PreviouslyPublished: PMID: 8471765

This proband has been previously published in the PMID listed above --> see that paper to get patient information. This patient can also be found in the GT database

Case4: Patient LW (found in GT database)

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0000421, HP:0006298

(Bruising, Epistaxis, Prolonged bleeding after tooth extraction)

CaseHPOFreeText: Blood transfusions were needed

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: 12% of normal GPIIIa and GPIIb surface expression

PlateletAggregation: N/A

CasePreviousTesting: N/A

Gene: ITGA2B

Variant: NM_000419.3:c.641T>C (p.Lue214Pro)

LegacyVariant: (p.Leu183Pro)

ClinVar: 2901

CAiD: CA115848

gnomAD: N/A

PreviouslyPublished: References 14 and 15

Case41: (GT-51) Female, age or ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Proband GT49-GT52 are related

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding severity: Information not available (See Supplementary Table 3)

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry performed and CD41 and CD61 were observed (See Supplementary Table 3)

PlateletAggregation: Minimal information (See Supplementary Table 3)

CasePreviousTesting: DNA was extracted from peripheral blood samples from patients and family members, and Sanger sequencing and PCR was performed. Samples were processed for targeted sequencing using the available SHGp heme panel of 393 genes.

Gene: ITGB3

Variant: NM_000212.2:c.2113del (p.Leu705Cysfs*4)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8623443

gnomAD: MAF in East Asian population: 0.0001087 http://gnomad.broadinstitute.org/variant/17-45380183-TC-T

Case24: Patient CI, gender and age are not specified, all of these patients are Caucasian (either Italian or European)

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: All patients presented with a current or past history of bleeding and a bleeding time >15 min. Bleeding symptoms were evaluated by examining available hospital records. Mild bleeders were defined as those who bled only after trauma or surgery or had minor symptoms, such as epistaxis. Moderate/severe bleeders were defined as those with a history of spontaneous or life threatening hemorrhages, such as gastrointestinal bleeding, or who had repeated episodes requiring platelet transfusions

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: See Table 1

PlateletAggregation: See Table 1

CasePreviousTesting: To identify point mutations responsible for GT, we have sequenced all coding regions of Ib and 3 genes and intron/exon boundaries.

Gene: ITGA2B

Variant: NM_000212.2:c.1801T>C

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8623361

gnomAD: MAF in the European non Finnish population is 0.00001758 https://gnomad.broadinstitute.org/variant/17-45376784-T-C

Case9: Patient MR, gender and age are not specified, all of these patients are Caucasian (either Italian or European)

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: All patients presented with a current or past history of bleeding and a bleeding time >15 min. Bleeding symptoms were evaluated by examining available hospital records. Mild bleeders were defined as those who bled only after trauma or surgery or had minor symptoms, such as epistaxis. Moderate/severe bleeders were defined as those with a history of spontaneous or life threatening hemorrhages, such as gastrointestinal bleeding, or who had repeated episodes requiring platelet transfusions

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: See Table 1

PlateletAggregation: See Table 1

CasePreviousTesting: To identify point mutations responsible for GT, we have sequenced all coding regions of Ib and 3 genes and intron/exon boundaries.

Gene: ITGA2B

Variant: NM_000419.3:c.1214T>C (p.Ile374Thr)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA290950815

gnomAD: N/A

Case1: GTP1, gender, age, or ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Sequencing of both parental genomic DNA confirmed patient was homozygous for IVS4+1G>A mutation

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed <5% αIIbβ3 expression, which was confirmed by western blot analysis

PlateletAggregation: N/A

CasePreviousTesting: Sequencing of patient genomic DNA was done on ITGA2B (no mention of ITGB3)

Gene: ITGA2B

Variant: NM_000419.3:c.574+1G>A (IVS4+1G>A)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399805691

gnomAD: MAF in the European non-Finnish population 0.00001235 http://gnomad.broadinstitute.org/variant/17-42462918-C-T

Case4: Patient 4, Female, 12 years old

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Affected sister is Patient 3

ParentalGenotype: N/A (Not consanguineous Caucasians, showed no increased bleeding tendency)

CasePresentingHPOs: HP:0000967

(Petechiae)

CaseHPOFreeText: Hematomas, prolonged in vitro bleeding time

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry analysis revealed that there was no surface expression of GPIIb/IIIa for Patient 4 and there was approx. 1520 of GPIIb/IIIa expression for Patient 4.

PlateletAggregation: All patients' platelets showed severely reduced platelet aggregation after stimulation with collagen and ADP in contrast to the normal range (See Table 1). Stimulation with epinephrine and arachidonic acid also demonstrated decreased platelet aggregation. In contrast, ristocetin-induced platelet aggregation was within a normal range.

CasePreviousTesting: Sequenced ITGA2B and ITGB3 genes from one patient of each family (Patient 2 and 3) and Patient 1 and 4 were screened for the identified mutation in the corresponding family.

Gene: ITGA2B

Variant: NM_000419.3:c.1787T>C (p.Ile596Thr)

LegacyVariant: N/A

ClinVar: 2900

CAiD: CA115846

gnomAD: MAF in the European (non-Finnish) population is 0.0001325 http://gnomad.broadinstitute.org/variant/17-42457148-A-G

Case1: Female, 20 years old, Chinese

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0000421,

(Easy bruising, epistaxis)

CaseHPOFreeText: Prolonged bleeding time (more than 20 minutes, absent clot retraction

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Decreased of surface expression of αIIb and β3 in patient's platelets

PlateletAggregation: Absent in vitro platelet aggregation in response to ADP, epinephrine, and collagen, but relatively normal ristocetin induced platelet aggregation

CasePreviousTesting: DNA fragments containing exons and flanking intronic regions of ITGA2B and ITGB3 genes were produced by PCR using primers. Amplified fragments were subjected to analysis by direct DNA sequencing

Gene: ITGA2B

Variant: NM_000419.3:c.527C>A (p.Pro157His)

LegacyVariant: (p.Pro126His)

ClinVar: N/A

CAiD: CA8603447

gnomAD: MAF in the African population is 0.00006689 http://gnomad.broadinstitute.org/variant/17-42462966-G-T

Case3: Patient 3, Female, 27 years old

DiseaseAssertion: Glanzmann thrombasthenia type I (Diagnosed at 10 years old)

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding phenotypes are not specified per patient in this article, rather, it states: "Petechia, epistaxis, and prolonged bleeding after trauma were the most common symptoms among studied patients"

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: This patient has type 1 Glanzmann thrombasthenia; therefore, according to this article, this proband had between 0-5% of normal levels of surface GPIIb/IIIa expression.

PlateletAggregation: Prolonged bleeding time, abnormal clot retraction, impaired platelet aggregation induced by most physiological agonists (ADP, epinephrine, and collagen) except ristocetin, mucosal bleeding, easy bruising, epistaxis, as well as normal prothrombin/activated partial thromboplastin time, and normal platelet count. (This is among inclusion criteria for this study)

CasePreviousTesting: To identify the underlying molecular mechanism of GPIIb/IIIa complex abnormalities among probands in this study, all the 30 exons of ITGA2B and the 15 exons of ITGB3 were analyzed using PCR–CSGE and DNA sequencing.

Gene: ITGA2B

Variant: NM_000419.3:c.113del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940264

gnomAD: N/A

Case1: Male, 7 years old, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: See pedigree Fig 5

ParentalGenotype: Parents heterozygous for the mutation proband has

CasePresentingHPOs:

(Petechia, bruising

CaseHPOFreeText: Mucocutaneous hemorrhages

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: There was a lack of platelet surface expression of the GPIIb-IIIa complex as shown by Western blotting

PlateletAggregation: Platelets fail to aggregate spontaneously or in response to agonists, although they agglutinate in response to ristocetin

CasePreviousTesting: Screening of mutations in both ITGA2B and ITGB3 was carried out by single stranded conformational polymorphism (SSCP) analysis

Gene: ITGA2B

Variant: NM_000419.3:c.1882C>T (p.Arg628Ter)

LegacyVariant: (p.Arg597Ter)

ClinVar: N/A

CAiD: CA399801310

gnomAD: MAF in the Latino population is 0.00003983 http://gnomad.broadinstitute.org/variant/17-42456075-G-A

Case#: II2 Figure 1A, Male, 7yo

DiseaseAssertion: Glanzmann's thrombasthenia

**FamilyInfo: ** Figure 1A, non-consanguineous, sibling (II1) died at 5yo, sibling (II3) in good health, mother and father heterozygous carriers

ParentalGenotype: both parents heterozygous carriers

CasePresentingHPOs: (HP:0001933) subcutaneous bleeding, (HP:0004406) spontaneous epistaxis, (HP:0011858) coagulation factor IX decreased

PlateletAggregation: Platelets were normal, coagulation factors normal, vWF factor normal, bone marrow normal. Platelet count via LH780 automatic blood analyzer, vWF via immunoturbidimetry, CD41(GPⅡb)/CD6l (GPⅢa) and CD42b via flow cytometry.

CaseHPOFreeText:Hemophilia B. Mutation in the F9 gene c.8G > A of unknown clinical significance, considered non-pathogenic.

CaseNotHPOs:

**CaseNotHPOFreeText: **

ProteinExpression: Flow cytometry results revealed that CD41 (GPⅡb) and CD6l (GPⅢa) were 2.05% and 0%, respectively (normal values ​​ranged from 95% to 97%), suggesting that the expression of platelet surface membrane glycoprotein GPIIb/IIIa was significantly reduced.

CasePreviousTesting: Whole exome sequencing verified by Sanger sequencing. Whole gene synthesis, qPRC analysis, Western blotting.

**PreviouslyPublished: **

Gene: ITGB3

Variant: c.1431C > T/p.Gly477 = in ITGB3 exon10 in the proband

HGVS: NM_000212.3:c.1431C>T

**ClinVar: ** 3242396

**CAID: ** CA500651220

gnomAD: Absent

Table 3 Molecular Diagnosis of Patients with Glanzmann Thrombasthenia:

Case3: GT-3, age, gender, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia type II

FamilyInfo: Segregation analysis confirmed in presence of heterozygous mutations in this proband.

ParentalGenotype: Although segregation analysis confirmed, we do not know which variant in particular came from mom or dad.

CasePresentingHPOs: N/A

CaseHPOFreeText: Patients presented with a variable bleeding diathesis; most patients had epistaxis (54%), cutaneous bleeding (58%), and menorrhagia (100% of women) while other common symptoms (oral cavity, GI, following dental extraction of mild injuries, postpartum, or hematomas) were in general milder. There is no specific phenotypes attached to probands in this paper.

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed that αIIbβ3 expression was between 5% and 20%.

PlateletAggregation: There was severely impaired aggregation in response to all physiological agonists, and ristocetin induced platelet agglutination was normal or reduced to some extent.

CasePreviousTesting: Total RNA from peripheral blood was used for cDNA synthesis for RT-PCR. Then, using specific oligonucleotides and conditions, they amplified and sequenced ITGA2B and ITGB3 by Sanger sequencing. Every mutation found in cDNA was confirmed in DNA samples.

Gene: ITGA2B

Variant: NM_000419.3:c.2113T>C (p.Arg705Cys)

LegacyVariant: (p.Cys674Arg)

ClinVar: N/A

CAiD: CA8602816

gnomAD: MAF in European non-Finnish population is 0.000008792

Case5: Patient DC

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs:

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

PlateletAggregation: N/A

CasePreviousTesting: The amplification of DNA fragments using PCR and their electrophoretic migration through a denaturing gradient was used to scan the entire coding region, splice site junctions and promoter regions of the GPIIb and GPIIIa genes for all 20 patients in this study

Gene: ITGA2B

Variant: NM_000419.3:c.1544+1G>A

LegacyVariant: N/A

ClinVar: 2895

CAiD: CA10575473

gnomAD N/A

Case4: P4, gender, age, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Article mentions all patients have a severe bleeding phenotype

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: αIIbβ3 expression levels were (0.6% in patient 4)

PlateletAggregation: N/A

CasePreviousTesting: Acknowledgements section mentions acknowledging the Genoscope team for sequencing both ITGA2B and ITGB3 genes of the GT patients in this article

Gene: ITGA2B

Variant: NM_000419.3:c.857T>A (p.Val268Asp)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399805011

gnomAD: N/A

Case1: Female, 29 years old, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Parents were heterozygous for mutation (parents are first cousins)

CasePresentingHPOs: HP:0001892, HP:0000421, HP:0000225, HP:0000132

(Severe hemorrhagic diathesis, epistaxis, gingival bleeding, menorrhagia)

CaseHPOFreeText: Patients severe hemorrhagic diathesis manifested as epistaxis

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: N/A

PlateletAggregation: N/A

CasePreviousTesting: Amplification of reversely transcribed platelet GP IIIa mRNA by the polymerase chain reaction and subsequent sequence analysis showed a 86-bp deletion, which corresponds to exon i of the GP IIIa gene.

Gene: ITGB3

Variant: NM_000212.2:c.165+1G>T (No other assertion was made about the 2 other variants in this article, just this variant that is mentioned in this annotation)

LegacyVariant: N/A

ClinVar: 13560

CAiD: CA400031853

gnomAD: N/A

Case9: (M1) Male, 9 years old, French Gypsy

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Mucocutaneous bleeding

CaseNotHPOs: N/A

ProteinExpression: Failed to express alphaIIbbeta3 on the surface of their platelets

Platelet Aggregation: Absent platelet aggregation to all agonists (no mention for which agonists or response to ristocetin)

CasePreviousTesting: All the information we are given is "mutation screening of the ITGA2B and ITGB3 genes" the method for sequencing etc. was not stated

Gene: ITGA2B

Variant: NM_000419.3:c.1544+1G>A

LegacyVariant: N/A

ClinVar: 2895

CAiD: CA10575473

gnomAD N/A

Case1: Female, 22 years old, Portugese

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Also studied were the patient’s mother (I.2),her father (1.1), and her sister (II.2). Of these family members, only her sister has reported excessive bleeding although platelet aggregation tests were normal for all of them. Consanguinity was present as her parents were cousins.

ParentalGenotype: Parents heterozygous for mutation

CasePresentingHPOs: HP:0000967

(Petechia)

CaseHPOFreeText: Mucocutaneous bleeding

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: <5% surface expression of aIIbb3

PlateletAggregation: Absent with physiologic agonists but agglutination with ristocetin was normal

CasePreviousTesting: We examined each of the 30 exons of the b3 gene and each of the 15 exons of the aIIb gene for migration changes in PCR-SSCP analysis

Gene: ITGB3

Variant:

LegacyVariant:

ClinVar:

CAiD:

gnomAD: N/A

Case#: 25 year old Female, Sikh, India, Punjab

DiseaseAssertion: EORSD

FamilyInfo: Family history for other disease were negative

CasePresentingHPOs: HP:0007401, HP:0007913

CaseHPOFreeText: Macular atrophy, scar and pigment OU, plus midperipheral pigmentation OU

CaseNotHPOs: N/a

CaseNotHPOFreeText: N/a

Genotyping Method: BGISeq-500 2 x 100-bp paired-end module, Burrows-Wheeler Aligner and Genome Analysis Tooklit HaploptypeCaller

PreviouslyPublished: N/a

Variant: NM_000350.3(ABCA4):c.6729+5_6729+19del

ClinVar: 283573

CAID: CA501163

SupplementalData: Family reported never saw well and had poor vision and nystagmus before the age of one.

Case#: German/British, 76

DiseaseAssertion: EOSRD

FamilyInfo: Grandparents from Germany and the United Kingdom

CasePresentingHPOs: HP:0007401, HP:0007913

CaseHPOFreeText: Macular atrophy and pigmentation, peripheral pigmentation, early-onset severe retinal dystrophy

CaseNotHPOs: N/a

CaseNotHPOFreeText: N/a

Genotyping Method: BGISeq-500 2 x 100-bp paired-end module, Burrows-Wheeler Aligner and Genome Analysis Tooklit HaploptypeCaller

PreviouslyPublished: n/a

Variant: c.1622T>C, c.4326C>A, and c.3113C>T

ClinVar: 99067, 417991, 7894

CAID: CA226911, CA957653, CA119135

SupplementalData: The c.1622T>C variants and c.3133C>T are thought to be same gene copy

Case#: 39 Year Old Female, India Punjab

DiseaseAssertion: EORSD

FamilyInfo: Family history for other disease was negative, husband was first cousin and their son had normal vision

CasePresentingHPOs: HP:0007401, HP:0007913

CaseHPOFreeText: Macular atrophy and pigmentation, yellowish flecks

CaseNotHPOs: N/a

CaseNotHPOFreeText: N/a

Genotyping Method: BGISeq-500 2 x 100-bp paired-end module, Burrows-Wheeler Aligner and Genome Analysis Tooklit HaploptypeCaller

PreviouslyPublished: N/a

Variant: NM_000350.3(ABCA4):c.6729+5_6729+19del

ClinVar: 283573

CAID: CA501163

SupplementalData: Confirmed that she had never seen properly or normally, marked horizontal nystagmus and poor pupil reaction to light

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#: Case 2, Sex: Male, Age:20

DiseaseAssertion: STGD

FamilyInfo: n/a

CasePresentingHPOs: HP:0007663, HP:0007401

CaseHPOFreeText: Text mentions visual acuity of 20/32 in right eye and 20/50 in left eye but later degrades to 20/200 in both eyes. pigmented changes in macula associated with flecks. Area of subretinal fibrosis in right eye. Subnormal scotopic and photopic responses. Instable fixation in both eyes with low retinal mean sensitivity. Hypofluorescent central area corresponding to macular atrophy and corresponding to flecks. Atrophic areas, some with pigment, localized in the temporal sector of the left eye which have become areas of subretinal fibrosis.

CaseNotHPOs:n/a

CaseNotHPOFreeText: Anterior segment showed a healthy ocular adnexa, and specular, transparent and 'in situ' lens, absence of any ocular trauma.

Genotyping Method: genetic analysis

PreviouslyPublished: n/a

Variant: Variant is a homozygous mutation given as NM_000350.3(ABCA4):c.571-2A>T

ClinVar: Variation ID: 1048133

CAID: CA958800

SupplementalData: n/a

Case#: Patient 62, female, Caucasian, onset at 40yo, Italy

DiseaseAssertion: STGD

FamilyInfo: co-segregation of variant in 2 affected siblings, unaffected children heterozygous or wild-type

CasePresentingHPOs: HP:0007754, HP:0000608, HP:0000548, HP:0000551, HP:0000510, HP:0000559

CaseHPOFreeText: macular atrophy OU, perifoveal and peripheral fundus flecks OU, RPE changes, thinning of outer nuclear layer OU, BCVA: 20/25 OD/OS, normal intraocular pressure, myopic refraction -3.50 sph -1 cyl, normal rod–cone and cone ERGs

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: WES with phenotype-driven filtering, variant confirmed by Sanger sequencing, segregation analysis performed, functional minigene splicing assay

PreviouslyPublished: n/a

Variant: RDH8 NM_015725.4 c.262+1G>A homozygous

ClinVar: SUB13728545

CAID: n/a

SupplementalData: phenotype and segregation info in supplemental data (Table S1, Figures S1–S5)

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#: 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#: 12, Somali, onset 5 years old

DiseaseAssertion: STGD

FamilyInfo: Parents were heterozygous for Arg212Cys, no family history of IRD

CasePresentingHPOs: HP:0011504, ORPHA:827, HP:0000608

CaseHPOFreeText: Bull's eye maculopathy, macular degredation, red-green color defecit, reduced cone function

CaseNotHPOs: n/a

CaseNotHPOFreeText: n/a

Genotyping Method: Whole exome sequencing

PreviouslyPublished: N/a

Variant:

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

ClinVar: 7888; 7898

CAID: CA119132, CA203216

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#: Somali origin, 11 years of age, onset age 8

DiseaseAssertion: STGD

FamilyInfo: Parents were heterozygous for Arg212Cys, asymptoamtic 32 year old father was found to be homozygous for Gly1961Glu

CasePresentingHPOs: HP:0011504, ORPHA:827, HP:0000608

CaseHPOFreeText: BCVA 20/70 and 20/80, atrophic zone of outer retinal and RPE atrophy, Bull's Eye Maculopathy, Macular atrophy

CaseNotHPOs: N/a

CaseNotHPOFreeText: N/a

Genotyping Method: Whole genome 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: CA119132, CA203216

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#: 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#: 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#: An 8-year old Hispanic female

DiseaseAssertion: Whole exome sequencing identified a homozygous ABCA4 missense variant (p.Arg602Trp) that has been identified as a Stargardt Disease mutation

FamilyInfo: consanguinity, her parents being first cousins, no family history of blindness. Familial cosegregation analysis was used, with both parents being heterozygous carriers.

CasePresentingHPOs: HP:0000529, HP:0000662, HP:0000556, HP:0002017,HP:0008046, HP:0031528, HP:0003678

CaseHPOFreeText: rapidly progressive vision loss, nyctalopia and retinal dystrophy, bilateral decreased vision following a febrile gastrointestinal illness with nausea and vomiting, Initial visual acuity was 20/60 at distance and 20/30 at near in both eyes, after 2 years visual acuities of 20/200 at distance in both eyes, attenuated vessels and multiple subretinal blister-like elevations, Cycloplegic retinoscopy detected very mild hyperopia and astigmatism in both eyes (OD: + 1.00 sphere + 1.00 cylinder axis 110 degrees; OS: + 0.75 sphere + 0.50 cylinder axis 60 degrees)

CaseNotHPOs: NR

CaseNotHPOFreeText: no evidence of a diffuse post-infectious/inflammatory process

Genotyping Method: DNA analysis by whole exomic sequencing

PreviouslyPublished: No

Variant: NM_000350.3:c.1804C>T

ClinVar:99084

CAID:CA226932

SupplementalData:

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 23, Female

DiseaseAssertion: STGD

FamilyInfo: Not evaluated

CasePresentingHPOs: HP:0000609, HP:0012632, HP:0007906

CaseHPOFreeText: The patient also had a history of bilateral optic nerve hypoplasia, labile intraocular pressure (IOP), and ocular hypertension without glaucoma.

CaseNotHPOs: n/a

CaseNotHPOFreeText:n/a

Genotyping Method: Not listed

PreviouslyPublished: n/a

Variant: p.Arg2107Cys:c.6319C>T and p.Gly607Arg:c.1819G>A

ClinVar: 635988, 99087

CAID: CA956906, CA226936

SupplementalData: Phenotype shown in case report with continued treatment below

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#: 10 years old

DiseaseAssertion:See Table 1

FamilyInfo: Not Mentioned

CasePresentingHPOs: Not specified

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/a

CasePreviousTesting: See Table 2

Variant: NM_000350.3(ABCA4):c.4139C>T (p.Pro1380Leu)

ClinVar: 7904 https://www.ncbi.nlm.nih.gov/clinvar/variation/7904/

CAID: CA129033

gnomAD: 0.00030430 https://gnomad.broadinstitute.org/variant/chr1-94031110-G-A?dataset=gnomad_r4

SupplementalData: Table 2

Case#: Age is not specified (Age of onset: 15 years old, with the time from onset: 8 years)

DiseaseAssertion: Presented with macular flecks and alterations in the retinal pigment epithelium (RPE) subretinal deposits.

FamilyInfo: Consanguinity within the family

CasePresentingHPOs: HP:0000608, HP:0008035 (Macular Degeneration, Retinis pigmentosa inversa)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: Visual Acuity: 20/20

CasePreviousTesting: See Table 2

Variant: NM_000350.3(ABCA4):C.4793C>A (p.Ala1598Asp)

ClinVar: 99321 https://www.ncbi.nlm.nih.gov/clinvar/variation/99321/

CAID: CA227239

gnomAD: 0.00002631 https://gnomad.broadinstitute.org/variant/1-94021695-G-T?dataset=gnomad_r3

SupplementalData: Table 2, Results Section

Case#: male, onset at or before age 12 months, ethnicity not specified DiseaseAssertion: Patient is asserted to have both "SHORT syndrome" and "X-linked agammaglobulinemia (XLA)" due to "absence of peripheral B cells" and "features of SHORT syndrome such as hyperextensibility, vision abnormalities, lack of fat tissue, triangular face, extroverted ears, ocular depression, [and] developmental and teething delay" CasePresentingHPOs: HP:0000974 (Hyperextensible skin), HP:0000504 (Abnormality of vision), HP:0005320 (Lack of facial subcutaneous fat), HP:0000325 (Triangular face), HP:0000430 (Underdeveloped nasal alae), HP:0000490 (Deeply set eye), HP:0000750 (Delayed speech and language development), HP:0002719 (Recurrent infections), HP:0030084 (Clinodactyly), HP:0045075 (Sparse eyebrow), HP:0000540 (Hypermetropia), HP:0000696 (Delayed eruption of permanent teeth) CaseHPOFreeText: A current 9 year old was diagnosed with XLA with SHORT at age 15 months after presenting with skin lesions, scrotal swelling and ulcers along with recurring upper and lower tract infections after 6 months of age. Evaluations for immunodeficiencies were performed. Basic immunoglobulin levels and lymphocyte subsets were measured, which suggested an XLA diagnosis. Delays in developmental milestones observed by the mother and physical examination suggested SHORT syndrome. CaseNotHPOs: HP:0000558 (Rieger anomaly), HP:0000364 (Hearing abnormality) GenotypingMethod: Genotyping was performed by whole exome sequencing, whivh revealed a novel pathogenic homozygous frameshift mutation in the PIK3R1 gene. PreviouslyPublished: No prior article is known to contain information on the same proband. Variant: The patient harbors NM_181523.3:c.244dup(p.(lle82Asnfs24) chr5:67522740) variant in the homozygous state. ClinVar: This variant was not found in ClinVar CAID: This variant was not found in the ClinGen Allele Registry. gnomAD:* The variant was not found in gnomAD v4.1.0.

Case#: 36 y.o male European

DiseaseAssertion: Limb Girdle

FamilyInfo: None

CasePresentingHPOs: HP:0003701,HP:0003560, HP:0006785, HP:0003236,HP:0003325, HP:0008981,

CaseHPOFreeText: Experienced two episodes of atrial fibrillation. High CADD scores. Exercise-induced myalgia and/or rhabdomyolysis

CaseNotHPOs:

CaseNotHPOFreeText:

MotorAchievement: Age 20 he developed exercise intolerance and sporadic myoglobinuria after intense exercise. Able to walk and cycle for long distances with little muscle pain.

CreatineKinase: Ranging from 1700 to 8000 UI/L), at the age of 10 years

CasePreviousTesting: Last neurological examination there was moderate calf hypertrophy.

GenotypingMethod: Muscle Biopsy using next generation sequencing and multiple gene panel. Minimal myopathic changes on histological assessment and normal immunofluorescence staining for muscle proteins including α-sarcoglycan

PreviouslyPublished:

Variant: NM_000023.4(SGCA):c.850C>T (p.Arg284Cys)

ClinVar: 9439

CAID:

gnomAD: 0.0007716