Case#: Patient 6, Gender N/A, Onset at 5-6 months. Death around 2 years old, Southeast Asian

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: P:0001639. HP:0005165, HP:0001270, HP:0011968

(Dyspnea, Shortened PR interval, Motor delay, Feeding difficulties,

CaseHPOFreeText: FTT, BVH, Severe MR)

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: GAA activity in leukocytes was 0.43% of normal control value.

PCR of all exons was performed and subsequently subjected to capillary Sanger sequencing in both directions

Variant: NM_000152.5(GAA):c.781G>A (p.Ala261Thr)

ClinVar: 456438

CAID: CA8815016

gnomAD: Highest population MAF = 0.00009799 (South Asian)

ParentalGenotype: Father and Mother were carriers of the variant c.781G>A (p.Ala261Thr)

PreviouslyPublished: N/A

Case#: Patient 10, Gender N/A, Onset at 1-2 months. Death at 10 months, Southeast Asian

DiseaseAssertion:Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001639. HP:0005165, HP:0002100

(Dyspnea, Shortened PR interval, Recurrent aspiration pneumonia)

CaseHPOFreeText: BVH, SDD

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting GAA enzyme activity is not available.

PCR of all exons was performed and subsequently subjected to capillary Sanger sequencing in both directions

Variant: NM_000152.5(GAA):c.876C>G (p.Tyr292Ter)

ClinVar: 637958

CAID: CA500127534

gnomAD: N/A

ParentalGenotype: Both parents are carriers of the variant c.876C>G (p.Tyr292Ter)

PreviouslyPublished: N/A

Case#: Patient 11, Gender N/A, Onset at 3-4 months. Death when 1-2 years old, Southeast Asian

DiseaseAssertion: Parents are

FamilyInfo: Proband parents are consanguineous family

CasePresentingHPOs: HP:0001252, HP:0002240 Muscular hypotonia, Hepatomegaly

CaseHPOFreeText: BVH, SDD

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: GAA enzyme activity is not available.

PCR of all exons was performed and subsequently subjected to capillary Sanger sequencing in both directions

Variant: NM_000152.5(GAA):c.1895T>G (p.Leu632Arg)

ClinVar: 637961

CAID: CA401369835

gnomAD: N/A

ParentalGenotype: Both parents were carriers of the variant c.1895T>G (p.Leu632Arg)

PreviouslyPublished:

Case#: Patient 9, Gender N/A, Onset at 3-4 months. Death around 1-2 years, Southeast Asian

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001252, HP:0001270, HP:0001640, HP:0005165

Muscular hypotonia, Motor delay, Cardiomegaly, Shortened PR interval)

CaseHPOFreeText: BVH, Ejection fraction 10%, Creatine kinase levels 1,010u/l

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: No GAA measurement . Ejection fraction 10%, Creatine kinase levels 1,010u/l

PCR of all exons was performed and subsequently subjected to capillary Sanger sequencing in both directions

Variant: NM_000152.5(GAA):c.1941C>G (p.Cys647Trp)

ClinVar: 550327

CAID: N/A

gnomAD: Highes population MAF = 0.0001427 (Others)

ParentalGenotype: Both parents were carriers for the viariant c.1941C>G (p.Cys647Trp)

PreviouslyPublished: N/A

Case#: 3, age 48, age 41 (report)

DiseaseAssertion: Pompe Disease

FamilyInfo: Family 3, no further information

CasePresenting HPOs:HP:0012378, HP:0003546, HP:0001324 (fatigue, exercise intolerance, muscle weakness)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: single gene sequencing/analysis, 63.85 NaG/AaGIA, 91% inhibition of GAA; NaG/AaGIA above 40 and %INH above 87 are in the affected range

Variants:

Variant 1:NM_000152.5(GAA):c.-32-3C>A

ClinVar: 371622

Variant 2:NM_000152.5(GAA):c.-32-3C>A

ClinVar: 371622

ParentalGenotypes: N/A

PreviouslyPublished: N/A

Case#: 4, age 24, age 18 (report)

DiseaseAssertion: Pompe Disease

FamilyInfo: Family 4, no further information

CasePresenting HPOs:HP:0012378, HP:0003546, HP:0001324 (fatigue, exercise intolerance, muscle weakness)

CaseHPOFreeText: vacuolar myopathy biopsy PAS +

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: single gene sequencing/analysis, 40.54 NaG/AaGIA, 90.54% inhibition of GAA; NaG/AaGIA above 40 and %INH above 87 are in the affected range

Variants:

Variant 1:NM_000152.5(GAA):c.2608C>T (p.Arg870Ter)

ClinVar: 189009

Variant 2: not reported

ParentalGenotypes: N/A

PreviouslyPublished: N/A

Case#: 2/a, age 20, age 14 (report)

DiseaseAssertion: Pompe Disease

FamilyInfo: Family 2, no further information

CasePresenting HPOs:HP:0002878, HP:0012378, HP:0003546, HP:0001324 (Respiratory failure, fatigue, exercise intolerance, muscle weakness)

CaseHPOFreeText: valvular myopathy, biopsy with vacuolar myopathy with PAS +

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: single gene sequencing/analysis, 64.47 NaG/AaGIA, 92.28% inhibition of GAA; NaG/AaGIA above 40 and %INH above 87 are in the affected range

Variants:

Variant 1:NM_000152.5(GAA):c.377G>A (p.Trp126Ter)

ClinVar: 932904

Variant 2: NM_000152.5(GAA):c.1655T>C (p.Leu552Pro)

ClinVar: 279811

ParentalGenotypes: N/A

PreviouslyPublished: N/A

Case1: Female, age and ethnicity is previously described in Ruan et al, 1993, but access not available to this article

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: The propositus' twin brother was also affected

ParentalGenotype: Article mentions, "Thus the two affected members are double heterozygote having inherited two different abnormal GPIIb alleles, one from the father and the other from the mother"

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding time > 15 minutes

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: Absent or reduced platelet GPIIb and GPIIIa assessed by Western blotting

PlateletAggregation: Absent platelet aggregation in response to ADP, epinephrine, and collagen and normal aggregation in response to ristocetin

CasePreviousTesting: PCR was used to amplify the defective segment of the GPIIb gene

Gene: ITGA2B

Variant: NM_000419.3:c.1750C>T (p.Arg584Ter)

LegacyVariant: c.9644C>T

ClinVar: 2892

CAiD: CA115834

gnomAD: MAF in the East Asian population is 0.0002176 https://gnomad.broadinstitute.org/variant/17-42457372-G-A

Case1: Female, 27 years old, Danish

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Information on father, mother, brother and sister. (See Figure 1 for pedigree)

ParentalGenotype: Pedigree from Figure 1 shows Father to have (p.Asn331Ser) and mother has (p.Arg786Trp) variant.

CasePresentingHPOs: HP:0000978, HP:0001934, HP:0006298

(Bruising, prolonged bleeding after minor trauma, prolonged bleeding after dental extraction)

CaseHPOFreeText: Lifelong bleeding history

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: αIIbβ3 expression and activation and αvβ3 expression were assessed by flow cytometry (See Figure 1 and 2 for results)

PlateletAggregation: Platelet aggregation was impaired in response to all stimuli except ristocetin, with low-normal response to collagen

CasePreviousTesting: To identify DNA variants, all exons of ITGA2B and ITGB3 were analyzed by Sanger sequencing

Gene: ITGB3

Variant: NM_000212.2:c.2356C>T (p.Arg786Trp) an NM_000212.2:c.992A>G (p.Asn331Ser)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA400034866 (p.Arg786Trp) and CA400025729 (p.Asn331Ser)

gnomAD: MAF for (p.Arg786Trp) in the African population is 0.000 https://gnomad.broadinstitute.org/variant/17-45387559-C-T

Case1: Female, 20 years old, Chinese

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Parents were heterozygous for mutation (See Fig 3)

CasePresentingHPOs: HP:0000421, HP:0000225, HP:0000967, HP:0000979, HP:0000132

(Epistaxis, gingival bleeding, petechiae, purpura, severe menorrhagia)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

ProteinExpression: Surface GPIIb/IIIa expression was < 15% of normal

Platelet Aggregation: Absent platelet aggregation in response to ADP, epinephrine, or collagen but normal response to ristocetin

CasePreviousTesting: Direct sequencing of PCR amplified cDNA and GPIIIa exon VIII indicated that the patient was homozygous for the mutation

Gene: ITGB3

Variant: NM_000212.2:c.1199G>A (p.Cys400Tyr)

LegacyVariant: (p.Cys374Tyr)

ClinVar: 13562

CAiD: CA123244

gnomAD N/A

Case1: Male, 2 years old, Korean

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Figure 1 shows haplotype analysis

CasePresentingHPOs: HP:0000978, HP:0000967

(Easy bruising, petechiae)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry analyses revealed markedly decreasedCD41/CD61 expression (<1%) in Patient 1 (type I GT).

PlateletAggregation: Platelet aggregation tests were performed to evaluate responses to ADP, collagen, epinephrine, and ristocetin agonists

CasePreviousTesting: Polymerase chain reaction for all exons ofITGA2Band/orITGB3were performed using primers. Sequence analysis was performed with reference to M_000419.3 andNP_000410.2 forITGA2Band NM_000212.2 and NP_000203.2 for ITGB3.

Gene: ITGB3

Variant: NM_000212.2:c.1913+5G>T

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8623377

gnomAD: MAF in the East Asian population is 0.0001633 http://gnomad.broadinstitute.org/variant/17-45376901-G-T

Case2: Male, 38 years old, Korean

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Figure 1 shows haplotype analysis

CasePresentingHPOs: HP:0004406, HP:0000225

(Recurrent epistaxis, gingival bleeding)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry analyses revealed markedly decreasedCD41/CD61 expression (<1%) in Patient 2 (type I GT).

PlateletAggregation: Platelet aggregation tests were performed to evaluate responses to ADP, collagen, epinephrine, and ristocetin agonists

CasePreviousTesting: Polymerase chain reaction for all exons ofITGA2Band/orITGB3were performed using primers. Sequence analysis was performed with reference to M_000419.3 andNP_000410.2 forITGA2Band NM_000212.2 and NP_000203.2 for ITGB3.

Gene: ITGB3

Variant: NM_000212.2:c.1913+5G>T

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8623377

gnomAD: MAF in the East Asian population is 0.0001633 http://gnomad.broadinstitute.org/variant/17-45376901-G-T

Case1: 30 year old, Female (primigravada), ethnicity not reported

DiseaseAssertion: Type-1 Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: See Table 1 (Father wild type and mother has frameshift mutation)

CasePresentingHPOs: HP:0000132 (Menorrhagia)

CaseHPOFreeText: Vaginal bleeding, haematochezia

CaseNotHPOs: N/A

CaseNotHPOsFreeText: Proband did not have any bleeding manifestations at the age of 16

ProteinExpression: Using flow cytometry, the test sample (normal plate-lets+patient plasma) showed only 28% GPIIb-IIIa expression as compared to 81.4% GPIIb-IIIa expression seen in the control sample(normal platelets+control plasma) (Fig. 1B) confirming the presence of GPIIbIIIa antibodies in patient plasma.

PlateletAggregation: Absent aggregation in response to ADP and collagen and normal response to ristocetin (Platelet aggregation information found in Table 1)

CasePreviousTesting: The mutation analysis was performed by Sanger sequencing of both ITGA2B and ITGB3 genes, which showed a frameshift mutation: c.1230_1230delC, cDNA.1262_1262delC (Y411Tfs*20) due to a single base deletion in exon 13 of ITGA2B

Gene: ITGA2B

Variant: NM_000419.3:c.1230del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940214

gnomAD: N/A

Case1: Male, 33 months old, French Gypsy

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Mother heterozygous for the c.1544+1G>A variant

CasePresentingHPOs: HP:0000967, HP:0000979, HP:0002094

(Petechiae, purpura, dyspnea,

CaseHPOFreeText: Hypoxia

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry analysis showed GPIIb/IIIa expression to be 22.6.

PlateletAggregation: Platelets failed to aggregate in response to ADP, epinephrine, collagen, calcium ionophore, and TRAP; however, ristocetin-induced aggregation was normal

CasePreviousTesting: Sequencing of coding regions of ITGA2B and ITGB3 genes was performed

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: 2895

CAiD: CA10575473

gnomAD: N/A

Case1: Male, French, age not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Son was heterozygous carriers of the p.Leu196Pro mutation (Sister died from nasal bleeding when she was a child)

ParentalGenotype: Mother is heterozygous for p.Leu196Pro mutation (Father not alive)

CasePresentingHPOs: HP:0000421 (Epistaxis)

CaseHPOFreeText: Lifelong history of mucocutaneous bleeding

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Expression showed 8% of normal platelet content for αIIbβ3

PlateletAggregation: Absent aggregation to physiologic agonists

CasePreviousTesting: Screened exons and splice sites of ITGB3 and ITGA2B genes of patient by single-strand conformation polymorphism analysis of PCR products.

Gene: ITGB3

Variant: NM_000212.2:c.665T>C (Leu222Pro) and NM_000212.2:c.1871G>A (p.Cys624Tyr)

LegacyVariant: p.Leu196Pro and p.Cys598Tyr

ClinVar: N/A

CAiD: CA291224887 and CA400032726

gnomAD: N/A

Case28: (GT30) Gender, age and ethnicity are not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Mother and father are heterozygous for the mutation

CasePresentingHPOs: N/A

CaseHPOFreeText: Inclusion criteria were patients with a history of mucocutaneous bleeding (Figure 1 shows a bar diagram of all the clinical manifestations in the patient cohort in this article)

CaseNotHPOs: N/A

ProteinExpression: Platelet receptor alphaIIbbeta3 protein was analyzed by flow cytometry followed by western blotting

Platelet Aggregation: Inclusion criteria for probands was absent or reduced platelet aggregation with agonists such as ADP, adrenaline, arachidonic acid, and collagen (no mention of ristocetin here-- this article does not tell us the specific aggregation for each proband in the paper)

CasePreviousTesting: For mutation analysis of ITGA2B and ITGB3 genes, DNA extraction from whole blood, PCR, heteroduplex PCR followed by CSGE and DNA sequencing were performed. All 30 exons of ITGA2B and 15 exons of ITGB3, as well as their promoters, were analyzed by CSGE following heteroduplex PCR.

Gene: ITGB3

Variant: NM_000212.2:c.674del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940689

gnomAD N/A

Table 3 Molecular Diagnosis of Patients with Glanzmann Thrombasthenia:

Case2: GT-2, age, gender, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia type I

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 less than 5%

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.2473_2481delinsTCACCTGGTC and NM_000419.3:c.641T>C (p.Leu214Pro)

LegacyVariant: p.Leu183Pro

ClinVar: (p.Leu214Pro is 2901)

CAiD: CA915940289 and CA115848

gnomAD: N/A

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

Case7: No assertion made on age, gender or ethnicity

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: The identified variants were heterozygote in parents.

CasePresentingHPOs: HP:0005542, HP:0000132, HP:0000421, HP:0000978

(Prolonged clotting, menorrhagia, epistaxis, easy bruising)

CaseHPOFreeText: Bleeding time greater than 20 minutes

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: Genetic study of patient was conducted using direct sequencing of entire coding and exon-intron boundaries of the ITGA2B and ITGB3 genes.

Gene: ITGA2B

Variant: NM_000419.3:c.1899del (p.Cys633TrpfsTer17)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940223

gnomAD: N/A

Case4: No assertion made on age, gender or ethnicity

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: The identified variants were heterozygote in parents.

CasePresentingHPOs: HP:0000978, HP:0000132, HP:0000421, HP:0000979

(Easy bruising, menorrhagia, epistaxis, purpura)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: Genetic study of patient was conducted using direct sequencing of entire coding and exon-intron boundaries of the ITGA2B and ITGB3 genes.

Gene: ITGB3

Variant: NM_000212.2:c.1303G>T (p.Glu435Ter)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA400028645

gnomAD: N/A

Case12: No assertion made on age, gender or ethnicity

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: The identified variants were heterozygote in parents.

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: Genetic study of patient was conducted using direct sequencing of entire coding and exon-intron boundaries of the ITGA2B and ITGB3 genes.

Gene: ITGA2B

Variant: NM_000419.3:c.1555C>T (p.Gln519Ter)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399802559

gnomAD: N/A

Case9: No assertion made on age, gender or ethnicity

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Table 1 mentions family history available for this proband.

ParentalGenotype: The identified variants were heterozygote in parents.

CasePresentingHPOs: HP:0030402, HP:0005542

(Abnormal platelet aggregation, prolonged clotting time)

CaseHPOFreeText: Bleeding time greater than 20 minutes and hematocrit of 38.1%.

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: Genetic study of patient was conducted using direct sequencing of entire coding and exon-intron boundaries of the ITGA2B and ITGB3 genes.

Gene: ITGA2B

Variant: NM_000419.3:c.286T>A (p.Cys96Ser)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8603504

gnomAD: N/A

Case5: No assertion made on age, gender or ethnicity

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: The identified variants were heterozygote in parents.

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: Genetic study of patient was conducted using direct sequencing of entire coding and exon-intron boundaries of the ITGA2B and ITGB3 genes.

Gene: ITGB3

Variant: NM_000212.2:c.538G>A (p.Gly180Arg) and NM_000212.2:c.155G>T (p.Cys52Phe)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8622972 (p.Gly180Arg) CA8622859 (p.Cys52Phe)

gnomAD: "Other" population (p.Gly180Arg) MAF is 0.0001630 https://gnomad.broadinstitute.org/variant/17-45361985-G-A and South Asian population p.Cys52Phe) MAF is 0.00003266.

Case1: Patient F1P1, Male, 11 years old, Tunisian

DiseaseAssertion: Glanzmann thrombasthenia type I

FamilyInfo: Table 1 states there is a family history of bleeding (we have minimal to no specific info on this)

ParentalGenotype: Mother and father are heterozygous for mutation

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

PlateletAggregation: GT diagnosis was based on absent platelet aggregation induced by ADP, collagen, and TRAP and subnormal or cyclical ristocetin induced agglutination

CasePreviousTesting: Using PCR they successfully amplified 20 DNA fragments for the ITGA2B gene (covering more than 48% of the ITGA2B gene constituting 30 exons) and15 DNA fragments of theITGB3gene (covering 15 exons)

Gene: ITGA2B

Variant: NM_000419.3:c.2702C>A (p.Ser901X) another variant this patient has is g.13944G>A --> I am noting this as Unknown Variant as I will need guidance curating this one

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399792888

gnomAD: N/A

Case2: Patient F2P1, Male, 34 years old, Tunisian

DiseaseAssertion: Glanzmann thrombasthenia type I

FamilyInfo: Table 1 states there is a family history of bleeding (we have minimal to no specific info on this)

ParentalGenotype: Mother and father are heterozygotes for the mutation here

CasePresentingHPOs, : HP:0000225, HP:0004406, HP:0000978,HP:0000790

(Gingival bleeding, recurrent epistaxis, easy bruising, hematuria)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

PlateletAggregation: GT diagnosis was based on absent platelet aggregation induced by ADP, collagen, and TRAP and subnormal or cyclical ristocetin induced agglutination

CasePreviousTesting: Using PCR they successfully amplified 20 DNA fragments for the ITGA2B gene (covering more than 48% of the ITGA2B gene constituting 30 exons) and15 DNA fragments of theITGB3gene (covering 15 exons)

Gene: ITGA2B

Variant: NM_000419.3:c.2702C>A (p.Ser901X) another variant this patient has is g.13944G>A --> I am noting this as Unknown Variant as I will need guidance curating this one

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399792888

gnomAD: N/A

Case1: Male, 14 years old, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia type 1

FamilyInfo: Sister is also heterozygous for this mutation but shows no bleeding symptoms

ParentalGenotype: Both parents are heterozygous for this mutation

Note: There is parental consanguinity

CasePresentingHPOs: HP:0000967, HP:0000225, HP:0000421

(Petechiae, ginigival bleeding, epistaxis)

CaseHPOFreeText: Haematoma,

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry analysis revealed 3.8 % platelet surface presentation of the αIIbβ3 complex for patient 1 and αIIb was not detected and β3 was significantly reduced in Western blots. Platelets from GT patients showed less than 5 % relative levels of the integrin subunit IIb and 5–9 % fibrinogen compared to controls.

PlateletAggregation: Article states agonist-induced platelet aggregation and binding of exogenous fibrinogen was pathological, too but does not mention specific agonists used or response to ristocetin

CasePreviousTesting: Molecular genetic analysis was done; however, no other information mentioned. In addition, the global proteome of highlight purified washed platelets was quantified by liquid chromatography-mass spectrometry and targeted MS-methods.

Gene: ITGA2B

Variant: NM_000419.3:c.175del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940266

gnomAD: N/A

Case2: Gender or age not specified, Thai ethnicity

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Parental information available in Table 2

ParentalGenotype: Father: p.Val206Asp/WT and Mother: also p.Val206Asp/WT (See Table 2)

Note: Yes to parental consanguinity

CasePresentingHPOs: N/A

CaseHPOFreeText: The article does not mention specific bleeding phenotypes for each of the 4 probands in the article, rather, there is a general statement that says: "The common presentations included recurrent epistaxis, bleeding in oral cavity, and easy-bruising spontaneously or after trauma"

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinEpression: General statement from the article that states that flow cytometry to assess the surface GPIIb/IIIa complex showed reduced expression for all probands.

PlateletAggregation: The platelet aggregation test was typically defective with all physiological agonists except ristocetin, for all patients.

CasePreviousTesting: Whole exome sequencing was performed on the 30 exons of ITGA2B and 15 exons in ITGB3. PCR and direct sequencing were then performed in the DNA samples of the patients and their available parents to verify the presence of the identified mutations.

Gene: ITGA2B

Variant: NM_000419.3:c.617T>A (p.Val206Asp)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399805578

gnomAD: N/A

PatientID: II.1

KindredID: 3

Case: M, 0Y4M, Ethnicity Unknown

DiseaseAssertion: Polycythemia

FamilyInfo: The patient had an affected brother (II.2) with the same mutation and polycythemia. Biologic material from parents were unavailable but Chuvash core haplotype analysis demonstrated that all patients were compound heterozygous, with 1 mutation being inherited from each parent. See Figure 2B for family pedigree.

CohortInfo: Patients with Chuvash polycythemia for whom VHL R200W had been found in a heterozygous state.

CasePresentingHPOs: HP:0001901 (Polycythemia)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: c.340+770T>C

LegacyVariant:N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 816685 https://www.ncbi.nlm.nih.gov/clinvar/variation/816685/

CAID: N/A

gnomAD: 0.00003186 https://gnomad.broadinstitute.org/variant/3-10184641-T-C

VariantEvidence: N/A

MutationType: intron_variant

CivicName: c.340+770T>C and R200W (c.598C>T)

MultipleGeneVariants: Germline, VHL, c.598C>T (p.Arg200Trp)

PatientID: II.1

KindredID: F10

Case: M, 4Y6M, Ethnicity Unknown

DiseaseAssertion: Polycythemia

FamilyInfo: This patient’s asymptomatic patients were both found to be carriers of the D143= (c.429C>T) germline variant in VHL. Their other child (II.2) also carried the gene. The current patient was the only one who was homozygous for the variant.

CasePresentingHPOs: HP:0001901; HP:0001744 (Polycythemia, Splenomegaly)

CaseHPOFreeText: Diagnosed with erythrocytosis (Polycythemia) and splenomegaly at 4.5 years old (DOB: 2002).

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.D143= (c.429C>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 416990, https://www.ncbi.nlm.nih.gov/clinvar/variation/416990/

CAID: N/A

gnomAD: 0.000007953, https://gnomad.broadinstitute.org/variant/3-10188286-C-T?dataset=gnomad_r2_1

VariantEvidence: Variant is present in allele 1 and 2 (i.e. homozygous).

MutationType: missense_variant;transition; synonymous_variant

CivicName: D143= (c.429C>T)

MultipleGeneVariants: Germline, Beta Thalassemia

PatientID: II.1

KindredID: F4

Case: M, 7Y0M, Ethnicity Unknown

DiseaseAssertion: Polycythemia

FamilyInfo: Variant c.340+694_340+711dup is inherited from mother (genetically confirmed) and variant R200W (c.598C>T) is assumed to be inherited from father.

CohortInfo: Patients with Chuvash polycythemia for whom VHL R200W had been found in a heterozygous state.

CasePresentingHPOs: HP:0001901; HP:0002625; HP:0001342 (Polycythemia, Deep venous thrombosis, Cerebral hemorrhage)

CaseHPOFreeText: Diagnosed with erythrocytosis (Polycythemia), deep vein thrombosis, intracerebral hemorrhage at age 7 (DOB: 1990).

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.R200W (c.598C>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 2232, https://www.ncbi.nlm.nih.gov/clinvar/variation/2232/

CAID: N/A

gnomAD: 0.0002016, https://gnomad.broadinstitute.org/variant/3-10191605-C-T

VariantEvidence: Variants are heterozygous.

MutationType: missense_variant;transition

CivicName: R200W (c.598C>T) and c.340+694_340+711dup

MultipleGeneVariants: Germline, VHL, c.340+694_340+711dup

MultipleGeneVariants: Germline, Factor V Leiden

PatientID: II.1

KindredID: F10

Case: M, 4Y6M, Ethnicity Unknown

DiseaseAssertion: Polycythemia

FamilyInfo: This patient’s asymptomatic patients were both found to be carriers of the D143= (c.429C>T) germline variant in VHL. Their other child (II.2) also carried the gene. The current patient was the only one who was homozygous for the variant.

CasePresentingHPOs: HP:0001901; HP:0001744 (Polycythemia, Splenomegaly)

CaseHPOFreeText: Diagnosed with erythrocytosis (Polycythemia) and splenomegaly at 4.5 years old (DOB: 2002).

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.D143= (c.429C>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 416990, https://www.ncbi.nlm.nih.gov/clinvar/variation/416990/

CAID: N/A

gnomAD: 0.000007953, https://gnomad.broadinstitute.org/variant/3-10188286-C-T?dataset=gnomad_r2_1

VariantEvidence: Variant is present in allele 1 and 2 (i.e. homozygous).

MutationType: missense_variant;transition; synonymous_variant

CivicName: D143= (c.429C>T)

MultipleGeneVariants: Germline, Beta Thalassemia

PatientID: II.1

KindredID: F4

Case: M, 7Y0M, Ethnicity Unknown

DiseaseAssertion: Polycythemia

FamilyInfo: Variant c.340+694_340+711dup is inherited from mother (genetically confirmed) and variant R200W (c.598C>T) is assumed to be inherited from father.

CohortInfo: Patients with Chuvash polycythemia for whom VHL R200W had been found in a heterozygous state.

CasePresentingHPOs: HP:0001901; HP:0002625; HP:0001342 (Polycythemia, Deep venous thrombosis, Cerebral hemorrhage)

CaseHPOFreeText: Diagnosed with erythrocytosis (Polycythemia), deep vein thrombosis, intracerebral hemorrhage at age 7 (DOB: 1990).

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.R200W (c.598C>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 2232, https://www.ncbi.nlm.nih.gov/clinvar/variation/2232/

CAID: N/A

gnomAD: 0.0002016, https://gnomad.broadinstitute.org/variant/3-10191605-C-T

VariantEvidence: Variants are heterozygous.

MutationType: missense_variant;transition

CivicName: R200W (c.598C>T) and c.340+694_340+711dup

MultipleGeneVariants: Germline, VHL, c.340+694_340+711dup

MultipleGeneVariants: Germline, Factor V Leiden

This paper is not publicly available. It was obtained via an institutional account and the relevant details annotated to the PubMed abstract.

PMID: 29393969

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

Case#: 1 (18 y, female, symptom onset/pain+movement limitation 10y, carpal tunnel syndrome surgery 16y, diagnosis 18y)

DiseaseAssertion: Scheie syndrome

FamilyInfo: "female patient, brother, and male cousin born to consanguineous parents" Based on pedigree (Figure 4), the cousins are related through their mothers but the degree of consanguinity is not clear

CasePresentingHPOs: 0034337

CaseHPOFreeText: claw hands with flexion contractures; electroneurology showed bilateral signs of severe median nerve suffering.

CaseNotHPOs: HP:0000280; HP:0001510; HP:0000943

CaseNotHPOFreeText: no coarse face, growth failure, other joint involvement, evidence of dysostosis multiplex of other bones. Normal intelligence, ophthalmologic, hearing and echocardiography, brain MRI

CaseEnzymeAssay: 0.36 (umol/g/h)

CaseUrineGAGs:

CaseERT: Yes, after diagnosis at 18y

CaseBMT:

Variant1:c.521delA

Variant1ClinVarID:

Variant1CAID: CA2586973518

Variant2: 521delA

Variant2ClinVarID:

Variant2CAID: CA2586973518

AdditionalVariants:

ParentalGenotype:

PreviouslyPublished

Case#: Male, 2-year old

DiseaseAssertion: MPS1-H

FamilyInfo: Not provided

CasePresentingHPOs: Not provided

CaseHPOFreeText: NA

CaseNotHPOs: Not provided

CaseNotHPOFreeText: NA

CaseEnzymeAssay: MPS1-H fibroblasts exhibited no activity of IDUAα (0.01 ± 0.02 nmol/mg/min); iPSC clones were devoid of IDUAα activity

CaseUrineGAGs: Not provided

CaseERT: Don't know

CaseBMT: Don't know

Variant1: NM_000203.5(IDUA):c.1073_1093del (p.His358_Thr364del)

Variant1ClinVarID:557260

Variant1CAID:

Variant2: NM_000203.4(IDUA):c.1205 G>A (p.Trp402Ter)

Variant2ClinVarID:11908

Variant2CAID:

ParentalGenotype: Not provided

PreviouslyPublished: Authors reference [30]: PMID: 31678774 DOI: 10.1016/j.scr.2019.101604

Case#: Elayaperumal_2018_V-283, M, 3 y.o. (onset), origin in India

DiseaseAssertion: VWD type 3

FamilyInfo: no consanguinity, no family history

ParentalGenotype: not reported

CasePresentingHPOs:

CaseHPOFreeText: bleeding score of 12, VWF:Ag of 0, FVIII:C 4.3%

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: not reported

GenotypingMethod: CSGE and Sanger sequencing of VWF gene only.

Gene: VWF

Variant: homozygous c.6321G>A (p.Trp2107*)

HGVS: NM_000552.3:c.6321G>A

ClinVarID: not reported

CAID: CA383491677

gnomAD: not reported

MultipleGeneVariants: not reported

Case#: 1, female, 44yo

DiseaseAssertion: VWD1

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0007420, HP:0000132, HP:0004846, HP:0012147, HP:0030129, HP:0030130 (spontaneous hematomas, Menorrhagia, Reduced quantity of VWF, Impaired ristocetin cofactor assay activity, Impaired von Willebrand factor collagen binding activity)

CaseHPOFreeText: Type O blood, VWF:Ag (0·55–2 iu/ml) pre = 0·47, VWF:RCo (0·55–2 iu/ml) pre = 0·5, FVIII:C (0·55–2 iu/ml) pre = 0·16, FVIII:C/VWF:Ag ratio = 0·32, VWF:FVIII binding (>20%) = 7%, VWF:FVIII binding/VWF:Ag (>0·7) = 0·15, patient died after motor vehicle accident

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: RFLP; confirmatory sequencing

Gene: VWF

Variant 1: NM_000552.4(VWF):c.2561G>A (p.Arg854Gln)

ClinVar: 296; https://www.ncbi.nlm.nih.gov/clinvar/variation/296/

gnomAD: MAF = 0.005692 (European Non-Finnish); https://gnomad.broadinstitute.org/variant/12-6143978-C-T

Variant 2: N/A - stated to be a compound heterozygote for a 2N VWD and a presumed null mutation

Case#: 3, female, 19yo

DiseaseAssertion: VWD1

FamilyInfo: brother diagnosed with VWD

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978; HP:0000132, HP:0004846, HP:0012147, HP:0030129 (Bruising susceptibility, Menorrhagia, Reduced quantity of VWF, Impaired ristocetin cofactor assay activity)

CaseHPOFreeText: Type O blood, VWF:Ag (0·55–2 iu/ml) pre = 0·14, VWF:RCo (0·55–2 iu/ml) pre = 0·15, FVIII:C (0·55–2 iu/ml) pre = 0·1, FVIII:C/VWF:Ag ratio = 0·71, VWF:FVIII binding (>20%) = n/a, VWF:FVIII binding/VWF:Ag (>0·7) = n/a, spinal surgery with VWF concentrate and adequate haemostasis

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: RFLP; confirmatory sequencing

Gene: VWF

Variant 1: NM_000552.4(VWF):c.2561G>A (p.Arg854Gln)

ClinVar: 296; https://www.ncbi.nlm.nih.gov/clinvar/variation/296/

gnomAD: MAF = 0.005692 (European Non-Finnish); https://gnomad.broadinstitute.org/variant/12-6143978-C-T

Variant 2: N/A - stated to be a compound heterozygote for a 2N VWD and a presumed null mutation

Case#: 4, male, 23yo

DiseaseAssertion: VWD1

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0004846, HP:0012147, HP:0030129 (Reduced quantity of VWF, Impaired ristocetin cofactor assay activity)

CaseHPOFreeText: Haemarthrosis in teens, Delayed bleeding after tonsillectomy (DDAVP given prior to procedure), VWF:Ag (0·55–2 iu/ml) pre = 0·35, VWF:RCo (0·55–2 iu/ml) pre = 0·32, FVIII:C (0·55–2 iu/ml) pre = 0·12, FVIII:C/VWF:Ag ratio = 0·34, VWF:FVIII binding (>20%) = n/a, VWF:FVIII binding/VWF:Ag (>0·7) = n/a, Surgery to repair a syringomyelia defect with VWF concentrate and no bleeding complications

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: RFLP; confirmatory sequencing

Gene: VWF

Variant 1: NM_000552.4(VWF):c.2561G>A (p.Arg854Gln)

ClinVar: 296; https://www.ncbi.nlm.nih.gov/clinvar/variation/296/

gnomAD: MAF = 0.005692 (European Non-Finnish); https://gnomad.broadinstitute.org/variant/12-6143978-C-T

Variant 2: N/A - stated to be a compound heterozygote for a 2N VWD and a presumed null mutation

Case: P7, Chinese, female, 27yo

DiseaseAssertion: VWD1

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type O blood, bleeding score = 9; VWF:Ag (%) = 5.4, VWF:RCo (%) = 5.3, FVIII:C (%) = 28, VWF:CB (%) = 4.1, VWFpp (%) = 4.8, VWF:RCo/VWF:Ag = 1.0, VWF:CB/VWF:Ag = 0.8, VWFpp/VWF:Ag = 0.9, FVIII:C/VWF:Ag = 5.2, RIPA (1.2 mg/ml, %) = 73.3

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant 1: c.711C>G (p.Cys237Trp)

HGVS: NM_000552.3:c.711C>G (p.Cys237Trp)

ClinVarID: NA

CAID: CA383509260; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA383509260

gnomAD: absent

Variant: c.1109+47T>A - Unregistered Variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Case: P10, Chinese, male, 5yo

DiseaseAssertion: VWD1

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type A blood, bleeding score = 2; VWF:Ag (%) = 4.2, VWF:RCo (%) = 3.8, FVIII:C (%) = 30.1, VWF:CB (%) = 3.5, VWFpp (%) = 4.1, VWF:RCo/VWF:Ag = 0.9, VWF:CB/VWF:Ag = 0.8, VWFpp/VWF:Ag = 1.0, FVIII:C/VWF:Ag = 7.4, RIPA (1.2 mg/ml, %) = 40.1

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant 1: c.7199delA (p.Asn2400Thrfs*4) - Unregistered Variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Variant 2: c.8155+5G>C - Unregistered Variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Case: P77, Chinese, female, 10yo

DiseaseAssertion: VWD3

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type B blood, bleeding score = 7; VWF:Ag (%) = 3.0, VWF:RCo (%) = 2.7, FVIII:C (%) = 6.8, VWF:CB (%) = 2.1, VWFpp (%) = 3.2, VWF:RCo/VWF:Ag = 0.9, VWF:CB/VWF:Ag = 0.7, VWFpp/VWF:Ag = 1.1, FVIII:C/VWF:Ag = 2.3

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant 1: c.6771C>A (p.Cys2257Ter)

HGVS: NM_000552.5:c.6771C>A (p.Cys2257Ter)

ClinVarID: NA

CAID: CA383489897; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA383489897

gnomAD: absent

Variant 2: c.8116-2delA - unregistered variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Case: P27, Chinese, female, 3yo

DiseaseAssertion: VWD2N

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type B blood, bleeding score = 6; VWF:Ag (%) = 9.5, VWF:RCo (%) = 8.9, FVIII:C (%) = 6.5, VWF:CB (%) = 6.9, VWFpp (%) = 10.8, VWF:RCo/VWF:Ag = 0.9, VWF:CB/VWF:Ag = 0.7, VWFpp/VWF:Ag = 1.1, FVIII:C/VWF:Ag = 0.7, VWF: FVIIIB (%) = 0.0

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant 1: c.2396G>A (p.Cys799Tyr)

HGVS: NM_000552.5:c.2396G>A (p.Cys799Tyr)

ClinVarID: NA

CAID: CA232300402; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA232300402

gnomAD: absent

Variant 2: c.3197_3201del - unregistered variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Case: P36, Chinese, male, 56yo

DiseaseAssertion: VWD3

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type A blood, bleeding score = 10; VWF:Ag (%) = 1.0, VWF:RCo (%) = 0.9, FVIII:C (%) = 4.1, VWF:CB (%) = 0.9, VWFpp (%) = 0.9, VWF:RCo/VWF:Ag = 0.9, VWF:CB/VWF:Ag = 0.9, VWFpp/VWF:Ag = 0.9, FVIII:C/VWF:Ag = 4.1

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant: c.5870delA - unregistered variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Case: P33, Chinese, female, 35yo

DiseaseAssertion: VWD3

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type A blood, bleeding score = 10; VWF:Ag (%) = 0.5, VWF:RCo (%) = <0.5, FVIII:C (%) = 5.0, VWF:CB (%) = <0.5, VWFpp (%) = <0.5, VWF:RCo/VWF:Ag = NA, VWF:CB/VWF:Ag = NA, VWFpp/VWF:Ag = NA, FVIII:C/VWF:Ag = 10.0

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant: c.813C>G (p.Tyr271Ter)

HGVS: NM_000552.5:c.813C>G (p.Tyr271Ter)

ClinVarID: NA

CAID: CA383508522; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA383508522

gnomAD: MAF = 0.0001088 (2/18380 alleles) in the East Asian popualtion; https://gnomad.broadinstitute.org/variant/12-6184562-G-C

Case#: Elayaperumal_2018_V-144, M, 1 y.o. (onset), origin in India

DiseaseAssertion: VWD type 3

FamilyInfo: consanguinity, family history of bleeding

ParentalGenotype: not reported

CasePresentingHPOs:

CaseHPOFreeText: bleeding score of 7, VWF:Ag of 0, FVIII:C of 5.9%

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: not reported

GenotypingMethod: CSGE and Sanger sequencing of VWF gene only.

Gene: VWF

Variant: homozygous c.1117C>T (p.Arg373*)

HGVS: NM_000552.3:c.1117C>T

ClinVarID: 100175

CAID: CA228261

gnomAD: MAF of 0.0001309 (4/30550 alleles, South Asian population) https://gnomad.broadinstitute.org/variant/12-6180502-G-A

MultipleGeneVariants:

Note: previously reported in LOVD

Case#: Elayaperumal_2018_V-115, female, 1 year old (onset), origin in India

DiseaseAssertion: VWD type 3

FamilyInfo: consanguinity

ParentalGenotype: not reported. family history of bleeding.

CasePresentingHPOs:

CaseHPOFreeText: bleeding score of 13. VWF:Ag of 0. FVIII:C of 1.9%

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: not reported

GenotypingMethod: CSGE and Sanger sequencing of VWF only.

Gene: VWF

Variant: homozygous c.6321G>A (p.Trp2107*)

HGVS: NM_000552.3:c.6321G>A (p.Trp2107*)

ClinVarID: not found

CAID: CA383491677

gnomAD: not found

MultipleGeneVariants: not reported

Case: Patient 3 (Family B), male, 55yo

DiseaseAssertion: VWD2B

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0030129, HP:0030130, HP:0011871, HP:0012147

(impaired ristocetin cofactor assay activity, Impaired von Willebrand factor collagen binding activity, Impaired RIPA, Reduced quantity of VWF)

CaseHPOFreeText: blood group O, Platelet count x103/μl = 204, PFA 100 sec = >300, SPA % = 0, MADR mg/mL = 0.45, VWF:Ag U/dL = 23.4, VWF:CB U/dL = 21.1, VWF:CB ratio = 0.9, VWF:RCo U/dL = 17.2, VWF:RCo ratio = 0.74, Platelet VWF U/dL = 42.6, FVIII U/dL = 60.5, BAT F/M = 20

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: Sequencing of exon 28 of VWF

PreviouslyPublished: NA

Gene: VWF

Variant 1: c.3797C>T (p.Pro1266Leu)

HGVS: NM_000552.4(VWF):c.3797C>T (p.Pro1266Leu)

ClinVarID: 314; https://www.ncbi.nlm.nih.gov/clinvar/variation/314/

CAID: NA

gnomAD: MAF = 0.003667 (92/25086 alleles; 1 homozygote) in the European (Finnish) population; https://gnomad.broadinstitute.org/variant/12-6128787-G-A?dataset=gnomad_r2_1

Variant 2: c.7085G>T (p.Cys2362Phe)

HGVS: NM_000552.4(VWF):c.7085G>T (p.Cys2362Phe)

ClinVarID: 315; https://www.ncbi.nlm.nih.gov/clinvar/variation/315/

CAID: NA

gnomAD: absent

Case#: Elayaperumal_2018_V-319, F, 8 y.o. (onset), origin in India

DiseaseAssertion: VWD type 3

FamilyInfo: Consanguinity: No, Family history: Yes

ParentalGenotype: not reported

CasePresentingHPOs:

CaseHPOFreeText: Bleeding score: 14, VWF:Ag 0, FVIII:C <1%

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: not reported

GenotypingMethod: CSGE and Sanger sequencing of VWF gene only.

Gene: VWF

Variant: homozygous c.6090dupT (p.Val2031Lysfs*19)

HGVS: NM_000552.3:c.6090dupT

ClinVarID: not present

CAID: CA2824998272

gnomAD: not present

MultipleGeneVariants:

Case#: Elayaperumal_2018_V-260 , M, 3y.o. (onset), origin in India

DiseaseAssertion: VWD type 3

FamilyInfo: consanguinity reported. No family history of bleeding

ParentalGenotype: not reported

CasePresentingHPOs:

CaseHPOFreeText: bleeding score of 9, VWF:Ag of 0, FVIII:C of 7.4%

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: not reported

GenotypingMethod: CSGE and Sanger sequencing of VWF gene only.

Gene: VWF

Variant: homozygous c.665G>A (p.Trp222*)

HGVS: NM_000552.3:c.665G>A

ClinVarID: not found

CAID: CA383509511

gnomAD: not found

MultipleGeneVariants: n/a

Case#: Elayaperumal_2018_V-312 , M, 2.5 y.o. (onset), origin in India

DiseaseAssertion: VWD type 3

FamilyInfo: Consanguinity: Yes, Family history: No

ParentalGenotype: not reported

CasePresentingHPOs:

CaseHPOFreeText: Bleeding score: 7, VWF:Ag 0, FVIII:C 3.6%

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: not reported

GenotypingMethod: CSGE and Sanger sequencing of VWF gene only.

Gene: VWF

Variant: homozygous c.3560delT

HGVS: NM_000552.3:c.3560delT (p.Leu1187Cysfs*28)

ClinVarID: not present

CAID: CA2580612141

gnomAD: not present

MultipleGeneVariants:

Case#: Elayaperumal_2018_V-316, F, 1.5 y.o. (onset), origin in India

DiseaseAssertion: VWD type 3

FamilyInfo: Consanguinity: Yes, Family history: Yes

ParentalGenotype: not reported

CasePresentingHPOs:

CaseHPOFreeText: Bleeding score: 0, VWF:Ag 0, FVIII:C 3.4%

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: not reported

GenotypingMethod: CSGE and Sanger sequencing of VWF gene only.

Gene: VWF

Variant: homozygous c.2749 2752dupCCCT (p.Val919Leufs*18)

HGVS: NM_000552.3:c.2749 2752dupCCCT

ClinVarID: not present

CAID: CA2695215955

gnomAD: not present

MultipleGeneVariants:

Case: Index Patient (IP), Female, 26 years old; described as from a genetically isolated population (not further specified), consistent with elevated homozygosity rates in that population. DiseaseAssertion: Type 3 VWD, confirmed by VWF:Ag <4 IU/dL (virtual absence of VWF). FamilyInfo: NA — no relatives' bleeding history or genotype reported ParentalGenotype(s): NA (not tested/not reported) CasePresentingHPOs: HP:0000421 (Epistaxis — frequent nosebleeds), HP:0000132 (Menorrhagia — heavy, prolonged, led to iron-deficiency anemia), HP:0001934 (Persistent bleeding after trauma — bleeding following injury), HP:0012147 (Reduced quantity of VWF; VWF:Ag <4 IU/dL), HP:0030129 (Impaired VWF:RCo-type activity; VWF:GPIbM <4 IU/dL) CaseHPOFreeText: Easy bruising (no matching HPO code in the approved list); FVIII:C 2.0 IU/dL (nv 70–157); referred to Hemophilia Centre at age 1 for bleeding complications; declined recommended lifelong prophylaxis due to injection discomfort, later underwent prophylaxis with plasma-derived VWF/FVIII concentrates and on-demand treatment (tranexamic acid, oral contraceptives, replacement therapy). Supporting functional evidence from patient-derived endothelial colony-forming cells (ECFCs): virtual absence of VWF mRNA (RQ ~0.04–0.05 vs. 1.00 in healthy controls, across 4 primer/probe sets); VWF secretion into ECFC medium 6.2% ± 0.4% of healthy controls (p<0.0001); near-total absence of Weibel-Palade bodies on immunofluorescence (only 1–3 small WPBs seen in some cells vs. normal stick-shaped WPBs in controls); altered intracellular trafficking of angiopoietin-2 (WPB inflammatory cargo) in the absence of WPBs. CaseNOTHPOs: NA CaseNOTHPOFreeText: NA CasePreviousTesting: Routine testing (Sanger sequencing of coding exons, ~50 bp flanking intronic regions, promoter, 5'/3'-UTR, plus MLPA) was negative — patient was "mutation-negative" prior to this study. Not genome-wide; targeted to VWF only, but comprehensive: this study's NGS covered the entire 176 kb VWF locus (all 52 exons, full intronic regions, promoter) at 30x coverage, going well beyond standard exon+flanking-intron approaches specifically to find deep intronic variants. GenotypingMethod: Illumina NovaSeq 6000 NGS (2×150 bp reads) of the whole VWF genomic region; variant annotation via Ensembl VEP with SpliceAI, PolyPhen-2, SIFT; splice effect independently confirmed with Neural Network Splicing, ASSP, and MaxEnt/HSF prediction tools. Functional validation via patient-derived ECFCs: RT-qPCR of VWF mRNA (4 primer/probe sets), cDNA sequencing, VWF:Ag ELISA of ECFC secretion, immunofluorescence microscopy, and whole-transcriptome RNA-seq. PreviouslyPublished: NA — no indication this patient was reported elsewhere; paper explicitly frames this variant/mechanism as a first report. Gene: VWF Variant: Novel homozygous deep intronic variant, intron 8, creating a new donor splice site that outcompetes the native donor site, causing inclusion of a 118-bp pseudoexon, frameshift, premature stop codon, and nonsense-mediated decay of the transcript. HGVS: NM_000552.5:c.997+118T>G (confirmed via ClinGen Allele Registry Community Standard Title; not explicitly stated in the paper's main text, which only gives cDNA/genomic coordinates without a transcript version). Genomic: g.6073501A>C (GRCh38/hg38; note the T>G/A>C discrepancy reflects VWF being transcribed from the minus strand of chr12). ClinVarID: NA CAID: CA3275979827 gnomAD: NA

Case: Patient B, male, 11 years old at WIL-29 study entry; ethnicity not reported.

DiseaseAssertion: VWD3. The patient was initially suspected to have VWD2A based on the family history but was reclassified as VWD3 after next-generation sequencing.

FamilyInfo: Patient B and Patient A are brothers from a consanguineous family. Both parents were diagnosed with VWD. Figure 2 shows both parents as heterozygous and Patient A and Patient B as homozygous for the familial VWF variant. The pedigree also includes another brother affected with VWD whose genetic testing was underway and a sister whose VWD diagnosis and genetic testing were pending.

ParentalGenotype: Both parents were heterozygous for the familial VWF variant, as shown in Figure 2.

CasePresentingHPOs: HP:0000421, HP:0030129 (Epistaxis, Impaired ristocetin cofactor assay activity)

CaseHPOFreeText: Recurrent spontaneous epistaxis. Historical VWF:RCo 1%; historical VWF:Ag not measured. VWF:RCo 1 IU/dL at WIL-31 screening. At the month 0 pharmacokinetic visit, pre-injection FVIII 16 IU/dL and VWF:RCo <5 IU/dL; after 60 IU/kg wilate, maximum VWF:RCo 65 IU/dL and in vivo recovery 1.02 kg/dL. VWF inhibitors were confirmed present at WIL-31 study entry; no VWF inhibitor was detectable at the 12-month visit.

CaseNotHPOs: NA

CaseNotHPOFreeText: No anaphylactic reactions or severe treatment-related adverse events were reported.

CasePreviousTesting: Diagnosed with VWD shortly after birth and initially suspected to have VWD2A based on family history. Historical VWF activity testing, and subsequent pharmacokinetic and VWF inhibitor testing, were performed. Historical VWF antigen was not measured. No earlier molecular genetic testing was reported.

GenotypingMethod: Next-generation sequencing performed in Bonn, Germany. Additional technical details regarding the sequencing assay or panel were not provided.

Gene: VWF

Variant: c.4094T>C p.Leu1365Pro, homozygous

HGVS: NM_000552.5:c.4094T>C (p.Leu1365Pro)

ClinVar: 2438545

CAID: NA

gnomAD: Absent (not reported in gnomAD; 0/251040 control chromosomes)

Case#: 1A

DiseaseAssertion:

FamilyInfo: Family 1. Her 2 offspring, 1B (son) and 1C (daughter), reported minor bleeding symptoms that had not required treatment. 1B was found to be heterozygous for Trp1745Cys only and 1C was heterozygous for Arg760His only, confirming that these mutations are in trans in 1A.

CaseHPOFreeText4: was an elderly woman with lifelong bleeding episodes, including epistaxis, ecchymosis, menorrhagia, and prolonged bleeding after dental extractions, requiring multiple medical interventions. The coexistence of both mutations appears to produce a more significant bleeding disorder as the bleeding score in 1A (8) was higher than that in either of her children (4 and 2). The position of Trp1745 in the A3 domain is shown in Figure 2. Both persons with this mutation (1A and 1B) had markedly reduced ratios of VWF collagen-binding activity to VWF antigen (CB:Ag) with type III collagen (0.1 and 0.3, respectively) and type I collagen (0.2 and 0.3, respectively). The ratio of VWF:RCo to VWF:Ag (RCo:Ag) was near unity in both persons, and VWF multimer analysis (Figure 1B) and RIPA were normal. Closure times in the PFA-100 were mildly prolonged with the ADP cartridge (1A = 173 seconds, 1B = 189 seconds, NR < 112 seconds). With the epinephrine cartridge, the closure time was prolonged in 1A only (1A = 271 seconds, 1B = 90 seconds, NR < 179 seconds).

CasePreviousTesting: Fifty-one primer sets were used to amplify the essential regions of VWF (52 exons, flanking intronic regions, 5′ promoter region, and the 3′ untranslated region).

Gene: VWF

Variant: 1A demonstrated compound heterozygosity for 2 mutations in the VWF gene. The first is a novel mutation in exon 30:c.5235 G → T resulting in Trp1745Cys and the second is c.2279 G → A resulting in Arg760His.

HGVS: NM_000552.5(VWF):c.5235G>T (p.Trp1745Cys), NM_000552.5(VWF):c.2279G>A (p.Arg760His)

ClinVar: 100421, 31011

CAID: CA228706, CA228316

gnomAD: 8.474e-7 in the european non finnish pop, 0.00002669 in the African American population

Gene:VWF

HGNCID:12726

Case:13 yo female

DiseaseAssertion: Type 2N

FamilyInfo:Fig. 1, family 2, patient 7

ParentalGenotype(s):Unknown, obligate carriers

CasePresentingHPOs:HP:0000421, HP:0004846, HP:0012147 HP:0030132, HP:0030130

CaseHPOFreeRext:Oral cavity and joint bleeding, VWF:Ag 0.07 U/mL, VWF:Ac 0 U/mL, VWF:CB 0.05 U/mL, FVIII 0.04 U/mL, No VWF Multimers

GenotypingMethod: NGS

Gene:VWF

Variant:c.2311A>G

HGVS:NM_000552.5(VWF):c.2311A>G

ClinVarID:1065273

CAID:CA383522481

Gene:VWF

HGNCID:12726

Case:27 yo male

DiseaseAssertion: Type 2N

FamilyInfo:Fig. 1, family 1, patient 2

ParentalGenotype(s):Unknown, obligate carriers

CasePresentingHPOs:HP:0000421, HP:0012147 HP:0030132, HP:0030130

CaseHPOFreeRext:Skin, oral cavity, and joint bleeding, Bleeding after tooth extractions and small wounds, VWF: Ag 0.07 U/mL, VWF:Act 0.05 U/mL, VWF:CB <0.05 U/mL, FVIII:C 0.01 U/mL, Less VWF Multimers

GenotypingMethod: NGS

Gene:VWF

Variant:c.2311A>G

HGVS:NM_000552.5(VWF):c.2311A>G

ClinVarID:1065273

CAID:CA383522481

Gene:VWF

HGNCID:12726

Case:17 yo male

DiseaseAssertion: Type 2N

FamilyInfo:Fig. 1, family 1, patient 3

ParentalGenotype(s):Unknown, obligate carriers

CasePresentingHPOs:HP:0000421, HP:0012147 HP:0030132, HP:0030130

CaseHPOFreeRext:Oral cavity, skin, and muscle bleeding, Bleeding after tooth extractions, VWF: Ag 0.09 U/mL, VWF:Act 0.05 U/mL, VWF:CB 0.04 U/mL, FVIII:C 0.01 U/mL, No VWF Multimers

GenotypingMethod: NGS

Gene:VWF

Variant:c.2311A>G

HGVS:NM_000552.5(VWF):c.2311A>G

ClinVarID:1065273

CAID:CA383522481

Case#: P 22, Female, 0.2 months old when started ERT (47.0 months old when last reported), German

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001639 , HP:0001252 , HP:0003701, HP:0001371

(Hypertrophic cardiomyopathy, Muscular hypotonia, Proximal muscle weakness, Flexion contracture )

CaseHPOFreeText: Flexion contractures were a complication during ERT

CaseNotHPOs: N/A

CaseNotHPOFreeText: No tube feeding nor ventilation needed

CasePreviousTesting: CRIM status is unknown

Antibody titer is 1:1.800

Variant 1: NM_000152.3:c.2004C>A

ClinVar: N/A

CAID: CA401370054

gnomAD: N/A

Variant: c.541545delTTAC

ClinVar: N/A

CAID: N/A

gnomAD: N/A

ParentalGenotype: Maternal allele carried the c.2004 C>A Variant

The paternal allele carried the c.541545delTTAC

PreviouslyPublished: N/A

Case7: GT-7, German and Jugoslav, gender or age not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Mother: c.1126-72C>T heterozygous and Father: c.1126-72C>T heterozygous

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding symptoms are severe and bleeding time is pathogenic (See Table 1) Abstract mentions patients' bleeding signs include epistaxis, mucocutaneous bleeding, haematomas, petechiae, GI bleeding and menorrhagia; however, not specified per proband.

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry was performed and expression is stated as pathogenic in Table 1

PlateletAggregation: Platelet aggregation was performed and is stated as pathogenic in Table 1; however, no specific agonists mentioned

CasePreviousTesting: All exons of ITGA2B and ITGB3 genes as well as surrounding intron regions were amplified by PCR using intronic primers as pre-viously described (12). The purified DNA fragments were then di-rectly sequenced.

Gene: ITGB3

Variant: NM_000212.2:c.1030dup and an Unregistered Variant (c.1126_72C>T) (Does not show up in CAR)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA658820875 and N/A

gnomAD: N/A

Case1: GT-1, Turkish, gender or age not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Mother: c.2374delG heterozygous and Father: c.2374delG heterozygous

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding symptoms are severe and bleeding time is pathogenic (See Table 1) Abstract mentions patients' bleeding signs include epistaxis, mucocutaneous bleeding, haematomas, petechiae, GI bleeding and menorrhagia; however, not specified per proband.

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry was performed and expression is stated as pathogenic in Table 1

PlateletAggregation: Platelet aggregation was performed and is stated as pathogenic in Table 1; however, no specific agonists mentioned

CasePreviousTesting: All exons of ITGA2B and ITGB3 genes as well as surrounding intron regions were amplified by PCR using intronic primers as pre-viously described (12). The purified DNA fragments were then di-rectly sequenced.

Gene: ITGA2B

Variant: NM_000419.3:c.2374del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940267

gnomAD: N/A

Case12: GT-12, Caucasian, gender or age not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: Mother: c.2326_2331dupGAGGCC and Father: deceased

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding symptoms are severe and bleeding time is pathogenic (See Table 1) Abstract mentions patients' bleeding signs include epistaxis, mucocutaneous bleeding, haematomas, petechiae, GI bleeding and menorrhagia; however, not specified per proband.

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry was performed and expression is stated as pathogenic in Table 1

PlateletAggregation: Platelet aggregation was performed and is stated as pathogenic in Table 1; however, no specific agonists mentioned

CasePreviousTesting: All exons of ITGA2B and ITGB3 genes as well as surrounding intron regions were amplified by PCR using intronic primers as pre-viously described (12). The purified DNA fragments were then di-rectly sequenced.

Gene: ITGA2B

Variant: NM_000419.3:c.957T>A and NM_000419.3:c.2326_2331dupGAGGCC

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399804780 and CA915940324

gnomAD: N/A

Case1: Female, 3 year old, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: An analysis of family members indicated that the Gln517Stop and Arg553Stop mutations were located on different alleles and inherited from the patient’s mother and father, respectively

CasePresentingHPOs: HP:0004406, HP:0002248, HP:0000978, HP:0000225

(Recurrent epistaxis, hematemesis, easy bruising, gingival bleeding)

CaseHPOFreeText: Petechial hemorrhages

CaseNotHPOs: HP:0001945, HP:0002014, HP:0005261

Fever, diarreah, hemarthrosis

CaseNotHPOsFreeText: N/A

ProteinExpression: A flow cytometry evaluation revealed marked reduction in glycoprotein IIb/IIIa (See Table 1 for Patient's Lab results)

PlateletAggregation: Patients platelets did not aggregate in response to ADP, epinephrine, arachidonic acid, or collagen but platelets had normal ristocetin induced aggregation

CasePreviousTesting: Molecular genetic analysis of ITGA2B was performed which revealed mutations

Gene: ITGA2B

Variant: NM_000419.3:c.1642C>T (p.Gln548Ter) and NM_000419.3:c.1750C>T (Arg584Ter)

LegacyVariant: Gln517Ter and Arg553Ter

ClinVar: 2892

CAiD: CA399802364 and CA115834

gnomAD: MAF in the East Asian population is 0.0002176

Case3: Male, Israeli-Arab, (age is either 10 or 14)

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: See Fig 1C for pedigree

ParentalGenotype: See Fig 1C for pedigree

CasePresentingHPOs: HP:0000421, HP:0031364, HP:0000967

(Severe epistaxis, ecchymosis, petechiae)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: No surface expression of αIIbβ3 was found in patients’ platelets (See Fig 3)

PlateletAggregation: Absent platelet aggregation in response to ADP, epinephrine, collagen and normal ristocetin-induced platelet agglutination

CasePreviousTesting: DNA fragments containing exons and flanking intronic regions of the aIIb and B3 genes were amplified by PCR using primers

Gene: ITGA2B

Variant: NM_000419.3:c.97A>G (p.Asn2Asp)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399806951

gnomAD: N/A

Case1: Male, 18 years old, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: See Figure 4 for family pedigree of patients carrying the 288delC mutation in GPIIb

ParentalGenotype: Heterozygous for variant

CasePresentingHPOs: HP:0000978 (Bruising)

CaseHPOFreeText: Mucocutaneous bleeding

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry analysis shown in Fig 1

PlateletAggregation: Platelets failed to aggregate either spontaneously or in response to ADP, adrenaline, collagen or arachidonic acid, but they showed agglutination in the presence of ristocetin

CasePreviousTesting: ITGA2B and ITGB3 both were sequenced

Gene: ITGA2B

Variant: NM_000419.3:c.291del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940464

gnomAD: N/A

Case#: Male, 62, Egyptian

DiseaseAssertion: GT with concurrent platelet CD36 deficiency (~1 in 100 million) and anti‐CD36 antibodies

CasePresentingHPOs: HP:0000421,Epistaxis. HP:0000978, Bruising susceptibility. HP:0000225, Gingival bleeding. HP:0001903, Anemia. HP:0001934, Persistent bleeding after trauma. HP:0001058, Poor wound healing. HP:0002573, Hematochezia. HP:0005261, Joint hemorrhage.

PlateletAggregation: See Table 1. Normal platelet count. Normal platelet size, modestly elevated mean platelet volume. Normal response to ristocetin.

ProteinExpression: Flow cytometry. GPIb/IX Expression 108% (range: 65-124%); GPIIb/IIIa expression 0% (range:65-124%).

Gene: ITGA2B

Variant: c.2148dup, p.Leu717Alafs3X

HGVS: NM_000419.5:c.2148dup

ClinVar: 627273

CAID: CA915940304

gnomAD: Absent

Variant: c.1234G>A, p.Gly412Arg

HGVS: NM_000419.5:c.1234G>A

ClinVar: 381748

CAID: CA8603182

gnomAD: 0.00003236, https://gnomad.broadinstitute.org/variant/chr17-44381038-C-T?dataset=gnomad_r4

Case1: Female, 9 years old, Japanese

DiseaseAssertion: Macrothrombocytopenia

FamilyInfo: Information given in Table 1 and Fig 2

ParentalGenotype: Mother: ITGA2B (p.Arg422Ter heterozygous) and Father: ITGA2B (p.Gly991Cys heterozygous) See Table 1 for this information

Sequencing of parental DNA indicated parental mutations. CasePresentingHPOs: HP:0000979, HP:0000421, HP:0000978

(Purpura, epistaxis, bruising)

CaseHPOFreeText: Hemorrhage after dental

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometric analysis showed that surface αIIbβ3 expression in platelets (was markedly impaired 3-11%)

PlateletAggregation: N/A

CasePreviousTesting: Sequence analysis of entire coding regions of exons and exon-intron boundaries of ITGA2B and ITGB3 gene of the patient revealed two novel mutations in ITGA2B.

Gene: ITGA2B

Variant: NM_000419.3:c.3064G>T (p.Gly1022Cys) and NM_000419.3:c.1357C>T (p.Arg453Ter)

LegacyVariant: (p.Gly991Cys legacy nomenclature for p.Gly1022Cys) and (p.Arg422Ter legacy nomenclature for p.Arg453Ter)

ClinVar: 631773

CAiD: CA399787943 and CA399803529

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

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

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

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

PatientID: 2

KindredID: 1

Case: M, 10Y0M, Ukrainian

DiseaseAssertion: Asymptomatic

FamilyInfo: His sister (patient 1) also had polycythemia and was heterozygeous for the mutation. Mutation inherited from father. The father was not polycythemic, but his BFU-Es were hypersensitive to Epo.

CasePresentingHPOs: HP:0001901 (polycythemia)

CaseHPOFreeText: Patient had a hematocrit of 63%, erythropoietin level of 271 mIU/mL, and had hypersensitivity of erythroid progenitors to Epo.

CaseNotHPOs: N/A

CaseNotHPOFreeText: No tumor masses were detected by repeated CT scans of his abdomen or chest and by magnetic resonance imaging (MRI) of the head.

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.D126Y(c.376G>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 2230 https://www.ncbi.nlm.nih.gov/clinvar/variation/2230/

CAID: CA020319 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.376G%3ET

gnomAD: N/A

VariantEvidence: Patient was heterozygous for the mutation.

MutationType: missense_variant;transversion

CivicName: D126Y(c.376G>T)

MultipleGeneVariants: N/A

PatientID: 2

KindredID: 1

Case: M, 10Y0M, Ukrainian

DiseaseAssertion: Asymptomatic

FamilyInfo: His sister (patient 1) also had polycythemia and was heterozygeous for the mutation. Mutation inherited from father. The father was not polycythemic, but his BFU-Es were hypersensitive to Epo.

CasePresentingHPOs: HP:0001901 (polycythemia)

CaseHPOFreeText: Patient had a hematocrit of 63%, erythropoietin level of 271 mIU/mL, and had hypersensitivity of erythroid progenitors to Epo.

CaseNotHPOs: N/A

CaseNotHPOFreeText: No tumor masses were detected by repeated CT scans of his abdomen or chest and by magnetic resonance imaging (MRI) of the head.

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.D126Y(c.376G>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 2230 https://www.ncbi.nlm.nih.gov/clinvar/variation/2230/

CAID: CA020319 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.376G%3ET

gnomAD: N/A

VariantEvidence: Patient was heterozygous for the mutation.

MutationType: missense_variant;transversion

CivicName: D126Y(c.376G>T)

MultipleGeneVariants: N/A

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.

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.