Case#: 19-year-old boy with coarctation of the aorta who complained of mild exertional dyspnea.

DiseaseAssertion: dilated cardiomyopathy (DCMP). LV systolic dysfunction.

FamilyInfo: The family history was positive to sudden death (his cousin died, aged 3 months) and to DCMP and heart transplant (HT): a maternal aunt and her son who then died at 42 and 24 years old. Cascade family screening revealed a TNNT2 variant in the mother (II.1) and his cousin (IV.3).

ParentalTesting: The 19 year old brother's was tested and carried the TNNT2 variant. She was also affected by DCM. The father’s testing status was not reported.

CasePresentingHPOs: HP:0001680, HP:0002875, HP:0025169, HP:4000141

CaseHPOFreeText: surgically repaired coarctation of the aorta who complained of mild exertional dyspnea repaired at birth (NYHA class II–III). Cardiac MRI showed a moderately dilated, hypokinetic LV with an ejection fraction of 45%; echocardiography showed an ejection fraction around 42%.

CaseNotHPOs: not reported

CaseNotHPOFreeText: Nothing was found that was correlated.

CasePreviousTesting: genetic investigations through next generation sequencing (NGS) with a panel of 325 genes, known to be associated with cardiomyopathies

Genotyping Method: targeted next generation sequencing

FunctionalAnalysis: not reported

Variant: c.518G>A (p. Arg173Gln)

ClinVar: 43649

CAID: CA004727

gnomAD: not reported

AdditionalInfo: not reported

Case1: 13 year old female

DiseaseAssertion: LVNC

FamilyInfo: No family history of cardiac disease

ParentalTesting:

CasePresentingHPOs: HP:0011664. HP:0002094. HP:0001279. HP:0031295

CaseHPOFreeText:Left Ventricular noncompaction, Dyspnea (shortness of breath), Fainting, Left atrial enlargement

CaseNotHPOs:HP:0000929. HP:0001712

CaseNotHPOFreeText:Abnormal skull morphology, left ventricular hypertrophy

CasePreviousTesting:

Genotyping Method:Next-Generation Sequencing (NGS)

FunctionalAnalysis:

Variant:c.575G>A

ClinVar:12424

CAID:CA021957

gnomAD:

AdditionalInfo:

Case#: V-1; male; age 68

DiseaseAssertion: Familial hypertrophic cardiomyopathy

FamilyInfo: HCM was reported in the proband’s father and three daughters. The same heterozygous TNNT2 Δ160E variant was identified in all three daughters

CasePresentingHPOs: HP:0001712 HP:0012664 HP:4000141 HP:0004756

CaseHPOFreeText: Left ventricular hypertrophy; progressive left ventricular systolic dysfunction; left ventricular enlargement; cardiomyocyte hypertrophy; sustained ventricular tachycardia; advanced heart failure

CasePreviousTesting: Diagnosed with HCM at age 25; no previous genetic testing reported

Genotyping Method: Ion AmpliSeq cardiovascular research panel screening 404 genes, with direct Sanger sequencing confirmation

FunctionalAnalysis: Patient-derived and isogenic CRISPR/Cas9-edited iPSC-derived cardiomyocytes showed prolonged calcium decay, impaired relaxation, cardiomyocyte hypertrophy, and altered calcium-regulated signaling. EGCG partially improved the calcium and relaxation abnormalities.

Variant: c.478_480del, p.Δ160E; in-frame 3-bp deletion

ClinVar: 43648

CAID: CA004651

Supplementary Table S1 & S2 Proband and Variant Information:

Case20: GT23, Male, 19, French

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0000225, HP:0000421

(Easy bruising, gingival bleeding, epistaxis)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed <5% expression of αIIbβ3 (See Supplementary Table 1)

PlateletAggregation: Absent platelet aggregation (See Supplementary Table 1)

CasePreviousTesting: Sanger sequencing of ITGA2B and ITGB3

Gene: ITGB3

Variant: NM_000212.2:c.1031A>C (p.Tyr344Ser)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA400025814

gnomAD: N/A

Supplementary Table S1 & S2 Proband and Variant Information:

Case39: GT40, Female, 17 years old, Pankistani

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000421, HP:0030140

(Epistaxis, bleeding from mouth)

CaseHPOFreeText: Heavy bleeding at menarche

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed <5% expression of αIIbβ3 (See Supplementary Table 1)

PlateletAggregation: Absent platelet aggregation (See Supplementary Table 1)

CasePreviousTesting: Sanger sequencing of ITGA2B and ITGB3

Gene: ITGA2B

Variant: NM_000419.3:c.857T>A (p.Val286Asp)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399805011

gnomAD: N/A

Supplementary Table S1 & S2 Proband and Variant Information:

Case57: GT58, Male, 14, Argentinian/European

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000421, HP:0000967, HP:0000225, HP:0011886

(Epistaxis, petechia, gingival bleeding, hyphema)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed <5% expression of αIIbβ3 (See Supplementary Table 1)

PlateletAggregation: Absent platelet aggregation (See Supplementary Table 1)

CasePreviousTesting: Sanger sequencing of ITGA2B and ITGB3

Gene: ITGA2B

Variant: NM_000419.3:c.601G>A (p.Gly201Ser)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399805612

gnomAD: N/A

Supplementary Table S1 & S2 Proband and Variant Information:

Case72: GT76, Male, 54 years old, French

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0002239, HP:0032551

(Gi bleeding, hemorrhoids)

CaseHPOFreeText: Moderate bleeding syndrome

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Type unknown for this proband

PlateletAggregation: Absent platelet aggregation (See Supplementary Table 1)

CasePreviousTesting: Sanger sequencing of ITGA2B and ITGB3

Gene: ITGA2B

Variant: NM_000419.3:c.2421G>A (p.Trp807Ter)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399796017

gnomAD: N/A

Supplementary Table S1 & S2 Proband and Variant Information:

Case68: GT72, Female, 56 years old, French

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000421, HP:0031364, HP:0000225, HP:0000132, HP:0002239, HP:0006298

(Epistaxis, ecchymosis, gingival bleeding, menorrhagia, GI bleeding, prolonged bleeding after dental extraction)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed <5% expression of αIIbβ3 (See Supplementary Table 1)

PlateletAggregation: Absent platelet aggregation (See Supplementary Table 1)

CasePreviousTesting: Sanger sequencing of ITGA2B and ITGB3

Gene: ITGA2B

Variant: NM_000419.3:c.2951C>A (P.Thr984Lys)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399790180

gnomAD: N/A

Supplementary Table S1 & S2 Proband and Variant Information:

Case60: GT62, Female, 58 years old, French

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Affected sister (that is all the information we are given)

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0000225, HP:0000132, HP:0006298

(Easy bruising, gingival bleeding, menorrhagia, bleeding after dental extraction)

CaseHPOFreeText: Esophageal bleeding

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed <5% expression of αIIbβ3 (See Supplementary Table 1)

PlateletAggregation: Absent platelet aggregation (See Supplementary Table 1)

CasePreviousTesting: Sanger sequencing of ITGA2B and ITGB3

Gene: ITGB3

Variant: NM_000212.2:c.31T>C (p.Trp11Arg)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA291240306

gnomAD: N/A

Supplementary Table S1 & S2 Proband and Variant Information:

Case53: GT53, Male, 16 years old, Argentenian/Brazilian

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000421

(Epistaxis)

CaseHPOFreeText: Hematomas

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed <5% expression of αIIbβ3 (See Supplementary Table 1)

PlateletAggregation: Absent platelet aggregation (See Supplementary Table 1)

CasePreviousTesting: Sanger sequencing of ITGA2B and ITGB3

Gene: ITGB3

Variant: NM_000212.2:c.356G>A (p.Gly201Ser) and NM_000212.2:c.1697G>A (p.Arg119Gln)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8622925 and CA400032338

gnomAD: MAF in the African population is http://gnomad.broadinstitute.org/variant/17-45360910-G-A

Case9: (GT-11) Male, age or ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Probands GT12 -GT14 are related to GT-11 see Table 1

ParentalGenotype: Parents may be included in Table 1; however, not specified so no information

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding severity: Moderate (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.727G>C (p.Asp243His)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA400023600

gnomAD: N/A

Case19: (GT-21) Male, age or ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Proband GT-22 is related to GT-21 see Table 1

ParentalGenotype: Parents may be included in Table 1; however, not specified so no information

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding severity: Moderate (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.2302-1G>A

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA400034626

gnomAD: N/A

Case: (Patient C), Male, age, and ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: 2 siblings (compound heterozygotes for the p.Cys674Arg and p.Ile374Thr mutation)

ParentalGenotype: Mother: (p.Ile374Thr) and Father: (p.Cys674Arg)

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: By immunoblot analysis, it was found that the platelets of the patient and his 2 siblings contained both αIIb and β3, but at reduced levels compared with a healthy control (Figure 1B)

CasePreviousTesting: Direct sequence analysis of the of the genes encoding αIIb were performed on DNA isolated from leukocytes obtained from Patient C and family members.

Gene: ITGA2B

Variant: NM_000419.3:c.1214T>C (p.Ile405Thr) and NM_000419.3:c.2113T>C (p.Cys705Arg)

LegacyVariant: (p.Ile374Thr) and (p.Cys674Arg)

ClinVar: N/A

CAiD: CA290950815 and CA8602816

gnomAD: MAF in the European (non-Finnish) population is 0.000008792 https://gnomad.broadinstitute.org/variant/17-42455140-A-G

Case9: 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: ITGA2B

Variant: NM_000419.3:c.189_236del (c.189-319_236del)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940231

gnomAD: N/A

Case1: Female, elderly (age not specified)

DiseaseAssertion: Glanzmann Thrombasthenia

FamilyInfo: Neither parent of the proband had a history of bleeding and there was no consanguinity, but her brother who is 3 years younger was quickly shown to also have both Glanzmann thrombasthenia and Macrothrombocytopenia. 3 children of Case1 are shown in Figure 1A pedigree.

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0000979, HP:0003010, HP:000042, HP:0000225, HP:0011877

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry confirmed that her platelets expressed <1% αIIbβ3 with GPIb normally present.

CasePreviousTesting: DNA analysis for mutations in ITGA2B and ITGB3 was performed, sequences with potential mutations were highlighted by high resolution melting curve analysis. As a part of an initial testing of this patient's gene panel (not specified which genes), DNA from this patient was submitted to ThromboGenetics in Cambridge UK. While confirming the two ITGB3 mutations described, an additional finding was a heterozygous mutation in TUBB1.

Gene: ITGB3

Variant: NM_000212.2:c.565C>T and NM_000212.2:c.629G>C

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA291224669 and CA400023389, respectively as written in variant section.

gnomAD: Maximum allele frequency for the variant NM_000212.2:c.565C>T: 0.00002638 https://gnomad.broadinstitute.org/variant/17-45362012-C-T

Case#: F7, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: partial loss of high molecular weight multimers, VWF:Ag = 88; VWF:RCo = 46; VWF:GPIbM = 81; 0.52; 0.93; 1.77

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[I1309V];[=]

HGVS: c.3925A>G (p.Ile1309Val)

CAID: CA228492

gnomAD: absent from gnomad v4.1.0

Case#: F6, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: partial loss of high molecular weight multimers, VWF:Ag = 56; VWF:RCo = 29; VWF:GPIbM = 75; 0.51; 1.34; 2.63

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[H1268D];[=]

HGVS: c.3802C>G (p.His1268Asp)

CAID: CA228445

gnomAD: absent from gnomad v4.1.0

Case#: F20, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: loss of high and intermediate MWMs, VWF:Ag = 34; VWF:RCo = 8; VWF:GPIbM = 23; 0.22; 0.68; 3.08

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[V1316M];[=]

HGVS: c.3946G>A (p.Val1316Met)

CAID: CA114127

gnomAD: absent from gnomad v4.1.0

Case#: F5, II:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: all mutimers present, VWF:Ag = 56; VWF:RCo = 48; VWF:GPIbM = 49; 0.86; 0.87; 1.01

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[I1372S];[=]

HGVS: c.4115T>G (p.Ile1372Ser)

CAID: CA228535

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019303-A-C?dataset=gnomad_r4

Case#: F19, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: loss of high and intermediate MWMs, VWF:Ag = 35; VWF:RCo = 5; VWF:GPIbM = 28; 0.14; 0.81; 5.68

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[V1316M];[=]

HGVS: c.3946G>A (p.Val1316Met)

CAID: CA114127

gnomAD: absent from gnomad v4.1.0

Case#: F5, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: all mutimers present, VWF:Ag = 105; VWF:RCo = 90; VWF:GPIbM = 87; 0.86; 0.82; 0.96

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[I1372S];[=]

HGVS: c.4115T>G (p.Ile1372Ser)

CAID: CA228535

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019303-A-C?dataset=gnomad_r4

Case#: F18, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: loss of high and intermediate MWMs, VWF:Ag = 95; VWF:RCo = 30; VWF:GPIbM = 70; 0.32; 0.73; 2.31

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1308C];[=]

HGVS: c.3922C>T (p.Arg1308Cys)

CAID: CA114125

gnomAD: absent from gnomad v4.1.0

Case#: F17, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: loss of high and intermediate MWMs, VWF:Ag = 30; VWF:RCo = 8; VWF:GPIbM = 23; 0.27; 0.75; 2.81

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1308C];[=]

HGVS: c.3922C>T (p.Arg1308Cys)

CAID: CA114125

gnomAD: absent from gnomad v4.1.0

Case#: F16, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: loss of high and intermediate MWMs, VWF:Ag = 48; VWF:RCo = 13; VWF:GPIbM = 48; 0.27; 1.00; 3.65

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1308C];[=]

HGVS: c.3922C>T (p.Arg1308Cys)

CAID: CA114125

gnomAD: absent from gnomad v4.1.0

Case#: F15, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: loss of high and intermediate MWMs, VWF:Ag = 43; VWF:RCo = 12; VWF:GPIbM = 30; 0.28; 0.70; 2.56

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1308C];[=]

HGVS: c.3922C>T (p.Arg1308Cys)

CAID: CA114125

gnomAD: absent from gnomad v4.1.0

Case#: F14, II:2

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: loss of high and intermediate MWMs, VWF:Ag = 12; VWF:RCo = 3; VWF:GPIbM = 9; 0.21; 0.71; 3.31

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[C275R];[P1337L]

HGVS: c.823T>C (p.Cys275Arg), c.4010C>T (p.Pro1337Leu)

CAID: CA228836, CA228510

gnomAD: absent from gnomad, https://gnomad.broadinstitute.org/variant/12-6019408-G-A?dataset=gnomad_r4

Case#: F4, I:3

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: all mutimers present, VWF:Ag = 34; VWF:RCo = 21; VWF:GPIbM = 31; 0.62; 0.92; 1.49

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1308L];[=]

HGVS: c.3923G>T (p.Arg1308Leu)

CAID: CA6402650

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019495-C-A?dataset=gnomad_r4

Case#: F4, I:2

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: all mutimers present, VWF:Ag = 40; VWF:RCo = 25; VWF:GPIbM = 38; 0.63; 0.95; 1.52

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1308L];[=]

HGVS: c.3923G>T (p.Arg1308Leu)

CAID: CA6402650

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019495-C-A?dataset=gnomad_r4

Case#: F3, II:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: all mutimers present, VWF:Ag = 45; VWF:RCo = 38; VWF:GPIbM = 45; 0.84; 1.00; 1.19

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[P1266L];[=]

HGVS: NM_000552.5(VWF):c.3797C>T (p.Pro1266Leu)

CAID: CA114170

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019621-G-A?dataset=gnomad_r4

Case#: F13, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 69; VWF:RCo = 50; VWF:GPIbM = 71; 0.72; 1.04; 1.43

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1341Q];[=]

HGVS: c.4022G>A (p.Arg1341Gln)

CAID: CA114129

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019396-C-T?dataset=gnomad_r4

Case#: F3, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: all mutimers present, VWF:Ag = 60; VWF:RCo = 57; VWF:GPIbM = 59; 0.95; 0.98; 1.03

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[P1266L];[=]

HGVS: NM_000552.5(VWF):c.3797C>T (p.Pro1266Leu)

CAID: CA114170

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019621-G-A?dataset=gnomad_r4

Case#: F2, II:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: all mutimers present, VWF:Ag = 68; VWF:RCo = 66; VWF:GPIbM = 61; 0.97; 0.90; 0.93

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[P1266L];[=]

HGVS: NM_000552.5(VWF):c.3797C>T (p.Pro1266Leu)

CAID: CA114170

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019621-G-A?dataset=gnomad_r4

Case#: F12, II:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 52; VWF:RCo = 18; VWF:GPIbM = 52; 0.34; 1.00; 2.92

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1341Q];[=]

HGVS: c.4022G>A (p.Arg1341Gln)

CAID: CA114129

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019396-C-T?dataset=gnomad_r4

Case#: F2, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: all mutimers present, VWF:Ag = 30; VWF:RCo = 29; VWF:GPIbM = 24; 0.97; 0.81; 0.84

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[P1266L];[=]

HGVS: NM_000552.5(VWF):c.3797C>T (p.Pro1266Leu)

CAID: CA114170

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019621-G-A?dataset=gnomad_r4

Case#: F11, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 35; VWF:RCo = 5; VWF:GPIbM = 27; 0.14; 0.78; 5.44

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F10, II:3

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 53; VWF:RCo = 13; VWF:GPIbM = 37; 0.25; 0.69; 2.82

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F10, II:2

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 40; VWF:RCo = 5; VWF:GPIbM = 16; 0.13; 0.40; 3.20

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F10, III:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 39; VWF:RCo = 12; VWF:GPIbM = 26; 0.31; 0.67; 2.18

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F10, II:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 30; VWF:RCo = 5; VWF:GPIbM = 17; 0.17; 0.57; 3.44

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F10, III:3

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 25; VWF:RCo = 6; VWF:GPIbM = 17; 0.23; 0.67; 2.95

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F10, I:3

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 50; VWF:RCo = 6; VWF:GPIbM = 29; 0.12; 0.58; 4.82

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F10, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 82; VWF:RCo = 27; VWF:GPIbM = 97; 0.33; 1.19; 3.62

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F9, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: complete loss of high MWM, VWF:Ag = 23; VWF:RCo = 7; VWF:GPIbM = 21; 0.29; 0.93; 3.18

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[R1306W];[=]

HGVS: c.3916C>T (p.Arg1306Trp)

CAID: CA114123

gnomAD: absent from gnomad v4.1.0

Case#: F20, II:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: loss of high and intermediate MWMs, VWF:Ag = 45; VWF:RCo = 7; VWF:GPIbM = 43; 0.16; 0.95; 6.11

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[V1316M];[=]

HGVS: c.3946G>A (p.Val1316Met)

CAID: CA114127

gnomAD: absent from gnomad v4.1.0

Case#: F8, I:1

DiseaseAssertion: Type 2 VWD

CaseHPOFreeText: partial loss of high molecular weight multimers, VWF:Ag = 37; VWF:RCo = 21; VWF:GPIbM = 34; 0.57; 0.92; 1.60

CasePreviousTesting: Not clearly described

Gene: VWF

Variant: p.[P1337L];[=]

HGVS: c.4010C>T (p.Pro1337Leu)

CAID: CA228510

gnomAD: https://gnomad.broadinstitute.org/variant/12-6019408-G-A?dataset=gnomad_r4

Case: P3, M/36

DiseaseAssertion: VWD2A

FamilyInfo: Positive family history, no details provided.

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 4, aPTT was 43 seconds, FVIII:C was 22%, VWF:RCo was not determined, and VWF:Ag was 14 IU/dL. The VWF:RCo/VWF:Ag ratio was not available. RIPA showed a loss of intermediate and high molecular weight multimers, VWF multimer analysis was 2, and platelet count was 265 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.3538+1G>A — heterozygous

HGVS: NM_000552.5(VWF):c.3538+1G>A

ClinVar: 100267

CAID: CA228420

gnomAD: absent from gnomad v4.1.0

Case: P7, M/41

DiseaseAssertion: VWD2A

FamilyInfo: Positive family history, no details provided.

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 7, aPTT was 36 seconds, FVIII:C was 36%, VWF:RCo was not determined, and VWF:Ag was 25 IU/dL. The VWF:RCo/VWF:Ag ratio was not applicable. The VWF multimer pattern showed a mild loss of high molecular weight multimers, RIPA was 4 ohms, and the platelet count was 301 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.4789C>T, p.R1597W — heterozygous

HGVS: NM_000552.5(VWF):c.4789C>T (p.Arg1597Trp)

ClinVar: 285

CAID: CA114117

gnomAD: https://gnomad.broadinstitute.org/variant/chr12-6018629-G-A?dataset=gnomad_r4

Case: P1, M/5

DiseaseAssertion: VWD1

FamilyInfo: No

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 0, aPTT was 41 seconds, FVIII:C was 60%, VWF:RCo was 22 IU/dL, and VWF:Ag was 27 IU/dL, resulting in a VWF:RCo/VWF:Ag ratio of 0.8. RIPA was nearly absent, VWF multimer analysis was not tested, and the platelet count was 250 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.6579G>C, p.W2193C — heterozygous

HGVS: NM_000552.5(VWF):c.6579G>C (p.Trp2193Cys)

ClinVar:

CAID: CA383490665

gnomAD: absent from gnomad v4.1.0

Case: P22, F/5

DiseaseAssertion: VWD2A

FamilyInfo: Positive family history, no details provided.

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 3, aPTT was 43 seconds, FVIII:C was 47%, VWF:RCo was 122 IU/dL, and VWF:Ag was 20 IU/dL, with a VWF:RCo/VWF:Ag ratio of 0.1. RIPA was normal, VWF multimer analysis was 2, and platelet count was 270 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.4825G>A, p.G1609R — heterozygous

HGVS: NM_000552.5(VWF):c.4825G>A (p.Gly1609Arg)

ClinVar: 100395

CAID: CA228665

gnomAD: https://gnomad.broadinstitute.org/variant/chr12-6018593-C-T?dataset=gnomad_r4

Case: P21, F/5

DiseaseAssertion: VWD2M

FamilyInfo: Positive family history, no details provided.

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 2, aPTT was 53 seconds, FVIII:C was 30%, and VWF:RCo was 25 IU/dL. The VWF:RCo/VWF:Ag ratio indicated a mild loss of high molecular weight multimers. RIPA was 4, VWF multimer analysis was 301, and platelet count was not specified.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.4121G>T, p.R1374L — heterozygous

HGVS: NM_000552.5(VWF):c.4121G>T (p.Arg1374Leu)

ClinVar: 100331

CAID: CA228543

gnomAD: https://gnomad.broadinstitute.org/variant/chr12-6019297-C-A?dataset=gnomad_r4

Case: P20, F/33

DiseaseAssertion: VWD1

FamilyInfo: No family history

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 4, aPTT was 25 seconds, FVIII:C was 6%, VWF:RCo was 19 IU/dL, and VWF:Ag was 19 IU/dL, with a VWF:RCo/VWF:Ag ratio of 1.0. RIPA was normal, VWF multimer analysis was not tested, and platelet count was 475 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.1135T>G, p.C379G, c.7390C>T, p.R2464C. Compound heterozygous

HGVS: NM_000552.5(VWF):c.1135T>G (p.Cys379Gly), NM_000552.5(VWF):c.7390C>T (p.Arg2464Cys)

ClinVar: 100467

CAID: CA6403534 , CA228786

gnomAD: https://gnomad.broadinstitute.org/variant/chr12-6071318-A-C?dataset=gnomad_r4, https://gnomad.broadinstitute.org/variant/chr12-5976158-G-A?dataset=gnomad_r4

Case: P18, F/39

DiseaseAssertion: VWD1

FamilyInfo: No family history

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 9, aPTT was 40 seconds, FVIII:C was 15%, VWF:RCo was 6 IU/dL, and VWF:Ag was 8 IU/dL, with a VWF:RCo/VWF:Ag ratio of 0.8. The VWF multimer pattern was absent, RIPA was 2 ohms, and the platelet count was 273 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.3943C>T, p.R1315C — heterozygous

HGVS: NM_000552.5(VWF):c.3943C>T (p.Arg1315Cys)

ClinVar: 100310

CAID: CA228502

gnomAD: https://gnomad.broadinstitute.org/variant/chr12-6019475-G-A?dataset=gnomad_r4

Case: P17, F/30

DiseaseAssertion: VWD2A

FamilyInfo: No family history

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 8, aPTT was 42 seconds, FVIII:C was 23%, VWF:RCo was 20 IU/dL, and VWF:Ag was 11 IU/dL, with a VWF:RCo/VWF:Ag ratio of 1.8. The VWF multimer pattern showed a loss of intermediate and high molecular weight multimers, RIPA was not tested, and the platelet count was 276 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.3814T>C, p.C1272R — heterozygous

HGVS: NM_000552.5(VWF):c.3814T>C (p.Cys1272Arg)

ClinVar: 301

CAID: CA114149

gnomAD: absent from gnomad v4.1.0

Case: P15, M/45

DiseaseAssertion: VWD1

FamilyInfo: Positive family history, no details provided.

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 11, aPTT was 59 seconds, FVIII:C was 3%, VWF:RCo was 11 IU/dL, and VWF:Ag was 6 IU/dL, with a VWF:RCo/VWF:Ag ratio of 1.8. The VWF multimer pattern was normal, RIPA was 2 ohms, and the platelet count was 378 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.2574C>G, p.C858W — heterozygous

HGVS: NM_000552.5(VWF):c.2574C>G (p.Cys858Trp)

ClinVar:

CAID: CA232299278

gnomAD: https://gnomad.broadinstitute.org/variant/chr12-6034799-G-C?dataset=gnomad_r4

Case: P11, M/19

DiseaseAssertion: VWD1

FamilyInfo: No family history

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 3, aPTT was 49 seconds, FVIII:C was 29%, VWF:RCo was 42 IU/dL, and VWF:Ag was 58 IU/dL, with a VWF:RCo/VWF:Ag ratio of 0.7. The VWF multimer pattern was normal, RIPA was not tested, and the platelet count was 234 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.2289dupG, p.S764Efs*16 — heterozygous

HGVS: NM_000552.5(VWF):c.2289dup (p.Ser764GlufsTer16)

ClinVar:

CAID: CA2695215960

gnomAD: absent from gnomad v4.1.o

Case: P9, M/26

DiseaseAssertion: VWD1

FamilyInfo: No family history

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 1, aPTT was 44 seconds, FVIII:C was 9%, VWF:RCo was 13 IU/dL, and VWF:Ag was 6 IU/dL, with a VWF:RCo/VWF:Ag ratio of 2.0. The VWF multimer pattern was normal, RIPA was 3 ohms, and the platelet count was 217 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.3614G>A, p.R1205H — heterozygous

HGVS: NM_000552.5(VWF):c.3614G>A (p.Arg1205His)

ClinVar: 308

CAID: CA114160

gnomAD: https://gnomad.broadinstitute.org/variant/chr12-6021960-C-T?dataset=gnomad_r4

Case: P8, M/32

DiseaseAssertion: VWD1

FamilyInfo: Positive family history, no details provided.

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 7, aPTT was 39 seconds, FVIII:C was 10%, VWF:RCo was 14 IU/dL, and VWF:Ag was 13 IU/dL, resulting in a VWF:RCo/VWF:Ag ratio of 1.1. The VWF multimer pattern showed a mild loss of high molecular weight multimers, RIPA was not tested, and the platelet count was 286 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.2665T>C, p.C889R — heterozygous

HGVS: NM_000552.5(VWF):c.2665T>C (p.Cys889Arg)

ClinVar:

CAID: CA383519992

gnomAD: absent from gnomad v4.1.0

Case: P10, M/2

DiseaseAssertion: VWD1

FamilyInfo: No family history

ParentalGenotype: NA

CaseHPOFreeText: The bleeding score was 1, aPTT was 33 seconds, FVIII:C was 96%, VWF:RCo was 30 IU/dL, and VWF:Ag was 36 IU/dL, resulting in a VWF:RCo/VWF:Ag ratio of 0.8. The VWF multimer pattern was normal, RIPA was not tested, and the platelet count was 222 × 10⁹/L.

CasePreviousTesting: NA

GenotypingMethod: Direct sequencing of all exons, flanking intronic sequences, and the promoter of VWF was performed.

Gene: VWF

Variant: c.3835G>A, p.V1279I — heterozygous

HGVS: NM_000552.5(VWF):c.3835G>A (p.Val1279Ile)

ClinVar: 100288

CAID: CA228459

gnomAD: https://gnomad.broadinstitute.org/variant/chr12-6019583-C-T?dataset=gnomad_r4

Case#: Patient 7, Gender N/A, Onset 3-4 months. Death around 1-2 years, Southeast Asian

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: P:0001639. HP:0005165, HP:0001270, HP:0002240

(Dyspnea, Shortened PR interval, Motor delay, Hepatomegaly

CaseHPOFreeText: BVH, Severe MR, SDD, CK 550u/l, EF

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: Creatine Kinase enzyme 550u/l, Ejection fraction 30%, GAA enzyme activity in leukocytes was 0.05% of normal control value.

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

Variant 1: NM_000152.5(GAA):c.1411_1414del (p.Glu471fs)

ClinVar: 188874

CAID: CA274067

gnomAD: Highest population MAF = 0.0002513 in East Asian

Variant 2: NM_000152.5(GAA):c.1933G>C (p.Asp645His)

ClinVar: 189013

CAID: CA274256

gnomAD: Highest population MAF = 0.00005534 (East Asian)

ParentalGenotype: Father was the carrier of variant 1 NM_000152.5(GAA):c.1411_1414del (p.Glu471fs)

mother was carrier of variant 2 NM_000152.5(GAA):c.1933G>C (p.Asp645His)

PreviouslyPublished: N/A

Case#: Patient 5, Gender N/A, Onset at 5-6 months. Death at 1.5 years of age, Southeast Asian

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0002094 HP:0001639. HP:0005165, HP:0001270, HP:0001252, HP:0001714, HP:0002090

(Hypertrophic Cardiomyopathy, Dyspnea, Shortened PR interval, Motor delay, Muscular hypotonia, Ventricular hypertrophy, Pneumonia )

CaseHPOFreeText: Death from heart failure and pneumonia

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: GAA activity in leukocytes was 0% of normal control value.

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

Variant 1: NM_000152.5(GAA):c.1538A>G (p.Asp513Gly)

ClinVar: 638014

CAID: CA401367134

gnomAD: N/A

ParentalGenotype: Both parents carried the .1538A>G (p.Asp513Gly) variant in the GAA gene. There was no parental consanguinity

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:

Case1: Female, 1 year old, Japanese

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000979, HP:0000421

(Purpura, epistaxis)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: The absence of platelet GPIIb-IIIa complexes was con-firmed by flow cytometric and immunoblotting analyses. Figure 1 shows the flow cytometric analysis of the platelets

PlateletAggregation: Absence of platelet aggregation in response to ADP, epinephrine, and collagen but the presence of a normal response to ristocetin

CasePreviousTesting: Genomic DNA was extracted by a standard protocol from the peripheral blood mononuclear cells of the patient and her parents. The flanking region of exon 25 of the GPIIb gene including the introns was amplified by PCR from the genomic DNA.

Gene: ITGA2B

Variant: NM_000419.3:c.2449-1G>C

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399795582

gnomAD: N/A

Case4: Male, 4 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 decreased expression at a level of 7.5%(type II GT)

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

CasePreviousTesting: Polymerase chain reaction for all exons of ITGA2Band/orITGB3were performed using primers. Sequence analysis was performed with reference to M_000419.3 andNP_000410.2 for ITGA2B and NM_000212.2 and NP_000203.2 for ITGB3.

Gene: ITGA2B

Variant: NM_000419.3:c.2333A>C (p.Gln778Pro) and NM_000419.3:c.1750C>T (p.Arg584Ter)

LegacyVariant: N/A

ClinVar: 225393 and 2892

CAiD: CA290947544 and CA115834

gnomAD: MAF in the East Asian population is 0.0001087 http://gnomad.broadinstitute.org/variant/17-42453691-T-G and MAF in the East Asian population is 0.0002176 http://gnomad.broadinstitute.org/variant/17-42457372-G-A

Case1: Female, 18 years old, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry showed mutated CD41 protein and lack of CD61 surface expression

PlateletAggregation: Platlets were stimulated by ADP and thromboxane A2 and stained with PAC-1, which specifically detects only the activated conformation of αIIbβ3. GT platelets from both sources showed diminished PAC-1 binding after both agonist treatments compared to corresponding CTR cells

CasePreviousTesting: PCR primers used for sequencing of exons containing mutations in ITGA2B gene

Gene: ITGA2B

Variant: NM_000419.3:c.1922C>T (p.Pro641Leu) and NM_000419.3:c.2478dup (p.Gly827Trp)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399801154 and CA915940290

gnomAD: N/A

Case1: Patient ET, gender, age, and ethnicity is not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: "However, ET platelets exhibited a normal surface expression of a-granule thrombospondin" this is all of the information we are given in this article; however Reference 13 might mention more on the protein expression. However, access is not available for article 13 at this time.

PlateletAggregation: ET's platelets fail to aggregate in response to stimuli (the article does not state which agonists/stimuli and does not mention response to ristocetin)

CasePreviousTesting: Two regions of ITGB3 were selected for amplification and sequence analysis. The first region, corresponding to exonIII encodes a fragment from D96 to D179 and the second region corresponding to exon IV, encodes a fragment from M180 to D233.

Gene: ITGB3

Variant: (NM_000212.2:c.719G>A (p.Arg240Gln)

LegacyVariant: (p.Arg214Gln)

ClinVar: 13553

CAiD: CA123224

gnomAD: N/A

PreviouslyPublished: Patient ET may have been previously published in PMID: 2512684; however, access is not available to this article

Case#: 2 (16 y, male - brother of Case 1, symptom onset/pain+movement limitation 8 y, diagnosis 16y)

DiseaseAssertion: Scheie syndrome

FamilyInfo: Male patient born to consanguineous parents

CasePresentingHPOs: 0034337

CaseHPOFreeText: claw hands with flexion contractures; electroneurology showed bilateral signs of mild 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: 0.64 (umol/g/h)

CaseUrineGAGs:

CaseERT: Yes, after diagnosis at 16y CaseBMT:

Variant1:c.1189+4A>T

Variant1ClinVarID:

Variant1CAID: CA2586965965

Variant2: 1189+4A>T

Variant2ClinVarID:

Variant2CAID: CA2586965965

AdditionalVariants:

ParentalGenotype:

PreviouslyPublished

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#: Variant not associated with a proband. Variant listed in supplementary materials in Supplementary Table 4

DiseaseAssertion: Mucopolysaccharidosis type I, MPS I

FamilyInfo: N/A

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: G84R

Variant1ClinVarID:

Variant1CAID: CA355946488

Variant2: N/A

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Variant not associated with a proband. Variant listed in supplementary materials in Supplementary Table 4

DiseaseAssertion: Mucopolysaccharidosis type I, MPS I

FamilyInfo: N/A

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: F188L

Variant1ClinVarID:

Variant1CAID: CA355961777

Variant2: N/A

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Patient 5 (see Table 2), 37 weeks, 5 days (Gestational age)

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: Inguinal hernia (HP:0000023)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 0.26 nmol x mg-1 × hr-1

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.1205G>A (p.W402X)

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.46_57del (p.Ser16_Ala19del) (c.134del12)

Variant2ClinVarID: 92643

Variant2CAID: CA220509

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished c.134del12 is based on old numbering. The variant is referred to as "134del12" in older papers. The correct name is: NM_000203.5(IDUA):c.46_57del (p.Ser16_Ala19del)

Case#: Patient 19 (see Table 2), 38 weeks (Gestational age)

DiseaseAssertion: MPS1-H/S

FamilyInfo: Sibling of Patient 20 (see Table 2)

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: Inguinal hernia (HP:0000023)

CaseNotHPOFreeText: Upper respiratory tract involvement

CaseEnzymeAssay: 0.92 nmol x mg-1 × hr-1

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.1205G>A (p.W402X)

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.1044C>A (p.N348K)

Variant2ClinVarID: N/A

Variant2CAID: CA:355963142

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case: IP #37 ((also in row 17 table 6)

DiseaseAssertion: type 2A (IIA) VWD

FamilyInfo:

ParentalGenotype(s):

CasePresentingHPOs: HP:0032440 - blood group B

CaseHPOFreeRext: VWF:Ag [IU/dL] = 22; VWF:Ac [IU/dL] = 14; FVIII:C [IU/dL] = 27

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting:

GenotypingMethod: Sequence variations in the VWF were identified through direct sequencing, while the detection of large rearrangements utilized the multiplex ligation-dependent probe amplification (MLPA) technique or assessed copy number variations (CNVs). Sanger sequencing methodology was applied for VWF analysis in patients investigated prior to 2016 (approximately 14% of IPs), whereas next-generation sequencing (NGS) was employed for the analysis of VWF in patients inspected from 2017 onwards (about 86% of IPs). In both strategies, the entire VWF, encompassing all 52 exons, intron/exon boundaries, and promoter regions, was analyzed.

PreviouslyPublished:

Gene: VWF

Variant: c.4541T>C p.Phe1514Ser

HGVS:

ClinVarID: not found

CAID: CA383501434

gnomAD: absent

Case2: Patient M2, Female, French Gypsy, age is not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: See Figure 2 for pedigree

ParentalGenotype: Unaffected parents see pedigree Fig 2

CasePresentingHPOs: N/A

CaseHPOFreeText: France, GT is particularly frequent in the Gypsy population, mainly represented by the Manouche tribe. Their clinical phenotype is the same as for classic type I disease, with a moderate and occasional severe bleeding syndrome

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry analysis has shown that these patients' surface expresses <5% of normal GPIIIa and GPIIb levels (we are not given an exact value for each proband)

PlateletAggregation: "Absent platelet aggregation" this is all the information we are given for platelet aggregation

CasePreviousTesting: N/A

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: 2895

CAiD: CA10575473

gnomAD: N/A

Case1: Female, 5 years old, Swiss (from Morocco)

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Affected brother

ParentalGenotype: Mother and father are heterozygous for the variant of interest

CasePresentingHPOs: HP:0001250, HP:0001270, HP:0000967, HP:0001892

(Seizures, retarded motor development, petechia, hemorrhagic diathesis)

CaseHPOFreeText: Subepndymal hematomas, cortical tubera, hydrocephalus internus

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry protein expression results can be seen in Figure 1

PlateletAggregation: Platelets failed to aggregate with ADP, collagen, or arachidonic acid; however, ristocetin induced platelet agglutination was normal

CasePreviousTesting: Amplified DNA fragments containing exon 11 of the GPIIIa gene were purified by PCR preps DNA purification resin and wizard.

Gene: ITGB3

Variant: NM_000212.2:c.1702T>C (p.Cys568Arg)

LegacyVariant: (p.Cys542Arg)

ClinVar: N/A

CAiD: CA400032350

gnomAD: N/A

Case1: Patient 1, Male, 6 years old

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Affected brother is Patient 2

ParentalGenotype: Mother and father revealed heterozygosity for c.1878G>C mutation. (Parents are consanguineous)

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

(Petechiae, epistaxis, gingival bleeding)

CaseHPOFreeText: Hematomas,

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry analysis showed that there was no surface expression of GPIIb/IIIa detectable on patient 1's platelets, indicating a lack of platelet GPIIb/IIIa expression

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 normal range for patient 1

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.1878G>C (p.Gln626His)

LegacyVariant: N/A

ClinVar: 2903

CAiD: CA115852

gnomAD: N/A

Case14: Patient ID N, Male, 7 years old, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000967, HP:0000979, HP:0000978, HP:0004406, HP:0000225

(Petechiae, purpura, easy bruising, recurrent epistaxis, gingival bleeding)

CaseHPOFreeText: Hemorrhage after dental, hemorrhage after trauma

CaseNotHPOs: HP:0002239, HP:0002239, HP:0000790, HP:0005261, HP:0002248

(GI bleeding, intracranial hemorrhage, hematuria, hemarthrosis, hematemesis)

CaseNotHPOsFreeText: Ear bleeding

ProteinExpression: N/A

PlateletAggregation: Defective response to ADP, adrenaline, collagen, arachidonic acid, and normal response to ristocetin

CasePreviousTesting: Exon PCR was used to amplify coding regions of the ITGA2B and ITGB3 genes. PCR products were purified and Sanger sequenced. Segregation using parental samples was undertaken when available

Gene: ITGB3

Variant: NM_000212.2:c.774T>A (p.Cys258Ter)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA400023704

gnomAD: N/A

Case#: Patient B, Male, Age 30, Chinese

Disease Assertion: VWD3

FamilyInfo: Consanguineous marriage between parents. Parents had 2 daughters and a son. One daughter died (1 year old) due to bleeding disorder. Mother's VWF:Ag 58% and VWF:RCo 36%. Family pedigree in Figure 2 (a). Both parents were heterozygous carriers of the variant.

Parental Genotype: Both Heterozygous

CasePresentingHPOs: HP:0003645

(Prolonged partial thromboplastin time)

CaseHPOFreeText: Hematoma in the lower extremity, VWF:Ag: 0.5%, VWF:RCo: 0.1%, FVIII:C 1.2%, APTT: 72.0 s

CaseNotHPOs:

CaseNotHPOFreeText: PT: 13.6 s, TT: 14.9s

Protein Expression: N/A

CasePreviousTesting: NGS targeting all exons and covered F8, F9, and VWF genes; and Sanger Sequencing

Gene: VWF

Variant: NM_000552.4:c.6450C>A

ClinVar: N/A

CAID: CA383491381 CAID

gnomAD:N/A

FamilyE

DiseaseAssertion: Left ventricular noncompaction (LVNC)

FamilyInfo: Presenting LVNC, Identified rare, protein changing mutations in MYH7, none of which have been previously reported but all of which were predicted to be pathogenic with multiple in silico prediction algorithms

GenotypingMethod: Whole exome sequencing analysis

Variant: NM_000257.4:c.2099A>G

ClinVar: not found

CAID: CA389049130

gnomAD: not found

Case1: 44 year old male

DiseaseAssertion: Dilated cardiomyopathy

FamilyInfo: Affected brother, two sisters and both parents unaffected, parents denied consanguinity and were assumed to be second cousins

CasePresentingHPOs: HP:0003704, HP:0009060, HP:0000218, HP:0000276, HP:0000819, HP:0003691

"Scapuloperoneal weakness, scapular muscle atrophy, high palate, long face, Diabetes mellitus, Scapular winging

CaseHPOFreeText: decreased cardiac systolic function, clinical symptoms of cardiac failure at 44 years old, left ventricular systolic and diastolic dysfunction, exertional dyspnoea, ymmetrical wasting of the sternocleidomastoideus, trapezius, supraspinatus, pectoralis, deltoid, triceps, biceps, paravertebral and tibialis muscles at age 56

CasePreviousTesting:

GenotypingMethod: genome scan using 730,000 single nucleotide polymorphism (SNP) markers. Sequence analysis for the last four MYH7 exons

Variant: NM_000257.4:c.5458C>T

ClinVar: 181282

CAID: CA016126

gnomAD: https://gnomad.broadinstitute.org/variant/14-23884305-G-A

0.00008011 African

Case#: Patient 4

DiseaseAssertion: Pompe Disease

FamilyInfo: None given

CasePresentingHPOs: None

CaseHPOFreeText: None

CaseNotHPOs: None

CaseNotHPOFreeText: None

CasePreviousTesting: Single gene sequencing with Ion Torrent Persional Genome Machine

Glucosidase activity: 0.0 nmol 5MU/hr/mL

Variant 1: NM_000152.5:c.596A>G

Variant 1 ClinVarID: 92486

Variant 1 CAid: CA145785

Variant 2: NM_000152.5:c.668G>A

Variant 2 ClinVarID: 92488

Variant 2 CAid: CA145791

ParentalGenotype: Not provided

Case#: Patient 2

DiseaseAssertion: Pompe Disease

FamilyInfo: None given

CasePresentingHPOs: None

CaseHPOFreeText: None

CaseNotHPOs: None

CaseNotHPOFreeText: None

CasePreviousTesting: Single gene sequencing with Ion Torrent Persional Genome Machine

Glucosidase activity: 0.0 nmol 5MU/hr/mL

Variant 1: NM_000152.5:c.596A>G

Variant 1 ClinVarID: 92486

Variant 1 CAid: CA145785

Variant 2: NM_000152.5:c.668G>A

Variant 2 ClinVarID: 92488

Variant 2 CAid: CA145791

ParentalGenotype: Not provided

PMID 16322474

Notes Recombinant full length p.Ile1628Thr expressed in HEK293 and purified from growth media was NOT digested by recombinant ADAMTS13 in non-denaturing conditions (Table 1, Fig 5a). However, the the A1-A3 p.Ile1628Thr truncations were digested by ADAMTS13 in non-denaturing conditions while WT recombinant VWF truncations were not (Fig 6).

Variant(1) NM_000257.4:c.1357C>T

ClinVar: 14089

CAID: CA010630

Variant(2) NM_000257.4:c.2146G>A

ClinVar: 14105

CAID: CA011770

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

PMID: 39421326 (PMCID: PMC11675205)

Gene: ABCA4

HGNC ID: 34

Case#: Patient 24 (male)

DiseaseAssertion: STGD (Stargardt disease)

FamilyInfo: Caucasian family from Germany. Patient has two siblings carrying the variant but they are not clinically affected according to pedigree information.

CasePresentingHPOs: Decreased central visual acuity (HP:0000545) Macular atrophy (HP:0007754) Retinal flecks (HP:0030638) Abnormal fundus autofluorescence (HP:0030647) Macular degeneration (HP:0007754) Abnormal electroretinogram (HP:0000763)

CaseHPOFreeText: Male patient diagnosed before age 50 with Stargardt disease. Best corrected visual acuity (BCVA) approximately 0.05–0.2. Fundus imaging shows paracentral scotoma, macular atrophy, and hyperfluorescent flecks with sparing of the fovea. Autofluorescence demonstrates hyperreflective spots and patchy lesions with parafoveal involvement.

CaseNotHPOs: None explicitly reported.

CaseNotHPOFreeText: Pattern-like distribution of lesions noted on clinical examination.

Genotyping Method: Whole-exome sequencing (WES) with an in-house RD-associated gene panel including 619 candidate and disease-associated genes.

PreviouslyPublished: No (novel complex deep-intronic allele described in this study).

Variant: c.[1555-5882C>A;1555-5784C>G]

ClinVar: Not reported in ClinVar in the provided information.

CAID: CA272741; CA227172

SupplementalData: Segregation data and functional splicing analysis available in the supplemental data (Table S1, Figure S1) of the article.

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

DiseaseAssertion: Stargardt disease (STGD1), early onset

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

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

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

CaseNotHPOs: HP:0007707

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

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

PreviouslyPublished: n/a

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

ClinVar: n/a

CAID: CA2837995439, CA227097

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

Case#: N/A

DiseaseAssertion: inherited arrhythmia syndromes, including Brugada syndrome, progressive cardiac conduction disease, and congenital sick sinus syndrome.

FamilyInfo: N/A

ParentalTesting: N/A

CasePresentingHPOs: HP:0011704, HP:0011675

CaseHPOFreeText: H558R may be over-represented among patients with Brugada syndrome in the Chinese Han population, S524Y, has been described in individuals of African ancestry.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: The antiarrhythmic drug mexiletine may have a therapeutic modulation of loss-of-function sodium channel defects; The antiarrhythmic drug mexiletine increased the expression level of both S524Y and H558R in Q1077 back to WT levels as demonstrated by current measurements and channel cell surface expression.

Genotyping Method: N/A

FunctionalAnalysis: N/A

Variant: SCN5A c.1571C>A (p.Ser524Tyr), SCN5A c.1673A>G (p.His558Arg)

ClinVar: 48286, 48289

CAID: CA014995, CA015145

gnomAD: p.Ser524Tyr - max AF: 0.03661 African American populations (https://gnomad.broadinstitute.org/variant/3-38604031-G-T?dataset=gnomad_r4), p.His558Arg - max AF: 0.3392 Amish populations (https://gnomad.broadinstitute.org/variant/3-38603929-T-C?dataset=gnomad_r4)

Case: 16 years diagnosis, Chinese

DiseaseAssertion: Charcot-Marie-Tooth disease

FamilyInfo: Mother（mild Pes Cavus）; Brother（Amyotrophy, Pes Cavus and so forth）

CasePresentingHPOs: HP:0001761, HP:0033526, HP:0001265

GenotypingMethod: Genomic DNA was extracted from the peripheral blood of the family members of a pedigree with autosomal dominant CMT disease, and 65 candidate genes of the proband were screened using target exon capture and the next generation sequencing, and the suspicious genes were verified using Sanger sequencing.

Variant: NM_018972.4:c.371A>G (p.Tyr124Cys)

CAID: CA371548535

gnomAD: NOT in gnomAD

n/a couldnt find

Case: patient is named case #2, male

Disease Assertion: UCD/OTCD

Family Info:

Case Presenting HPOs: Hyperammonemia (HP:0001987), oriticaciduria (HP:0003218), low plasma citrulline (HP:0003572), neonatal onset(HP:0003623), Hyperglutaminemia (HP:0003217)

Case HPO FreeText:

Case NOT HPOs:

Case NOT HPO Free Text:

Case Previous Testing: GDNA was isolated from lymphocytes. To examine the small mutations in the coding region of the OTC gene, all 10 exons and their flanking intron regions were amplified using PCR, and the nucleotide sequences of the amplified products were determined. To determine the intron 5 sequence of case 2, PCR was performed using primers OTCex5F and OTCint5R, and primers OTCint5F and OTCex6R (Table 1, Fig. 3). The amplified products were subcloned into the pT7 vector and the inserted DNA was sequenced using an automated DNA sequencer. Allopurinol test

Supplemental Data: TABLE 1, Notes:

Variant: NM_000531.6: c.540+265G>A

ClinVarID: NA

CAID: CA658658977

gnomAD:

Gene Name: OTC (ornithine transcarbamylase)

Case: Patient #8, Female, Spanish

DiseaseAssertion: UCD/OTCD

FamilyInfo: Family history of disease

CasePresentingHPOs: Hyperammonemia (HP:0001987), Hyperglutaminemia (HP:0003217), Low plasma citrulline (HP:0003572), Oroticaciduria (HP:0003218), Childhood onset (HP:0011463)

CaseHPOFreeText:

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: Patients referred for mutational study because of enzymatically proven and/or laboratory proven OTC deficiency; genomic DNA extracted using commercial kit; amplified through PCR; SSCP analysis; sequenced using ABI Prism 3100 automated sequencer

SupplementalData: Table 1

Variant: NM_000531.6: c.391_397dup (p.Ser133Ilefs*3)

ClinVarID: 597358

CAID: CA913190354

gnomAD:

Case: Patient Proband SS, Female, Caucasian

DiseaseAssertion: UCD/OTCD

FamilyInfo: De novo inheritance, no family history of disease

CasePresentingHPOs: Hyperammonemia (HP:0001987), oroticaciduria (HP:0003218), Childhood onset (HP:0011463)

CaseHPOFreeText:

CaseNOTHPOs: Positive allopurinol test

CaseNOTHPOFreeText:

CasePreviousTesting: Genomic DNA isolated from peripheral blood leukocytes or cultured skin fibroblasts. Amplification by PCR used. SSCP analysis performed. Sequencing of both free and immobilized single strands carried out by dideoxy chain termination method.

SupplementalData: Table 1: Mutations in the Ornithine Transcarbamylase Gene of 17 Females

Variant: NM_000531.6:c.77+1G>A

ClinVarID: 97313

CAID: CA224773

gnomAD:

Case: Female Patient #1, Female, Japanese

DiseaseAssertion: UCD/OTCD

FamilyInfo: N/A

CasePresentingHPOs: Childhood onset (HP:0011463)

CaseHPOFreeText: Onset at 2 years

CaseNOTHPOs:

CaseNOTHPOFreeText: 16% OTC activity

CasePreviousTesting:

Variant: NM_000531.5:c.67C>T (p.Arg23*)

ClinVarID: 97292

CAID: CA224742

gnomAD:

Case: Patient #38, Female, Chinese

DiseaseAssertion: UCD/OTCD

FamilyInfo: No family history of disease, mutation is inherited

CasePresentingHPOs: Hyperammonemia (HP:0001987), oroticaciduria (HP:0003218), vomiting (HP:0002013), coma (HP:0001259), lethargy (HP:0001254), seizures (HP:0001250), childhood onset (HP:0011463)

CaseHPOFreeText: Elevated plasma ammonia at 190 umol/L (Normal: 9-30 umol/L), Elevated urinary orotate at 202 mmol/mmol creatinine (Normal: 0-1.5 mmol/mmol creatinine)

CaseNOTHPOs:

CaseNOTHPOFreeText: Normal plasma glutamine at 13.5 umol/L (Normal: 6-30 umol/L), Normal plasma citrulline at 15.75 umol/L (Normal: 7-35 umol/L)

CasePreviousTesting: gDNA extracted from peripheral blood leukocytes. PCR all coding exons and exon–intron boundaries of the OTC gene using 9 pairs of synthetic oligonucleotide primers, and the primer sequences and annealing temperature. PCR products were then purified and bidirectionally sequenced. The library was sequenced using Illumina HiSeq4000 and generated 150 bp paired-end reads. Data analysis was performed as previously described [Sun Y, Hu G, Liu H, Zhang X, Huang Z, Yan H, et al. Further delineation of the phenotype of truncating KMT2A mutations: the extended Wiedemann–Steiner syndrome. Am J Med Genet A. 2017;173:510–4.]. Multiplex ligation-dependent probe amplification analysis was performed for samples in which Sanger sequencing or WES failed to detect any disease-causing mutation.

Variant: NM_000531.6:c.67C>T (p.Arg23*)

ClinVarID: 97292

CAID: CA224742

gnomAD:

Case: Patient #4, Female, Caucasian

DiseaseAssertion: UCD/OTCD

FamilyInfo: N/A

CasePresentingHPOs: Hyperammonemia (HP:0001987),

CaseHPOFreeText: Elevated plasma ammonia concentration at 123 uM/L

CaseNOTHPOs:

CaseNOTHPOFreeText: Anxiety, plasma citrulline at 2 uM/L

CasePreviousTesting: N/A

Variant: NM_000531.5:c.67C>T (p.Arg23*)

ClinVarID: 97292

CAID: CA224742

gnomAD:

Case: Patient #16, Male

DiseaseAssertion: UCD/OTCD

FamilyInfo: N/A

CasePresentingHPOs: Neonatal onset (HP:0003623), Hyperammonemia (HP:0001987)

CaseHPOFreeText:

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: N/A

Variant: NM_000531.6: c.77+2dupT

ClinVarID: 567293

CAID: CA891844248

gnomAD:

Case: Patient #50, Male

DiseaseAssertion: UCD/OTCD

FamilyInfo: N/A

CasePresentingHPOs: Neonatal onset (HP:0003623), Hyperammonemia (HP:0001987)

CaseHPOFreeText:

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: N/A

Variant: NM_000531.6: c.174G>A (p.Trp58*)

ClinVarID: 97127

CAID: CA224490

gnomAD:

Case: Patient #85, Male

DiseaseAssertion: UCD/OTCD

FamilyInfo: N/A

CasePresentingHPOs:

CaseHPOFreeText:

CaseNOTHPOs: Late Onset

CaseNOTHPOFreeText: Milder phenotype

CasePreviousTesting: N/A

Variant: NM_000531.6: c.298+1G>T

ClinVarID: 97160

CAID: CA224544

gnomAD:

Case: Patient #7, Female

DiseaseAssertion: UCD/OTCD

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText:

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: N/A

Variant: NM_000531.6: c.29_32del (p.Asn10fs)

ClinVarID: 97157

CAID: CA224540

gnomAD:

Gene Name: OTC (ornithine transcarbamylase)

Case: Patient #15, Female

DiseaseAssertion: UCD/OTCD

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText:

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting:

Variant: NM_000531.6: c.77+1G>A

ClinVarID: 97313

CAID: CA224773

gnomAD:

Case: patient #10, Male, Argentine

Disease Assertion: UCD/OTCD

Family Info: family history of the disease,

Case Presenting HPOs: Neonatal onset(HP:0003623), Hyperammonemia HP:0001987

Case HPO FreeText:

Case NOT HPOs:

Case NOT HPO Free Text:

Case Previous Testing: The OTC gene mutations were identified using PCR amplification, classical sequencing (Sanger), and multiplex ligation-dependent probe amplification.10,11 Mutations were identified by comparison with the GenBank reference sequence for human OTC (GenBank entries: NG_008471.1, NP 000522.3, NM 000531.5, NC 000023.11) Missense mutations were analyzed using different computational algorithms: CLUSTALW2 (http://www.clustal.org/clustal2/), SIFT (http://blocks.fhcrc.org/sift/SIFT.html),Polyphen2(http://genetics.bwh.harvard.edu/pph/),PoPMuSiC(http://babylone.ulb.ac.be/popmusic/), and SIFT Indel(http://siftdna.org/www/SIFT_indels2.html).

Supplemental Data: Table 1 Notes: died at 6 months and had 2 brothers that died a neonatal stage

Variant: NM_000531.6: c.540+1G>A

ClinVarID: 1458773

CAID: CA412724226

gnomAD: X-38381340-A-T

Gene Name: OTC (ornithine transcarbamylase)

Case: patient#5 , female, Italian

Disease Assertion: UCD/OTCD

Family Info:

Case Presenting HPOs: irritability(HP:0000737), lethargy(HP:0001254), vomiting(HP:0002013), Oriticaciduria (HP:0003218), low plasma citrulline (HP:0003572), Elevated circulating alanine aminotransferase concentration(HP:0031964), Elevated circulating aspartate aminotransferase concentration (HP:0031956), childhood onset (HP:0011463)

Case HPO FreeText:

Case NOT HPOs:

Case NOT HPO Free Text:

Case Previous Testing: Total RNA was isolated from peripheral blood lymphocytes or lymphoblastoid cell lines and from frozen liver biopsy as described in Chomczynski and Sacchi (1987). For each patient two cDNA syntheses were performed: 10mg of total RNA with 800-1000 ng of oligo dT or 500ng of specific primer NR, mapping in the 3’UTR of OTC cDNA Identification of genetic lesions by amplification of the OTC mRNA, expressed in the liver tissue and intestine, from a non-specific tissue like PBL or lymphoblastoid cell lines. Some mutations, particularly those affecting splicing sites, may have a different expression in liver and PBL . In females, including manifesting carriers, this method allows the identification of deletions and gene rearrangements with certainty, but mutations, decreasing mRNA stability, are unlikely to be detected because the normal allele will constitute the majority of the RNA available for RT-PCR and will be preferentially amplified.

Supplemental Data: Case report section Notes: Hepatomegaly. This mutation, previously reported (Reish et al., 1993), has been correlated with a lethal disease form in a male patient, therefore the mild phenotype in our patient could be explained by a not completely unfavorable X-lyonization

Variant: NM_000531.6: c.928G>T(p.Glu310*)

ClinVarID: 97361

CAID: CA224838

gnomAD:

Gene Name: OTC (ornithine transcarbamylase)