PreviouslyPublished: PMID: 8471765

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

Case17: Patient MO (patient found in the GT database as well) gender and age are not specified here

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0000132 (Bruising, menorrhagia)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

PlateletAggregation: N/A

CasePreviousTesting: N/A

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: 2892

CAiD: CA115834

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

PreviouslyPublished: Reference numbers 29 and 30 in this article

Case10: Patient LeM (found in the GT database) gender and age are not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000979, HP:0000967 (Purpura/petechiae)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: <5% of normal expression

PlateletAggregation: N/A

CasePreviousTesting: N/A

Gene: ITGA2B

Variant: NM_000419.3:c.1366_1371del

LegacyVariant: N/A

ClinVar: 2898

CAiD: CA8603160

gnomAD: MAF in the European (non-Finnish) population is 0.000008791 https://gnomad.broadinstitute.org/variant/17-42458268-TGTCTAC-T

PreviouslyPublished: Reference number 21 in this article

Case20: Patient CG (Found in GT database) also gender and age are not specified for this patient

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: Gingival bleeding and menorrhagia HP:0000225, HP:0000132

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: About 5% of normal GPIIIa and GPIIb surface expression

PlateletAggregation: N/A

CasePreviousTesting: N/A

Gene: ITGA2B

Variant: NM_000419.3:c.1787T>C and M_000419.3:c.3060+2T>C

LegacyVariant: N/A

ClinVar: 2900

CAiD: CA115846 and CA290944108

gnomAD: MAF in the European (non-Finnish) population is 0.0001325 https://gnomad.broadinstitute.org/variant/17-42457148-A-G and MAF in the European (non-Finnish) population is 0.00003876 https://gnomad.broadinstitute.org/variant/17-42451720-A-G

PreviouslyPublished: References 34 and 35 in this article

Case4: Patient LW (found in GT database)

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

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

(Bruising, Epistaxis, Prolonged bleeding after tooth extraction)

CaseHPOFreeText: Blood transfusions were needed

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: 12% of normal GPIIIa and GPIIb surface expression

PlateletAggregation: N/A

CasePreviousTesting: N/A

Gene: ITGA2B

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

LegacyVariant: (p.Leu183Pro)

ClinVar: 2901

CAiD: CA115848

gnomAD: N/A

PreviouslyPublished: References 14 and 15

Supplementary Table S1:

Case17: GT20, French, gender and age not specified

DiseaseAssertion: Glanzmann thrombasthenia type I

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: All patients had a life-long history of mucocutaneous bleeding

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: All patients in this study met the clinical and platelet function requirements for GT-- this includes an absent or strongly reduced expression of alphaIIbBeta3 in platelets

PlateletAggregation: All patients in this study met the clinical and platelet function requirements for GT-- this includes absent or severely reduced platelet aggregation with at least three physiological agonists

CasePreviousTesting: Sanger sequencing was performed. Sanger sequencing ensured coverage of all exons and splice sties of the ITGA2B and ITGB3 genes and extended 300-500 bp into the introns as well as including the UTR. They sequenced 416 bp upstream of the ITGA2B promoter and 463 bp upstream of the ITGB3 promoter. In total they sequenced 51.2% of the ITGA2B gene and 19.4% of the larger ITGB3 gene

Gene: ITGA2B

Variant: M_000419.3:c.2800G>T (p.Val934Phe)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA290946484

gnomAD: N/A

Supplementary Table S1:

Case39: GT45, French, age and gender not specified

DiseaseAssertion: Glanzmann thrombasthenia type I

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: All patients had a life-long history of mucocutaneous bleeding

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: All patients in this study met the clinical and platelet function requirements for GT-- this includes an absent or strongly reduced expression of alphaIIbBeta3 in platelets

PlateletAggregation: All patients in this study met the clinical and platelet function requirements for GT-- this includes absent or severely reduced platelet aggregation with at least three physiological agonists

CasePreviousTesting: Sanger sequencing was performed. Sanger sequencing ensured coverage of all exons and splice sties of the ITGA2B and ITGB3 genes and extended 300-500 bp into the introns as well as including the UTR. They sequenced 416 bp upstream of the ITGA2B promoter and 463 bp upstream of the ITGB3 promoter. In total they sequenced 51.2% of the ITGA2B gene and 19.4% of the larger ITGB3 gene

Gene: ITGA2B

Variant: NM_000419.3:c.551_626del (p.Arg184_Gln208del) and the other variant is noted as "LR deletion" and that is all the information we are given so I will note it as an Unknown Variant

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940373

gnomAD: N/A

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

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Proband GT49-GT52 are related

ParentalGenotype: N/A

CasePresentingHPOs: N/A

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

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

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

PlateletAggregation: Minimal information (See Supplementary Table 3)

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

Gene: ITGB3

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

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8623443

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

Case11: (GT-13) Male, carrier, age or ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Probands GT11 -GT14 are related to GT-13 see Table 1

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

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding severity: Not available (See Supplementary Table 3)

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

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

PlateletAggregation: Minimal information (See Supplementary Table 3)

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

Gene: ITGB3

Variant: NM_000212.2:c.727G>C (p.Asp243His)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA400023600

gnomAD: N/A

Case3: Male, 40 years old, Indian

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000421, HP:0002239, HP:0002248

(Epistaxis, GI bleeding, hematemesis)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: Diagnosis of GT was made on the basis of quantitive determination of receptor count by flow cytometric analysis of GPIIb-IIIa

PlateletAggregation: Diagnosis of GT was made on the basis of impaired platelet aggregation (platelet aggregation was tested against ristocetin, ADP, collagen, epinephrine and arachidonic acid)

CasePreviousTesting: Multiplex PCR by using GPIIb primers and CSGE analysis were performed

Gene: ITGA2B

Variant: NM_000419.3:c.310+1G>A (IVS2(+1)G>A)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8603502

gnomAD: MAF in the European (non-Finnish) population is 0.00001771 https://gnomad.broadinstitute.org/variant/17-42463377-C-T

Case2: Male, 3 years old, Indian

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0030137 (Prolonged bleeding following circumcision)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: Diagnosis of GT was made on the basis of quantitive determination of receptor count by flow cytometric analysis of GPIIb-IIIa

PlateletAggregation: Diagnosis of GT was made on the basis of impaired platelet aggregation (platelet aggregation was tested against ristocetin, ADP, collagen, epinephrine and arachidonic acid)

CasePreviousTesting: Multiplex PCR by using GPIIb primers and CSGE analysis were performed

Gene: ITGA2B

Variant: NM_000419.3:c.1652G>A (p.Arg551Gln)

LegacyVariant: (p.Arg520Gln)

ClinVar: N/A

CAiD: CA8602986

gnomAD: MAF in the South Asian population is 0.00006536 https://gnomad.broadinstitute.org/variant/17-42457470-C-T

Case10: Female, 7 years old, Indian

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000421, HP:0000790 (Epistaxis, hematuria)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: Diagnosis of GT was made on the basis of quantitive determination of receptor count by flow cytometric analysis of GPIIb-IIIa

PlateletAggregation: Diagnosis of GT was made on the basis of impaired platelet aggregation (platelet aggregation was tested against ristocetin, ADP, collagen, epinephrine and arachidonic acid)

CasePreviousTesting: Multiplex PCR by using GPIIb primers and CSGE analysis were performed

Gene: ITGA2B

Variant: NM_000419.3:c.2415del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940581

gnomAD: N/A

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

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

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

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: See Table 1

PlateletAggregation: See Table 1

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

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8623361

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

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

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

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

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: See Table 1

PlateletAggregation: See Table 1

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

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA290950815

gnomAD: N/A

Case29: GT40, Female, India, age of onset is 6 years old

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Patients were recruited as they presented consecutively from 1996 to 1998 for evaluation of a mucocutaneous bleeding disorder

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

PlateletAggregation: All patients examined had defective ADP, epinephrine, and collagen induced aggregation and normal ristocetin induced aggregation

CasePreviousTesting: Mutations were detected by the method of single strand conformation polymorphism (SSCP) analysis, followed by nucleotide sequencing and confirmation by restriction fragment length polymorphism (RFLP) assays. The sequences of the primers employed and the reaction conditions for PCR amplification of the exons, adjacent intronic regions, and 50 and 30 untranslated regions of the aIIb and b3 gene

Gene: ITGB3

Variant: NM_000212.2:c.428T>G (p.Leu143Trp)

LegacyVariant: N/A

ClinVar: 13567

CAiD: CA123252

gnomAD: MAF in the Other population is 0.0001629 https://gnomad.broadinstitute.org/variant/17-45361875-T-G)

Case18: GT09, Female, India, age of onset is 21 years old

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Patients were recruited as they presented consecutively from 1996 to 1998 for evaluation of a mucocutaneous bleeding disorder

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

PlateletAggregation: All patients examined had defective ADP, epinephrine, and collagen induced aggregation and normal ristocetin induced aggregation

CasePreviousTesting: Mutations were detected by the method of single strand conformation polymorphism (SSCP) analysis, followed by nucleotide sequencing and confirmation by restriction fragment length polymorphism (RFLP) assays. The sequences of the primers employed and the reaction conditions for PCR amplification of the exons, adjacent intronic regions, and 50 and 30 untranslated regions of the aIIb and b3 gene

Gene: ITGB3

Variant: NM_000212.2:c.428T>G (p.Leu143Trp) and NM_000212.2:c.1261G>A (p.Val422Met)

LegacyVariant: N/A

ClinVar: 13567

CAiD: CA123252 and CA400028437

gnomAD: MAF in the Other population is 0.0001629 https://gnomad.broadinstitute.org/variant/17-45361875-T-G

Case1: Female, 25 years old, Japanese

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A per Table 1

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Prolonged ivy bleeding times, bleeding diathesis since early childhood

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: Surface expression of αIIbβ3 was analyzed by flow cytometry which was < 5% of normal

PlateletAggregation: Aggregation in response to ADP, epinephrine and collagen was absent but normal in response to ristocetin

CasePreviousTesting: Nucleotide sequences of the αIIb and β3 coding regions were determined by direct sequencing of RT-PCR products from platelet RNA.

Gene: ITGA2B

Variant: NM_000419.3:c.959T>C (p.Phe320Ser)

LegacyVariant: (p.Phe289Ser)

ClinVar: N/A

CAiD: CA399804774

gnomAD: N/A

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

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

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

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

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

PlateletAggregation: N/A

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

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399805691

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

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.

Case4: Patient 4, Female, 12 years old

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Affected sister is Patient 3

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

CasePresentingHPOs: HP:0000967

(Petechiae)

CaseHPOFreeText: Hematomas, prolonged in vitro bleeding time

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

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

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

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

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: 2900

CAiD: CA115846

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

Case1: Female, 20 years old, Chinese

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0000421,

(Easy bruising, epistaxis)

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

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

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

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

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

Gene: ITGA2B

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

LegacyVariant: (p.Pro126His)

ClinVar: N/A

CAiD: CA8603447

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

Case6: (GT6), Male, 82 years old, French

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Mucocutaneous bleeding

CaseNotHPOs: N/A

ProteinExpression: 40-55% surface expression levels of αIIbβ3

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

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

Gene: ITGB3

Variant: NM_000212.2:c.665T>C (p.Leu222Pro) and NM_000212.2:c.1871G>A (p.Cys592Tyr)

LegacyVariant: (p.Leu196Pro) and (p.Cys624Tyr) (The paper gives legacy and current nomenclature)

ClinVar: N/A

CAiD: CA291224887 and CA400032726

gnomAD MAF in the European (non-Finnish) population is 0.00006482 https://gnomad.broadinstitute.org/variant/17-45363676-T-C

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

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Mucocutaneous bleeding

CaseNotHPOs: N/A

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

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

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

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: 2895

CAiD: CA10575473

gnomAD N/A

PMID: 33600779

Case7: Patient FO

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.2153dup and NM_000419.3:c.1234G>A (p.Gly412Arg)

LegacyVariant: (p.Gly381Arg)

ClinVar: 381748

CAiD: CA913189170 and CA8603182

gnomAD MAF in the Latino population is 0.0001453 https://gnomad.broadinstitute.org/variant/17-42458406-C-T

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

Case14: Patient MB

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

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.1211-78A>G

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940720

gnomAD: N/A

Supplementary Tables 1 and 2 combined information:

Case3: GT3, Female, 12 years old

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Not available per supplementary table 1

ParentalGenotype: Parents are not consanguineous, no other genotype information available

CasePresentingHPOs: HP:0000978, HP:0000979, HP:0031364, HP:0000421, HP:0000225

(Bruising, purpura, ecchymosis, epistaxis, gingival bleeding)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Showed <5% of αIIbβ3 expression measured by flow cytometry

PlateletAggregation: Platelet aggregation showed no response to ADP and collagen but normal response to ristocetin

CasePreviousTesting: All exons from ITGA2B and ITGB3 genes were amplified by PCR using intronic primers. DNA sequencing was determined by Sanger sequencing.

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: 2892

CAiD: CA115834

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

Supplementary Tables 1 and 2 combined information:

Case6: GT6, Male, 7 years old

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: Not available per supplementary table 1

ParentalGenotype: Parents are not consanguineous, no other genotype information available

CasePresentingHPOs: HP:0000978, HP:0000979, HP:0031364, HP:0000421

(Bruising, purpura, ecchymosis, epistaxis)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Showed 10-20% of αIIbβ3 expression measured by flow cytometry

PlateletAggregation: Platelet aggregation showed a small amount of response to ADP and collagen but normal response to ristocetin

CasePreviousTesting: All exons from ITGA2B and ITGB3 genes were amplified by PCR using intronic primers. DNA sequencing was determined by Sanger sequencing.

Gene: ITGA2B

Variant: NM_000419.3:c.812C>G (p.Ala271Gly) and NM_000419.3:c.2172G>A (p.Met724Gln)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399805123 (p.Ala271Gly) and CA399798895 (p.Met724Gln)

gnomAD: N/A

Case3: Patient 3, Female, 27 years old

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

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

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

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

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

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

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

Gene: ITGA2B

Variant: NM_000419.3:c.113del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA915940264

gnomAD: N/A

Case21: (ProbandGT-21) Male, age not specified, Caucasian

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

ProteinExpression: Flow cytometry showed <5% GPIIIa and GPIIIb surface expression

Platelet Aggregation: N/A

CasePreviousTesting: Promoter and exon sequences of aIIb and b3 genes were amplified and directly sequence

Gene: ITGB3

Variant: NM_000212.2:c.191G>A (p.Cys64Tyr) the second mutation was not identified

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA291224490

gnomAD N/A

Case12: (Proband CabGT-12), Female, age not specified, Caucasian

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

ProteinExpression: Flow cytometry showed 19% GPIIb and 40% GPIIIa surface expression

Platelet Aggregation: N/A

CasePreviousTesting: Promoter and exon sequences of aIIb and b3 genes were amplified and directly sequence

Gene: ITGA2B

Variant: NM_000419.3:c.2113T>C (p.Cys705Arg) and NM_000419.3:c.3060+2T>C (p.Val982_Lys1020del)

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8602816 and CA290944108

gnomAD MAF in the European (non-Finnish) population is 0.000008792 https://gnomad.broadinstitute.org/variant/17-42455140-A-G and MAF in the European non Finnish population for (p.Val982_Lys1020del) is 0.00003876 https://gnomad.broadinstitute.org/variant/17-42451720-A-G

Case13: Female, African, age not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: N/A

PlateletAggregation: Minimal information, not specific enough

CasePreviousTesting: Sanger sequencing identified disease-causing variants in 18 out of 20 patients (Probands 6 and 14 excluded) with istoantibodies to αIIbβ3. The mutations were evenly distributed between ITGB3 and ITGA2B.

Gene: ITGA2B

Variant: NM_000419.3:c.1357C>T (p.Arg453Ter)

LegacyVariant: N/A

ClinVar: 631773

CAiD: 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

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

Case1: Female, 48 years old, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000421, HP:0000225, HP:0000978, HP:0000132, HP:0006298, HP:0005261

(Epistaxis, gingival bleeding, easy bruising, menorrhagia, bleeding after tooth extraction, hemarthrosis

CaseHPOFreeText: Hemorrhage after surgery

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Platelet surface glycoprotein analysis by flow cytometry revealed a severe αIIbβ3 deficiency (Table 3 shows specific values)

PlateletAggregation: There was a failure of ADP, collagen and adrenalin to induce platelet aggregation, but ristocetin-induced platelet aggregation (RIPA) was normal

CasePreviousTesting: Integrin alphaIIb subunit gene (ITGA2B) sequencing showed that this proband was a compound heterozygote

Gene: ITGA2B

Variant: NM_000419.3:c.1214T>C (p.Ile405Thr) and NM_000419.3:c.1234G>A (p.Gly412Arg)

LegacyVariant: (p.Ile374Thr) (p.Gly381Arg)

ClinVar: 381748

CAiD: CA290950815 (p.Ile403Thr) and CA8603182 (p.Gly412Arg)

gnomAD: MAF in Latino population 0.0001453 http://gnomad.broadinstitute.org/variant/17-42458406-C-T

Case4: P4, gender, age, ethnicity not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Article mentions all patients have a severe bleeding phenotype

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

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

PlateletAggregation: N/A

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

Gene: ITGA2B

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

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA399805011

gnomAD: N/A

Case35: (GT14) Gender, age and ethnicity are not specified

DiseaseAssertion: Glanzmann thrombasthenia

FamilyInfo: N/A

ParentalGenotype: N/A

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:

Variant: NM_000419.3:c.188+8del

LegacyVariant: N/A

ClinVar: N/A

CAiD: CA8603523

gnomAD MAF in the South Asian population is 0.0002613 https://gnomad.broadinstitute.org/variant/17-42466645-AC-A

Case1: Female, 56 years old, Japanese

DiseaseAssertion: Glanzmann thrombasthenia (Diagnosed at 21 years of age)

FamilyInfo:

ParentalGenotype:

CasePresentingHPOs: HP:0004406, HP:0000225

(Recurrent epistaxis, gingival bleeding)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOsFreeText: N/A

ProteinExpression: Flow cytometry demonstrated significantly decreased expression of CD41 and CD61 to less than 20% of normal levels (See Figure 2)

PlateletAggregation: An in vitro assay revealed no platlet aggregation in response to agonists except ristocetin.

CasePreviousTesting: DNA sequencing analysis revealed compound heterozygous mutations confirming a diagnosis of Glanzmann thrombasthenia

Gene: ITGA2B

Variant: NM_000419.3:c.2602-3C>G and NM_000419.3:c.641T>C (p.Leu214Pro)

LegacyVariant: N/A

ClinVar: 2893 and 2901

CAiD: CA10575472 and CA115848

gnomAD: MAF in East Asian population 0.00006523 http://gnomad.broadinstitute.org/variant/17-42453087-G-C

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

Case#: Male, 48

Disease: Glazmann's Thrombasthenia Like Syndrome

CasePresentingHPOs: HP:0001873, HP:0000421, HP:0031364, HP:0000225

Thrombocytopenia, Epistaxis, Ecchymosis, Gingival bleeding

CaseNotHPOs: NA

FamilyInfo: Pedigree figure 1. Family history of thrombocytopenia.

PlateletAgreggation: Decreased PLT aggregation and diminished ATP release with the agonists ADP, collagen, and AA, with normal ristocetin agglutination

GenotypingMethod: Genetic analysis of ITGA2B and ITGB3 genes was performed by next-generation sequencing (NGS). Sanger sequencing used to confirm variants.

ClinVar: 50232

CAID: CA10575572

Variant: NM_000419.5:c.3077G>A

GnomAD: European non-Finnish 0.000008801 (1/113618)

ExpressionEvidence: Level of expression on PLT surface determined by FCM: CD41a (GPIIb/IIIa) 49%, CD61 (GPIIIa) 44%, and CD42b (GPIb) 105%. Healthy control value range: CD41a (GPIIb/IIIa) (85-115%); CD61 (GPIIIa) (80-120%); CD42b (GPIb) (70-130%).

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

CaseCII-1: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 1515 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.194T>C (p.Ile65Thr)

ClinVar: 636 https://www.ncbi.nlm.nih.gov/clinvar/variation/636/

gnomAD: 0.0005574, https://gnomad.broadinstitute.org/variant/12-102894893-A-G?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.1065+1G>A

ClinVar: 102501 https://www.ncbi.nlm.nih.gov/clinvar/variation/102501/

gnomAD: 0.00004622, http://gnomad.broadinstitute.org/variant/12-103238113-C-T

CaseAII-2: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 375 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.165del (p.Phe55fs)

ClinVar: 611 https://www.ncbi.nlm.nih.gov/clinvar/variation/611/

gnomAD: 0.00002639, https://gnomad.broadinstitute.org/variant/12-103306571-CA-C?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

ClinVar: 92751 https://www.ncbi.nlm.nih.gov/clinvar/variation/92751/

gnomAD: 0.006318, https://gnomad.broadinstitute.org/variant/12-102851701-C-A?dataset=gnomad_r3

CaseBII-2: N/A

CasePresentingHPOs: N/A

HPOsFreeText: Pretreatment phenylalanine level at 270 umol/L

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: N/A

Variant1: NM_000277.3(PAH):c.688G>A (p.Val230Ile)

ClinVar: 102784 https://www.ncbi.nlm.nih.gov/clinvar/variation/102784/

gnomAD: 0.0009025, https://gnomad.broadinstitute.org/variant/12-102855154-C-T?dataset=gnomad_r3

Variant2: NM_000277.3(PAH):c.1241A>G (p.Tyr414Cys)

ClinVar: 593 https://www.ncbi.nlm.nih.gov/clinvar/variation/593/

gnomAD: 0.0005264, https://gnomad.broadinstitute.org/variant/12-102840474-T-C?dataset=gnomad_r3

Case3:

CasePresentingHPOs:

HPOFreeText: Identified by NBS with elevated C5-carnitine levels. Asymptomatic up to 3 year follow up. Levels of C5-carnitine decreased with time.

CaseNotHPOs:

CasePreviousTesting: Followup C5 carnitine 0.25 nM/ml (ref 0.33). Additional testing was performed on patients identified by NBS: all either had elevation of 2-methylbutyrlglycine in urine (with no intermediates consistent with isovaleric acidemia), or increase in 2-methylbutyrylcarnitine in culture from fibroblasts.

CaseGenotypingMethod: Bidirectional sequence analysis of genomic DNA.

Variant: 1. NM_001609.3(ACADSB):c.621G>A (p.Trp207Ter) 2. unknown

ClinVar: 299075

gnomAD:

VariantEvidence: Genomic DNA showed heterozygosity for this variant, but cDNA indicated homozygosity. The variant on the second allele must result in loss of transcription, abnormal splicing, unstable RNA, or deletion containing exon 5.

CaseAddInfo:

CasePMIDs:

Case 10 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.658_660delAAG (p.Lys220del)

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

CaseAddInfo: proband genotype, homozygous, no phenotypic info, sibling (fetus) also homozygous for variant

Case 4 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

__

Variant2: NM_015506.2(MMACHC):c.467G>A (p.Gly156Asp)

ClinVar: 554696

CAID: CA340133108

gnomAD: not in gnomAD

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info given, sibling (fetus) carrier of both variants. variant 2 is not in the table of 31 variants (Table 1).

Case61(Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.599G > A (p.Trp200Ter)

ClinVar: n/a

CAID: n/a

gnomAD: 0.000008829 (European non-Finnish)

Variant2: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier of p.W203X paternal variant

Case 21 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.467G > A (p.Gly156Ala)

ClinVar: n/a

in ClinVar it says that this nucleotide change corresponds to p.Gly156Asp (p.G156D), which is the paternal variant listed in case 4 that I mentioned was not also listed in Table 1 (list of all 31 variants found). I am wondering if p.G156A is a typo in case 21 Table 2 and Variant 18 Table 1

CAID: CA340133108

gnomAD: n/a

Variant2: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for p.G156A (possible typo??) maternal variant

Case52(Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.658_660delAAG (p.Lys220del)

ClinVar: 95707

CAID: CA223197

gnomAD: 0.0003071 (East Asian)

Variant2: NM_015506.2(MMACHC):c.365A > T (p.His121Leu)

ClinVar: n/a

CAID: n/a

gnomAD: n/a

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier of p.K220del maternal variant

Case 26 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.440_441delGT

ClinVar: n/a

CAID: CA312741

gnomAD: n/a

Variant2: NM_015506.2(MMACHC):c.609G > A (p.Trp203Ter)

ClinVar: 30800

CAID: CA259906

gnomAD: 0.0005562 (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for p.W203X paternal variant

Case32 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group

Variant1: NM_015506.2(MMACHC):c.666C > A (p.Tyr222Ter)

ClinVar: 496436

CAID: CA827827

gnomAD: 0.00006537 (South Asian)

Variant2: NM_015506.2(MMACHC):c.80A>G (p.Gln27Arg)

ClinVar: 552467

CAID: CA827620

gnomAD: not in gnomAD

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier of p.Y222X maternal variant

Case 17 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: PCR

CaseGenotypingMethod: same as group __

Variant1: NM_015506.2(MMACHC):c.445_446insA (p.Cys149Ter)

ClinVar: n/a

CAID: n/a

gnomAD: n/a

Variant2: NM_015506.2(MMACHC):c.567dupT (p.Ile190Tyrfs*13)

ClinVar: 556708

CAID: CA522810899

gnomAD: [0.0001024] (https://gnomad.broadinstitute.org/variant/1-45974604-G-GT) (East Asian)

CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for c.567dupT paternal variant

CaseF1P: Female, 8 yrs report, India

CasePresentingHPOs: N/A

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband for Family 1, Variant is demonstrated to activate a cryptic splice site and abolish the canon splice site leading to a premature termination and nonsense-mediated decay

CasePreviousTesting: Blood phenylalanine before treatment was 1174 μmol/l, Blood tyrosine before treatment was 33 μmol/l

CaseGenotypingMethod: N/A

Variant: NM_000277.3(PAH):c.169-2A>G

ClinVar: 555212 https://www.ncbi.nlm.nih.gov/clinvar/variation/555212/

gnomAD: 0.00003267, http://gnomad.broadinstitute.org/variant/12-103288698-T-C

CaseF6P: 1 yr report, India

CasePresentingHPOs: HP:0001010, HP:0000750, HP:0001249, HP:0006801, HP:0004923 (Hypopigmentation of the skin, Delayed speech and language development, Intellectual disability, Brisk deep tendon reflexes, Hyperphenylalaninemia)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Family is consanguinous, Predicted to undergo NMD

CasePreviousTesting: Blood phenylalanine before treatment was 1260 μmol/l, Blood tyrosine before treatment was N/A μmol/l, PKU diagnosis was based on ferric chloride test on patient urine samples and detection of elevated Phenylalanine levels in blood samples by using HPLC, in addition to analysis of clinical features.

CaseGenotypingMethod: Genomic DNA was isolated from blood samples of proband and family members. PCR amplification and sequencing was used to screen for mutations. Each mutation was confirmed by bi-directional DNA sequencing.

Variant: NM_000277.3(PAH):c.526C>T (p.Arg176Ter)

ClinVar: 102723 https://www.ncbi.nlm.nih.gov/clinvar/variation/102723/

gnomAD: 0.00008012, http://gnomad.broadinstitute.org/variant/12-103249094-G-A

Case# P4, 4yr onset, Pakistani

CasePresentingHPOs HP:0002151, HP:0001946, HP:0001942, HP:0001987

CasePreviousTesting negative for NAGS and CPS1 genes.

CaseGenotypingMethod sequence analysis of coding exons, including flanking intronic regions of CA5A and CA5B, was performed.

Variant NM_001739.1:c.555+4_555+183del180bp

CAID CA658820661

VariantEvidence intronic splice site

CaseAddInfo consanguineous

Case3b: Female, 9 d at initiation of follow up, East Indian ancestry, sibling of Case 3a (Family 1)

HPOsFreeText: NBS C4-acylcarnitine 2.1 umol/L, Plasma C4-acylcarnitine 2.47 umol/L, urine C4-acylcarnitine 21.66 mmol/mol creatinine, Urine C4/C3 ratio 42

NotHPOsFreeText: normal urine isobutyrylgycine ug/mg creatinine

CaseAddInfo: unremarkable clinical condition

Case3b (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_014384.2(ACAD8):c.867C>A (p.His289Gln)

ClinVar: 5358

CAID: CA117441

gnomAD: not in gnomAD

CaseAddInfo: homozygous mutations, no data for SCAD gene variants

Case8: Male, 6 wks at initiation of follow up, European ancestry

HPOsFreeText: NBS C4-acylcarnitine 1.8 umol/L, plasma C4 acylcarnitine 1.52 umol/L, in vitro probe isoC4-acylcarnitine 0.187 umol/ g protein, in vitro probe C4-acylcarnitine 0.573 umol/g protein, elevated urine C4-acylcarnitine 25.09 mmol/mol creatinine, Urine C4/C3 ratio 88

NotHPOsFreeText: normal urine isobutyryglycine

CaseAddInfo: unremarkable clinical condition

Case8 (Level 2)

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2(ACAD8):c.512C>G (p.Ser171Cys)

ClinVar: 95589

CAID: CA223125

gnomAD: 0.02252 (European non-Finnish)

Variant2: NM_014384.2(ACAD8):c.455T>C (p.Met152Thr)

ClinVar: 5355

CAID: CA117433

gnomAD: 0.0001395 (European Non-Finnish)

CaseAddInfo: compound heterozygote specified allele 1 and 2, but not maternal and paternal. Potential splice-site alteration at exon 3(+3A>G). ACADS (SCAD-deficient) gene variants 625G>A/625G>A.

Case765: Female, 9 years report, Spain

CasePresentingHPOs: HP:0003153, HP:0001256, HP:0007359, HP:0012000 (Cystathioninuria, Mild mental retardation, Partial seizures, EEG with generally recognized spikes)

HPOsFreeText: Elevated urine cystathionine (750 umol/g creatine; reference <46) and Elevated tHcys in urine (61 umol/g creatine; reference <20), Elevated plasma tHcys (19 umol/l; reference <7.5), Elevated plasma cystathionine (10 umol/l; reference =0), Post treatment normal urine cystathionine (34 umol/g creatine)

CaseNotHPOs: HP:0003345 (Glutathione synthetase deficiency)

NotHPOsFreeText: N/A

CaseAddInfo: Patient is homozygous for this variant

CasePreviousTesting: Karyotype, magnetic resonance imaging, specific genetic tests for neurogenetic diseases and screening for inborn errors of metabolism (lactate, pyruvate, ammonium, uric acid, amino acids, organic acids, glycosaminoglycanes, creatine and guanidinoacetate, purines and pyrimidines, and isoelectric focusing pattern of transferrin), as well as folate, pyridoxine and cobalamine deficiencies, neural tumors and genetically determined homocystinurias, were all ruled out.

CaseGenotypingMethod: All twelve exons of the CTH gene and the intronic flanking sequences of the subjects and their parents was PCR amplified and directly sequenced.

Variant: NM_001902.5:c.200C>T (p.Thr67Ile)

ClinVar: 2939 https://www.ncbi.nlm.nih.gov/clinvar/variation/2939/

gnomAD: Ashkenazi Jewish 9.934e-3, Overall 6.308e-3 https://gnomad.broadinstitute.org/variant/1-70881670-C-T

Case# P2, M, 1mo onset, Indian

CasePresentingHPOs HP:0001263, HP:0001250, HP:0001298, HP:0008344

CasePreviousTesting Biochemical testing (Leu + Ile- 1235 Val- 591) on Tandem Mass Spectrometry (TMS) and/or abnormal metabolites (elevated BCKAs, 2-keto isocaproate, 3-hydroxy butyrate, 2-hydroxy isovalerate, 2-hydroxy caproate, 2-keto 3-methyl valerate) on a urinary organic acid profile using Gas Chromatography Mass Spectrometry (GC–MS) was performed to make the diagnosis.

CaseMethod1 PCR

CaseMethod2 Direct

CaseGenotypingMethod Coding regions as well as flanking exon–intron boundaries of genes (BCKDHA- 9 exons, BCKDHB- 10 exons, and DBT- 11 exons) were amplified by PCR. Bidirectional Sequencing on products

Variant NM_000709.3(BCKDHA):c.844G>C (p.Asp282His)

ClinVar 204377

VariantEvidence none

CaseAddInfo consanguineous

Case#: P4, F, 13 days (onset)

CasePresentingHPOs: HP:0001250, HP:0007105

CasePresentingHPOs (free text): TMS/GC-MS: Leu+Ile- 1810, Val- 275. Diagnosed with classic form of MSUD.

CasePreviousTesting: Biochemical testing (elevated BCAAs) used to make diagnosis.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, coding regions (and flanking exon-intron boundaries) of BCKDHA, BCKDHB, and DBT were PCR-amplified, followed by bidirectional sequencing.

Variant: NM_001918.3(DBT):c.939G>C (p.Lys313Asn) (homozygous)

ClinVar: 94017

gnomAD: MAF (South Asian) 9.747e-5

VariantEvidence: None

Case#: P15, F, 2 months (onset)

CasePresentingHPOs: HP:0001263, HP:0200134

CasePresentingHPOs (free text): TMS/GC-MS: Leu+Ile- 517, Val- 315. Diagnosed with intermediate form of MSUD.

CasePreviousTesting: Biochemical testing (elevated BCAAs) used to make diagnosis.

CaseMethod1: PCR

CaseMethod2: Sequencing

CaseGenotypingMethod: Genomic DNA extracted, coding regions (and flanking exon-intron boundaries) of BCKDHA, BCKDHB, and DBT were PCR-amplified, followed by bidirectional sequencing.

Variant: NM_001918.3(DBT):c.939G>C (p.Lys313Asn) (homozygous)

ClinVar: 94017

gnomAD: MAF (South Asian) 9.747e-5

VariantEvidence: None

Case10 age/gender unknown, Caucasian, Germany

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Probable PDE: either pyridoxine-responsive seizures and an affected sibling or neonatal seizures responsive to a single dose of pyridoxine with later recurrence of seizures again responsive to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 7.5(nv 0.4-4.9µmol/liter), AASA in plasma 5.5(nv<0.2µmol/liter), urine AASA 26(nv<1mmol/molcreatinine). Normal urine PA after pyridoxine treatment.

Variant NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), homozygous

ClinVar 17994

gnomAD not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case9 age/gender unknown, Caucasian, Germany

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Definite PDE: formal pyridoxine withdrawal had resulted in reoccurrence of seizures that again responded to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 5.5(nv 0.7-2.6µmol/liter), AASA in plasma 5.8(nv<0.2µmol/liter). Normal urine PA after pyridoxine treatment.

Variant 1. NM_001182.4:c.696-2A>G (p.=), 2. NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), compound heterozygous

ClinVar 1. n/a 2. 17994

CAID 1. CA360730346

gnomAD neither in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case6 age/gender unknown, Caucasian, Germany

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Definite PDE: formal pyridoxine withdrawal had resulted in reoccurrence of seizures that again responded to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 23(nv 0.8-5.5µmol/liter), AASA in plasma 4.6(nv<0.2µmol/liter). Normal urine PA after pyridoxine treatment.

Variant 1. NM_001182.4(ALDH7A1):c.328C>T (p.Arg110Ter), 2. NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), compound heterozygous

ClinVar 1. 17995 2. 17994

gnomAD 1. MAF=0.0001385(Other), no homozygotes 2. not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Case5 age/gender unknown, Caucasian, Italy

CasePresentingHPOs HP:0001250

(Seizures)

HPOsFreeText seizure onset in neonatal period from minutes after birth until 3 weeks of age. Definite PDE: formal pyridoxine withdrawal had resulted in reoccurrence of seizures that again responded to pyridoxine.

CaseNotHPOs n/a

CasePreviousTesting post treatment testing: Pipecolic acid in plasma 7.8(nv 0.4-4.9µmol/liter), AASA in plasma 5.8(nv<0.2µmol/liter), urine AASA 28(nv<1mmol/molcreatinine). Normal urine PA after pyridoxine treatment.

Variant NM_001182.4(ALDH7A1):c.1279G>C (p.Glu427Gln), homozygous

ClinVar 17994

gnomAD not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

Patient8: Male, 2yo, sibling to patient 9

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 6.4 μmol l−1, Ammonium (μmol l−1) = 30, pH = 7.36, Protein intake (g kg−1 per day) = 1.5, PDI/IQ in follow-up = 108

CaseNotHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

(poor feeding, vomiting, dehydration, lethargy, coma)

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS at 11 days old, homozygous

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_002225.3:c.941C>G

CAID: CA391721562, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391721562

gnomAD: n/a

Patient15: Female, 15yo

CasePresentingHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001941

(poor feeding, vomiting, dehydration, acidosis)

HPOsFreeText: intermittent isovaleric acidemia, C5 (DBS) = 7.8 μmol l−1, IVA incorp (%) = 4.9, IVG in urine mmol permol creatinine = 4653, Ammonium (μmol l−1) = 28, pH = 7.18, Protein intake (g kg−1 per day) = 0.8, treated with carnitine and glycine supplements, PDI/IQ in follow-up = 92

CaseNotHPOs: HP:0001254, HP:0001259 (lethargy, coma)

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: diagnosed via clinical findings at 6yo, hospitalized outside of detection period

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group, nucleotide changes detected in homozygosity in mRNA

Variant1: NM_002225.3:c.1099T>C

CAID: CA391723803, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391723803

gnomAD: n/a

Variant2: c.1-?_c.295+? (Delexons 1–3) no ClinVar or CAID

Patient9: Female, 3yo, sibling to patient 8

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 3.5 μmol l−1, Ammonium (μmol l−1) = 32, pH = 7.34, Protein intake (g kg−1 per day) = 1.8, PDI/IQ in follow-up = 95

CaseNotHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

(poor feeding, vomiting, dehydration, lethargy, coma)

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed via family evaluation at 3yo, homozygous

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_002225.3:c.941C>G

CAID: CA391721562, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391721562

gnomAD: n/a

Patient5: Male, 11mo, sibling to patient 4

CasePresentingHPOs:

HPOsFreeText: Asymptomatic, C5 (DBS) = 6.0 μmol l−1, IVA incorp (%) = 64, IVG in urine mmol permol creatinine = 955, Ammonium (μmol l−1) = 65, pH = 7.41, Protein intake (g kg−1 per day) = 1.5, treated with carnitine supplements, PDI/IQ in follow-up = 85

CaseNotHPOs: HP:0011968, HP:0002013, HP:0001944, HP:0001254, HP:0001259

(poor feeding, vomiting, dehydration, lethargy, coma)

NotHPOsFreeText: sweaty feet odor

CaseAddInfo: Diagnosed with NBS at 10 days old

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_001159508.1:c.1214T>C

CAID: CA268781818, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA268781818

gnomAD: 0.000003977, http://gnomad.broadinstitute.org/variant/15-40710485-T-C

Variant2: NM_001159508.1:c.500T>C

CAID: CA391717541, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391717541

gnomAD: n/a

CaseREU3: Male, 6 yrs report, United Kingdom

CasePresentingHPOs: HP:0001337, HP:0001263, HP:0000717, HP:0001382, HP:0012120 (Tremor, Global developmental delay, Autism, Joint hypermobility, Methylmalonic aciduria)

HPOsFreeText: Malonic aciduria

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this variant

CasePreviousTesting: All participants had undergone multiple standard and specialized biochemical tests, invasive procedures (e.g. muscle and/or skin biopsy, lumbar puncture) and targeted gene testing; MRI head not performed

CaseGenotypingMethod: 16 broad classes of IEM was target enriched and sequenced. Any suspected pathogenic variants were confirmed with Sanger sequencing.

Variant: NM_001243279.3:c.1453A>C (p.Ser485Arg)

CAID: CA397148172, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA397148172

gnomAD: Not in gnomAD

CasePA007 4do onset, Taiwan

CasePresentingHPOs HP:0003571, HP:0011968, HP:0002098, HP:0001290, HP:0002240, HP:0002789, HP:0004372, HP:0001987, HP:0003811

(propionicacidemia, poor feeding, respiratory distress, hypotonia, hepatomegaly, tachypnea, disturbed consciousness, hyperammonemia, neonatal death)

HPOsFreeText poor activity and other phenotypes presented at 4 days old. Died at 6 days old

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1301C>T (p.Ala434Val),2. NM_000532.4(PCCB):c.838dup (p.Leu280Profs)

ClinVar 1. 554490, 2. 552435

gnomAD 1. MAF= 0.0003510(East Asian), no homozygotes, 2. not in gnomAD

CaseAddInfo n/a

CasePMIDs n/a

CasePA006 2yo report, Taiwan

CasePresentingHPOs HP:0011343, HP:0003571

(moderate global developmental delay, propionicacidemia)

HPOsFreeText did not experience other classical PA phenotype after liver transplant(10mo) during 12-month follow up. Urine methylcitrate levels and serum propionylcarnitine levels have not markedly decreased

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1301C>T (p.Ala434Val), 2. NM_000532.4(PCCB):c.1534C>T (p.Arg512Cys)

ClinVar 1. 554490, 2. 38879

gnomAD 1. MAF=0.0003510(East Asian), no homozygotes, 2. MAF=0.00005440(East Asian), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

CasePA005-2 8yo report, Taiwan

CasePresentingHPOs HP:0003571, HP:0011968, HP:0002013, HP:0001987, HP:0011343

(propionicacidemia, poor feeding, vomiting, hyperammonemia, moderate developmental delay)

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1301C>T (p.Ala434Val), 2. NM_000532.4:c.-4156_183+3713del

ClinVar 1. 554490, 2. n/a

CAID 2. n/a

gnomAD 1. MAF=0.0003510(East Asian), no homozygotes, 2. n/a

CaseAddInfo Older sister presented at two weeks old with poor feeding, vomiting, hyperammonemia, metabolic acidosis, recurrent infection, and elevated urine 3-hydroxypropionic and 2-methyl-3-hydroxybutyric acids suggestive of PA. Died of severe infection at 1yr 6mo without genetic testing

CasePMIDs n/a

CasePA004 40do onset, Taiwan

CasePresentingHPOs HP:0003571, HP:0001987, HP:0011968, HP:0001263, HP:0000952, HP:0001942, HP:0001522

(propionicacidemia, hyperammonemia, poor feeding, developmental delay, jaundice, metabolic acidosis, death in infancy)

HPOsFreeText severe jaundice and other symptoms at 40days old. Death at 1yr 6mo

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant NM_000532.4(PCCB):c.1301C>T (p.Ala434Val), homozygous

ClinVar 554490

gnomAD MAF= 0.0003510(East Asian), no homozygotes

CaseAddInfo n/a

CasePMIDs n/a

CasePA003 3do onset, Taiwan

CasePresentingHPOs HP:0003571, HP:0000952, HP:0011968, HP:0001290, HP:0001942, HP:0002154, HP:0001987, HP:0001522

(propionicacidemia, jaundice, poor feeding, hypotonia, metabolic acidosis, hyperglycinemia, hyperammonemia, death in infancy)

HPOsFreeText died at 5m 15days (also check 2178070 first)

CaseNotHPOs "

NotHPOsFreeText "

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger + "

Variant 1. NM_000532.4(PCCB):c.1301C>T (p.Ala434Val), 2. NM_000532.4:c.580T>C (p.Ser194Pro)

ClinVar 1. 554490, 2. n/a

CAID 2. CA354641839

gnomAD 1. MAF=0.0003510(East Asian), no homozygotes, 2. not in gnomAD

CaseAddInfo "

CasePMIDs 2178070

CasePA002-2 prenatal diagnosis, Taiwan

CasePresentingHPOs HP:0003571

(propionicacidemia)

CaseNotHPOs n/a

CasePreviousTesting coding regions and flanking areas of PCCA also analyzed with PCR and Sanger

Variant 1. NM_000532.4(PCCB):c.1316A>G (p.Tyr439Cys), 2. NM_000532.4:c.-4156_183+3713del

ClinVar 1. 225429, 2. n/a

CAID 2. n/a

gnomAD 1. MAF=0.0001631(South Asian), no homozygotes, 2. n/a

CaseAddInfo aborted after prenatal diagnosis. Older sibling presented with recurrent vomiting, conscious disturbance, hyperventilation, metabolic acidosis, and elevated urine 3-hydroxypropionate, 3-hydroxybutyrate, and 3-hydroxyvalerate suggestive of PA. Died at 2yr 8mo without genetic testing.

CasePMIDs n/a

CaseGM01566: Female, 16 years report, Caucasian, Europe

CasePresentingHPOs: HP:0003153 (Cystathioninuria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is a compound heterozygote for this variant, Variants were confirmed in trans by parental testing

CasePreviousTesting: N/A

CaseGenotypingMethod: Primers were developed and the CTH exons 1-12 and exon-intron boundaries were PCR amplified and sequenced. All sequence variations were verified by restriction enzyme analysis and/or repeat sequencing.

Variant1: NM_001902.5:c.200C>T (p.Thr67Ile)

ClinVar: 2939 https://www.ncbi.nlm.nih.gov/clinvar/variation/2939/

gnomAD: Ashkenazi Jewish 9.934e-3, Overall 6.308e-3 https://gnomad.broadinstitute.org/variant/1-70881670-C-T

Variant2: CTH, 1-BP DEL, 1220C AKA: NM_001902.5:c.1064del (p.Thr355Ilefs*19)

ClinVar: 2938 https://www.ncbi.nlm.nih.gov/clinvar/variation/2938/

gnomAD: European (Non-Finnish) 1.551e-4, Overall 8.845e-5 https://gnomad.broadinstitute.org/variant/1-70904381-AC-A

Case27 Male, 3do onset, Ethnicity: Turkish

CasePresentingHPOs HP:0003571, HP:0008872, HP:0008947, HP:0002789, HP:0002789

(propionicacidemia, feeding difficulties in infancy, infantile hypotonia, tachypnea)

HPOsFreeText feeding difficulties, hypotonia, somnolence, tachypnea (3do)

CaseNotHPOs n/a

CasePreviousTesting Diagnosis by selective metabolic screen.

Variant NM_000532.4:c.1309G>A (p.Gly437Ser), homozygous

ClinVar n/a

CAID CA354649286

gnomAD MAF= 0.00008674(Latino), no homozygotes

CaseAddInfo parental consanguinity

CasePMIDs n/a

Case22 Male, 13.5yo report, Ethnicity: German

CasePresentingHPOs HP:0003571, HP:0008872, HP:0001531, HP:0002240

(propionicacidemia, feeding difficulties in infancy, failure to thrive in infancy, hepatomegaly)

HPOsFreeText feeding difficulties, failure to thrive, hepatomegaly(4do), 55 IQ on Snijders-Omen Test

CaseNotHPOs n/a

CasePreviousTesting Diagnosed by selective metabolic screening. PCC activity was 0.81 in patient fibroblasts vs control.

Variant NM_000532.4:c.1218_1231delins12 (p.Gly406fs), homozygous

ClinVar n/a

CAID link to register the deletion, but the insertion is not described

gnomAD not in gnomAD

CaseAddInfo no parental consanguinity

CasePMIDs n/a

Case21 Female, 8.8yo report, Ethnicity: Italian

CasePresentingHPOs HP:0003571, HP:0012523, HP:0002013, HP:0008947, HP:0001259, HP:0002789

(propionicacidemia, oral aversion, vomiting, infantile hypotonia, coma, seizures, tachypnea)

HPOsFreeText feeding refusal, vomiting, hypotonia, coma, seizures, tachypnea, exanthema (14do). 55 IQ on Snijders-Omen Test.

CaseNotHPOs n/a

CasePreviousTesting Diagnosed by selective metabolic screen. PCC activity in patient fibroblasts was 1.1% of control.

Variant NM_000532.4(PCCB):c.562G>A (p.Gly188Arg), homozygous

ClinVar 558327

gnomAD MAF= 0.00006152(African), no homozygotes

CaseAddInfo no parental consanguinity

CasePMIDs n/a

CaseBI2K: N/A

CasePresentingHPOs: HP:0001875, HP:0001644, HP:0003756 (Neutropenia, Dilated cardiomyopathy, Skeletal myopathy)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseGenotypingMethod: Five genes noted to have high heart and skeletal muscle expression were sequenced and ORFs created. After PCR amplification and direct sequencing of the TAZ gene (G4.5.), a unique missense variant was found in this proband.

CasePreviousTesting: N/A

CaseAddInfo: N/A

Variant: NM_000116.5(TAZ):c.239-1G>C

ClinVar: 11102, https://www.ncbi.nlm.nih.gov/clinvar/variation/11102/

gnomAD: Not in gnomAD

Case2: female, Turkish, neonatal screening

CasePresentingHPOs: HP:0000403

HPOFreeText: Neonatal screening suggestive of MBD deficiency. Normal free carnitine. No treatment, but normal at 6 years. Adenotomy and bilateral paracentesis at 5.5 years.

CaseNotHPOs:

CasePreviousTesting: Neonatal screening: elevated C5 acylcarnitine (0.75 umol/l, ref <0.31). Urinary organic acids showed increased N-methylbutyrylglycine.

CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced.

Variant: NM_001609.3(ACADSB):c.443C>T (p.Thr148Ile) (homozygous)

ClinVar: 9202

gnomAD: South Asian 0.002678; Overall 0.0008097, no homozygotes

VariantEvidence: Decreases ACADSB enzymatic activity to 2.8% of wild type in vitro (PMID: 20547083).

CaseAddInfo: Consanguinity. 7 year old brother also found to have enzyme deficiency. No symptoms.

CasePMIDs:

Case4: female, Turkish, neonatal screening

CasePresentingHPOs:

HPOFreeText: Neonatal screening suggestive of MBD deficiency. Treatment of 100 mg L-carnitine/kg body weight and has shown normal development until 3 years.

CaseNotHPOs:

CasePreviousTesting: Neonatal screening: elevated C5 acylcarnitine (0.68 umol/l and 2.08 umol/l , ref <0.31). Urinary organic acids showed increased N-methylbutyrylglycine.

CaseGenotypingMethod: Genomic DNA extracted from DBS or peripheral blood. All exons and intron-exon boundaries of ACADSB sequenced.

Variant: NM_001609.3(ACADSB):c.1159G>A (p.Glu387Lys) (homozygous)

ClinVar: 9203

gnomAD: Latino 0.0004797, Overall 0.0002404, no homozygotes

VariantEvidence: In vitro expression in E. coli shows no protein on Western blot, reduced enzymatic activity to 2% and defects in protein folding and stability (PMID: 20547083).

CaseAddInfo:

CasePMIDs:

Case3: Female, 1y 5m, Chinese

HPOsFreeText: (at 21 days) 1.96 C4, 0.17 C4/C2, 2.09 C4/C3

NotHPOsFreeText: normal urine isobutyrylglycine

Case3 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_014384.2:c.286G>A (p.Gly96Ser)

ClinVar: n/a

CAID: CA6372895

gnomAD: 0.001453 (East Asian)

CaseAddInfo:

Case6: Male, 8y 11m, Chinese, part of Family 1

CasePresentingHPOs: HP:0000750, HP:0001328 (speech delay, learning disability)

HPOsFreeText: (at 8y 8m) 1.07 C4 umol/L, 0.13 C4/C2, 1.20 C4/C3

Case6 (Level 2):

CasePreviousTesting: same as group

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant1: NM_014384.2:c.286G>A (p.Gly96Ser)

ClinVar: n/a

CAID: CA6372895

gnomAD: 0.001453 (East Asian)

Variant2: NM_014384.2:c.1092+1G>A

ClinVar: n/a

CAID: CA6373205

gnomAD: 0.00005790 (Latino)

CaseAddInfo: older brother of patient 5. Had not undergone expanded NBS at birth but presented with symptoms by age 8 and was diagnosed later since his younger sister has IBDHD. Trans heterozygous, inherited one allele from each parent