: n/a

Variant: c.4139C>T (p.P1380L), BoldM1: c.5603A>T(p.N18681)[NM_000350.3(ABCA4):c.5603A>T (p.Asn1868Ile) - Variation ID 99390], M2: c.[1622T>C; 3113C>T] (p.[L541P; A1308V])

ClinVar: M1) 99390 M2) 99067

CAID: n/a

SupplementalData: Fig 1: Pedigree illustrating ABCA4 variants and the associated Stargardt phenotype for 5 families. Proband Labeled w/ white arrow for each family. Fig 2: retinal scan measuring melanin in 4 patients of family 2. Panel shows bull's-eye ring of RPE atropy. Fig 3: Macular SD-OCT line profile from b-scans. Reflectivity plotted against function of retinal depth. Table 1: table shows patients with p.N18681 variant, type of mutation, and pathogenicity class. Table 2: Patients, age on-set and first symptom

Case#: Female, Family #4, patient #8

DiseaseAssertion: STGD

FamilyInfo: Proband's daughter shares ABCA4 variant and struggled with difficulty focusing at age 19. BVCA 20/200 R.E and 20/80 in L.E.

CasePresentingHPOs: HP:0030500, HP:0007663, HP:0000608

CaseHPOFreeText: Proband's first symptom was difficulty with night vision occurring at 45 y.o, BVCA at 50 y.o in both eyes was 20/20. atrophy in macula and Stage 2 fundus flecks identified.

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: Genotyping performed at Columbia University, sequencing technology used is not disclosed.

PreviouslyPublished: n/a

Variant: NM_000350.3(ABCA4):c.1622T>C (p.Leu541Pro), NM_000350.3(ABCA4):c.1957C>T (p.Arg653Cys)

ClinVar: M2) 99067, M5) 99108

CAID: n/a

SupplementalData: Fig 1: Pedigree illustrating ABCA4 variants and the associated Stargardt phenotype for 5 families. Proband Labeled w/ white arrow for each family. Fig 2: retinal scan measuring melanin in 4 patients of family 2. Panel shows bull's-eye ring of RPE atropy. Fig 3: Macular SD-OCT line profile from b-scans. Reflectivity plotted against function of retinal depth. Table 1: table shows patients with p.N18681 variant, type of mutation, and pathogenicity class. Table 2: Patients, age on-set and first symptom

Case#: Male, Family#3, Proband M1, M2: II,1 on pedigree

DiseaseAssertion: STGD

FamilyInfo: mother of proband has p.N18681 and p.P1380L mutations and is asymptomatic with no changes to NIR-AF and SD-OCT. Treated with 400mg of hydroxychloroquine for lupus prior to imaging. Non-affected father.

CasePresentingHPOs:HP:0007663, HP:0000493

CaseHPOFreeText: Proband has reduced visual acuity and issues reading with BCVA 20/200 in R.E and 20/50-2 in L.E. Oval foveal lesions with stage 2 flecks. Visual acuity reducing starting at age 10.

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: Genotyping performed at Columbia University, sequencing technology used is not disclosed.

PreviouslyPublished: n/a

Variant: M1:p.P1380L, complex allele: M2: p.N18681 and IVS38:c.5461-10T>C. M3: c.4139C>T(p.P1380L)

ClinVar: M1) 99390 M2) 99067 M3) Variation ID: 7904

CAID: n/a

SupplementalData: Fig 1: Pedigree illustrating ABCA4 variants and the associated Stargardt phenotype for 5 families. Proband Labeled w/ white arrow for each family. Fig 2: retinal scan measuring melanin in 4 patients of family 2. Panel shows bull's-eye ring of RPE atropy. Fig 3: Macular SD-OCT line profile from b-scans. Reflectivity plotted against function of retinal depth. Table 1: table shows patients with p.N18681 variant, type of mutation, and pathogenicity class. Table 2: Patients, age on-set and first symptom

Case#: Female, family #5, Patient #20

DiseaseAssertion: STGD

FamilyInfo: Proband's sister presented with same clinical prognosis. Sister diagnosed with pattern dystrophy and photoaversion at age 57, with difficulty seeing at night. Sister has nuclear sclerotic and cortical cataracts in both eyes.

CasePresentingHPOs: HP:0000662, HP:0000603, HP:0000603, HP:0000493

CaseHPOFreeText: Proband presented with localized blur at age 62, (late onset) in her left eye. BVCA 20/20-3 and 20/20-2 at age 70. Also has macular lesions with stage 2 fundus flecks.

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: Genotyping performed at Columbia University, sequencing technology used is not disclosed.

PreviouslyPublished: n/a

Variant: p.N18681, IVS36:c.5196+1G>A

ClinVar: M2) 99067, M6) 99351

CAID: N/A

SupplementalData: Fig 1: Pedigree illustrating ABCA4 variants and the associated Stargardt phenotype for 5 families. Proband Labeled w/ white arrow for each family. Fig 2: retinal scan measuring melanin in 4 patients of family 2. Panel shows bull's-eye ring of RPE atropy. Fig 3: Macular SD-OCT line profile from b-scans. Reflectivity plotted against function of retinal depth. Table 1: table shows patients with p.N18681 variant, type of mutation, and pathogenicity class. Table 2: Patients, age on-set and first symptom

Case#: Two affected sisters/Female siblings/Progressive onset initially presenting as Stargardt disease

DiseaseAssertion: ABCA4

FamilyInfo: Large American family pedigree with two affected sisters. Both sisters were compound heterozygous for two novel ABCA4 variants. Unaffected relatives carried one variant or neither variant, supporting autosomal recessive inheritance.

CasePresentingHPOs: HP:0000556, HP:0000572, HP:0007754, HP:0000648, HP:0000510, HP:0001133, HP:0000610

CaseHPOFreeText: Proband initially showed phenotype compatible with Stargardt disease with progressive central vision loss. Over several years disease advanced into severe cone-rod dystrophy with worsening retinal degeneration, abnormal visual fields, and reduced electroretinography responses.

CaseNotHPOs: n/a

CaseNotHPOFreeText: Unaffected family members with only one mutation had no retinal disease phenotype.

Genotyping Method: Genome-wide linkage analysis using 408 microsatellite markers followed by direct Sanger DNA sequencing of all ABCA4 exons and exon-intron boundaries. Segregation analysis performed in family members.

PreviouslyPublished: No, both variants were novel at time of publication.

Variant: ABCA4 (RefSeq: NM_000350.3): c.655A>T ; ABCA4 (RefSeq: NM_000350.3): c.5312+3A>T

ClinVar: 632118

CAID: n/a

SupplementalData: Variants absent in 200 unrelated controls. Clinical testing included visual acuity, fundus examination, fluorescein angiography, visual field testing, and electroretinography. Compound heterozygous state associated with severe progressive phenotype.

Case#: Female, 54 yo

FamilyInfo: No family members were available

CasePresentingHPOs: HP:0007924, HP:0000519,HP:0001105, HP:0030825,

CaseHPOFreeText: diagnosed with HIV 15 years ago. She was initially diagnosed with HIV following recurrent respiratory infections and an unintentional weight loss of 12 kg over six months. The diagnosis was confirmed via a positive HIV antibody test, followed by a Western blot confirmation and a CD4 count of 400 cells/mm³ at the time of diagnosis. Antiretroviral therapy (ART) was initiated shortly after confirmation of the diagnosis. Her condition has since progressed to AIDS, with a recent CD4 count of 80 cells/mm³. She was on ART, including tenofovir, emtricitabine, and efavirenz.

CaseNotHPOs: n/a

GenotypeMethod: NGS, Sanger Sequencing

Variant: c.2588G>C in exon 13, c.5461-10T>C in intron 39

ClinVar: Not reported in ClinVar

**SupplementalData: ** indicative of significant loss of central retinal structure (Figure 4).

PMID:39991341

Gene: ABCA4

Disease: Stargardt

PMID: 38694055 Gene: ABCA4

Case #: Eldest sister/Female/Onset at 3yo

DiseaseAssertion: SLC26A2

FamilyInfo: Family pedigree showing consanguinity of the proband's parents. The osteochondrodysplasia genotype, derived from a homozygous variant in the SLC26A2 gene and compound heterozygous variants in the ABCA4 gene, is responsible for the retinal phenotype

CasePresentingHPOs: HP:0034345, HP:0000556, HP:0002098, HP:0001903, HP:0001385, HP:0007754, HP:0002650, HP:0000939, HP:0025388, HP:0007987, HP:0003124, HP:0007401

CaseHPOFreeText: Visual acuity was 1/50 and 2/50 for both eyes, knee dysplasia, sticky platelet syndrome type II

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

GenotypyingMethod: genetic screening by next‐generation sequencing (NGS) was performed on a panel of genes involved in retinal dystrophy and macular degeneration

PreviouslyPublished: n/a

Variant: ABCA4 (RefSeq: NM_000350.3(ABCA4):c.203C>T (p.Pro68Leu))

CAID: n/a

SupplementalData: Comparison of phenotypes (table 1)

Case#: Patient 231, Female, age of onset at 7 y.o, Poland

DiseaseAssertion: STGD1

FamilyInfo: Mother was a carrier, unaffected father.

CasePresentingHPOs: HP:0007722, HP:0000608, HP:0025158

CaseHPOFreeText: RPE atrophy, macular degeneration, central hyper-autofluorescence in fundus autofluorescence

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a, non-proband identified HPO's mentioned, but not assignable to individual proband.

Genotyping Method: DNA isolated from peripheral blood from patients and relatives via MagNA Pure 24, samples screened with MIPs targeting 108 genes involved in pathogensis of IRD's. PCR completed on library, analysed with NGS fragment analysis kit.

PreviouslyPublished: yes

Variant: c.4234C>T , p.(Gln1412*)

ClinVar: 99263

gnomeAD 0.00001984 allelic frequency

CAID: n/a

SupplementalData: Fig1: List of families displaying pseudo-dominant inheritance. Fig2: Number of alleles for most common variants.

Case#: Patient 225, Female, age of onset 7 y.o, Poland

DiseaseAssertion: STGD-1

FamilyInfo: no given family information.

CasePresentingHPOs: HP:0007722, HP:0000608, HP:0025158

CaseHPOFreeText: RPE atrophy, macular degeneration, central hyper-autofluorescence in fundus autofluorescence

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a, non-proband identified HPO's mentioned, but not assignable to individual proband.

Genotyping Method: DNA isolated from peripheral blood from patients and relatives via MagNA Pure 24, samples screened with MIPs targeting 108 genes involved in pathogensis of IRD's. PCR completed on library, analysed with NGS fragment analysis kit.

PreviouslyPublished: yes

Variant: c.634C>T,p.(Arg212Cys)

ClinVar: 7898

CAID: n/a

gnomeAD 0.0001177 allele frequency

SupplementalData: Fig1: List of families displaying pseudo-dominant inheritance. Fig2: Number of alleles for most common variants.

Case#: Patient 231, Female, age of onset at 7 y.o, Poland

DiseaseAssertion: STGD1

FamilyInfo: Mother was a carrier, unaffected father.

CasePresentingHPOs: HP:0007722, HP:0000608, HP:0025158

CaseHPOFreeText: RPE atrophy, macular degeneration, central hyper-autofluorescence in fundus autofluorescence

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a, non-proband identified HPO's mentioned, but not assignable to individual proband.

Genotyping Method: DNA isolated from peripheral blood from patients and relatives via MagNA Pure 24, samples screened with MIPs targeting 108 genes involved in pathogensis of IRD's. PCR completed on library, analysed with NGS fragment analysis kit.

PreviouslyPublished: yes

Variant: c.5882G>A

ClinVar:7888

gnomeAD: 0.00310 allelic freq.

CAID: n/a

SupplementalData: Fig1: List of families displaying pseudo-dominant inheritance. Fig2: Number of alleles for most common variants.

Case#: Patient 225, Female, age of onset 7 y.o, Poland

DiseaseAssertion: STGD-1

FamilyInfo: no given family information.

CasePresentingHPOs: HP:0007722, HP:0000608, HP:0025158

CaseHPOFreeText: RPE atrophy, macular degeneration, central hyper-autofluorescence in fundus autofluorescence

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a, non-proband identified HPO's mentioned, but not assignable to individual proband.

Genotyping Method: DNA isolated from peripheral blood from patients and relatives via MagNA Pure 24, samples screened with MIPs targeting 108 genes involved in pathogensis of IRD's. PCR completed on library, analysed with NGS fragment analysis kit.

PreviouslyPublished: yes

Variant: c.[1622T>C;3113C>T]

ClinVar: 99067, 7894

CAID: n/a

gnomeAD 0.0001266 allele frequency

SupplementalData: Fig1: List of families displaying pseudo-dominant inheritance. Fig2: Number of alleles for most common variants.

PMID: 35243166

Gene: ABCA4

HGNC: 34

PMID: 19352439

Gene: ABCA4

PMID: 28050124 Gene: ABCA4 HGNC: HGCN:34

Case#: Patient 1, Female, age 40

DiseaseAssertion: STGD1

FamilyInfo: n/a

CasePresentingHPOs: HP:0007722, HP:0000608, HP:0000007

CaseHPOFreeText: Patient diagnosed with STGD type 1, presenting with retinal pigment atrophy as well as other symptoms typical of STGD1 with reduced visual acuity. Patient daignosed at age 16.

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: Patient ABCA-4 gene sequenced via Sanger sequencing of all 50 exons, Splice variants were identified by synthesized cDNA from RNA isolation with RT-PCR analysis with exonic primers.

PreviouslyPublished: Variant 1 identified in association with retinal dystrophy in these PMC articles: 23982839, 25082829, 25082885, 28327576

Variant: NM_000350.3(ABCA4):c.859-9T>C, NM_000350.3(ABCA4):c.303-3C>G

ClinVar: 3249248, 859348

gnomAD total allele frequency: 0.005% of var . 1

CAID: n/a

SupplementalData: Fig 1: Minigene RNA analysis of splice variants. A: genomic region of exon 40 on ABCA-4. B: genomic regions of exons 39-41 to investigate specific variant:oncanonical splice site variant c.5714+5G>A Fig 2: overview of wild-type midigene splice constructs of ABCA-4 and locations of 47 different non canonical splice site variants Fig 3: Overview of splice defects from nine different non canonnical splice variants in ABCA-4 gene. Fig 4: percentages of normal ABCA-4 transcripts as a result of noncanonical splice variants using electrophoresis system analysis. Table 1: Non canonical splice variants and observed protein affects.

**Case#: ** Female, 35yo

FamilyInfo: Unremarkable

CasePresentingHPOs: HP:0000529 Progressive visual loss, HP:0030532 Visual acuity, HP:0007401 Macular atrophy

CaseHPOFreeText: 35-year-old woman presented with symptom of gradually progressive diminution of vision in both eyes since childhood. Patient gave no history of defective night vision.

CaseNotHPO n/a

GenoTypeMethod: n/a (optical coherence tomography (OCT))

PMID:36910710 Gene: ABCA4 HGNC: 34

PMID: 10612508

Gene: ABCA4

Case#: Patient 2, 46-year-old female

DiseaseAssertion: STGD1

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

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

CaseHPOFreeText: Progressive visual decline since age 16. Best-corrected visual acuity 20/400 in both eyes. Fundus examination showed bilateral symmetrical central chorioretinal atrophy (~3 disc diameters) with prominent pigment deposits and numerous yellow flecks in the posterior pole. Fluorescein angiography demonstrated central hypofluorescence with surrounding hyperfluorescence and peripheral dark choroid.

CaseNotHPOs: Not reported

CaseNotHPOFreeText: Not reported

GenotypingMethod: PCR amplification and direct sequencing of ABCA4 after 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 and sequencing data shown in Figures 1 and 4

Case#: Patient 3, 37-year-old female

PMID: 10612508

DiseaseAssertion: STGD1

FamilyInfo: Affected sibling in autosomal recessive family.

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

CaseHPOFreeText: Gradual visual decline beginning at age 12. Visual acuity 20/400 in both eyes. Fundus examination revealed bilateral macular atrophy with pigment deposits and numerous yellow flecks in the posterior pole and midperiphery. Fluorescein angiography showed large hypofluorescent regions with surrounding hyperfluorescence and peripheral dark choroid.

CaseNotHPOs: Not reported

CaseNotHPOFreeText: Not reported

GenotypingMethod: PCR and direct sequencing of ABCA4

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 and sequencing data (Figures 1, 4)

PMID: 17562343 GeneName: ABCA4

PMID: 23949494 HGNC: 34 Gene: ABCA4 DiseaseAssertion: Stargardt Disease