5,487 Matching Annotations
  1. Oct 2026
    1. GT-2

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

      DiseaseAssertion: Glanzmann thrombasthenia type I

      FamilyInfo: N/A

      ParentalGenotype: Segregation analysis confirmed the presence of heterozygous mutations in carrier parents

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Article mentions patients presented with variable bleeding diathesis and Table 1 shows the several phenotypes that were seen among the cohort of 13 patients in this study (this article does not state a specific bleeding phenotype for each proband) "Most of the patients had gross blood loss due to epistaxis (54%), cutaneous bleeding (58%) and menorrhagia (100% of women), while other common symptoms (oral cavity, gastrointestinal, following dental extraction or mild injuries, postpartum, or hematomas) were in general milder."

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry showed <5% αIIbβ3 expression

      PlateletAggregation: Article mentions the disorder was indentified by platelet testing consisting in severely impaired aggregation in response to all physiological agonists and also TMA (See Table 4). Ristocetin-induced platelet aggregation was normal or reduced to some extent.

      CasePreviousTesting: To detect mutations in ITGA2B or ITGB3, total RNA from peripheral blood was used for cDNA synthesis for RT-PCR. Using specific oligonucleotides and conditions, they amplified and sequenced ITGA2B and ITGB3 by Sanger sequencing, and every mutation found in cDNA was confirmed on DNA samples

      Gene: ITGA2B

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

      LegacyVariant: (p.Leu183Pro) + 31= 214

      ClinVar: 2901

      CAiD: CA115848 and CA915940289

      gnomAD: N/A

      PreviouslyPublished PMID: 9473221 (p.Leu214Pro)

    2. GT-1

      Case1: GT-1, gender, age, ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia type II

      FamilyInfo: N/A

      ParentalGenotype: Segregation analysis confirmed the presence of heterozygous mutations in carrier parents

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Article mentions patients presented with variable bleeding diathesis and Table 1 shows the several phenotypes that were seen among the cohort of 13 patients in this study (this article does not state a specific bleeding phenotype for each proband) "Most of the patients had gross blood loss due to epistaxis (54%), cutaneous bleeding (58%) and menorrhagia (100% of women), while other common symptoms (oral cavity, gastrointestinal, following dental extraction or mild injuries, postpartum, or hematomas) were in general milder."

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry revealed αIIbβ3 expression between 5% and 20%

      PlateletAggregation: Article mentions the disorder was indentified by platelet testing consisting in severely impaired aggregation in response to all physiological agonists and also TMA (See Table 4). Ristocetin-induced platelet aggregation was normal or reduced to some extent.

      CasePreviousTesting: To detect mutations in ITGA2B or ITGB3, total RNA from peripheral blood was used for cDNA synthesis for RT-PCR. Using specific oligonucleotides and conditions, they amplified and sequenced ITGA2B and ITGB3 by Sanger sequencing, and every mutation found in cDNA was confirmed on DNA samples

      Gene: ITGB3

      Variant: NM_000212.2:c.448A>G (p.Met150Val) and NM_000212.2:c.774_775del (p.Cys258Ter)

      LegacyVariant: (p.Met124Val)

      ClinVar: N/A

      CAiD: CA8622961 and CA915940285

      gnomAD: MAF in South Asian population is 0.00003266 http://gnomad.broadinstitute.org/variant/17-45361895-A-G

      PreviouslyPublished PMID: 15583747 (p.Met124Val)

    3. Table 3 Molecular Diagnosis of Patients with Glanzmann Thrombasthenia:

      Case4: GT-4, age, gender, ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia type I

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

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

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry showed that αIIbβ3 expression was less than 5%

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

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

      Gene: ITGB3

      Variant: NM_000212.2:c.569A>G (p.Tyr190Cys)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA400023236

      gnomAD: N/A

    1. F

      Case6: Patient ID F, Female, 16 years old, ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000978,

      (Easy bruising, recurrent epistaxis, gingival bleeding)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0000967, HP:0000979, HP:0004406, HP:0002239, HP:0002239, HP:0000790, HP:0005261, HP:0002248

      (Petechiae, purpura, recurrent epistaxis, GI bleeding, Intracranial hemorrhage, hematuria, hemarthrosis, hematemesis)

      CaseNotHPOsFreeText: Hemorrhage after dental, hemorrhage after trauma, ear bleeding, hematoma

      ProteinExpression: N/A

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

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

      Gene: ITGA2B

      Variant: NM_000419.3:c.1608del (p.Asn536Lysfs*29)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940296

      gnomAD: N/A

    1. Type I thrombasthenic patient, FLD

      Case3: Patient FLD

      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: N/A

      Gene: ITGA2B

      Variant: NM_000419.3:c.818G>A (p.Gly273Asp)

      LegacyVariant: (G242D)

      ClinVar: 2894

      CAiD: CA115837

      gnomAD: N/A

    1. 23CabGT-23

      Case23: (Proband CabGT-23) 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 10% GPIIb and 14% GPIIIa 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.665T>C (p.Leu222Pro)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA291224887

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

    2. 8CabGT-8

      Case8: (Proband CabGT-8) Gender, age and ethnicity were not mentioned (See Supp Table S1) for confirmation of this

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      ProteinExpression: N/A

      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.1672C>T (p.Gln558Ter)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA290949843

      gnomAD N/A

    1. GT-71c

      Case52: (GT-71) Gender, age, or ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Bleeding severity: Information not given (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: ITGA2B

      Variant: NM_000419.3:c.1142C>T (p.Thr381Ile)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399804396

      gnomAD: N/A

    2. GT-33

      Case28: (GT-33) Female, age or ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Proband GT31-GT34 are related

      ParentalGenotype: N/A

      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.2113del (p.Leu705Cysfs*4)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA8623443

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

    3. GT-74

      Case55: (GT-74) Gender, age, or ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Bleeding severity: Information not given (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.985A>G (p.Asn329Asp)

      LegacyVariant: N/A

      ClinVar: 323865

      CAiD: CA8623107

      gnomAD: MAF in Other population 0.0005534 http://gnomad.broadinstitute.org/variant/17-45367092-A-G

    1. GT 48

      Case31: GT48, Male, India, age of onset is 5 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)

    1. Supplementary Tables 1 and 2 combined information:

      Case39: GT39, Male, 25 years old

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Available per Table 1; however, very minimal information

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

      CasePresentingHPOs: HP:0100309 (Subdural hematoma)

      CaseHPOFreeText: Post traumatic hemorrhage

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Showed 50-100% (variant) 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.2570G>T (p.Cys857Phe) and NM_000419.3:c.1769G>A (p.Arg590Gln)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399794409 (p.Cys857Phe) and CA8602943 (p.Arg590Gln)

      gnomAD: MAF for (p.Arg590Gln) in the Latino population 0.0002314 https://gnomad.broadinstitute.org/variant/17-42457166-C-T

    2. Supplementary Tables 1 and 2 combined information:

      Case34: GT34, Male, 3 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: Post traumatic hemorrhage

      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.432G>A (p.Trp144Ter)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399805999

      gnomAD: N/A

    3. Supplementary Tables 1 and 2 combined information:

      Case14: GT14, Female, 5 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.2333A>C

      LegacyVariant: N/A

      ClinVar: 225393

      CAiD: CA290947544

      gnomAD: N/A

    4. Supplementary Tables 1 and 2 combined information:

      Case7: GT7, Female, 31 years old

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Not available per supplementary table 1

      ParentalGenotype: Parents are consanguineous, no other genotype information available

      CasePresentingHPOs: HP:0000978, HP:0000979, HP:0031364, HP:0000421, HP:0000132

      (Bruising, purpura, ecchymosis, epistaxis, menorrhagia)

      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.1652G>A (p.Arg551Gln)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA8602986 (p.Arg551Gln)

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

    5. Supplementary Tables 1 and 2 combined information:

      Case5: GT5, Female, 25 years old; however, now deceased

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Not available per supplementary table 1

      ParentalGenotype: Parents are consanguineous, no other genotype information available

      CasePresentingHPOs: HP:0000132, HP:0000421, HP:0002239, HP:0002170

      (Menorrhagia, epistaxis, gastrointestinal bleeding, intracranial hemorrhage)

      CaseHPOFreeText: Post traumatic hemorrhage

      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) and NM_000419.3:c.2159T>C (p.Leu720Pro)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA115834 (p.Arg584Ter) and CA399798955 (p.Leu720Pro)

      gnomAD: N/A

    6. Supplementary Tables 1 and 2 combined information:

      Case2: GT2, Male, 13 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 <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

    7. Supplementary Tables 1 and 2 combined information:

      Case28: GT28, Female, 6 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, HP:0002239

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

      CaseHPOFreeText: Post traumatic hemorrhage

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Showed 10-20% 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: ITGB3

      Variant: NM_000212.2:c.1728del (p.S577Pfs*92) and NM_000212.2:c.892C>T (p.Gln298Ter)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940253 (p.S577Pfs*92) and CA400025098 (p.Gln298Ter)

      gnomAD: N/A

    1. Case7: Patient CT, 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.1096C>T (p.Arg366Ter)

      LegacyVariant: (p.Arg335Ter)

      ClinVar: N/A

      CAiD: CA399804480

      gnomAD: N/A

    2. Case1: Patient FN, 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: IVS3(-3)418del (Ala106_Gln111del)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: Unregistered

      gnomAD: N/A

    3. Case3: 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 and ITGB3

      Variant: NM_000419.3:c.526C>G (p.Pro176Ala) and NM_000212.2:c.224del ,

      LegacyVariant: (p.Pro145Ala)

      ClinVar: N/A

      CAiD: CA399805793 and CA8622899

      gnomAD: MAF in the European non Fin pop is 0.000008795 for the ITGB3 variant

    1. Supplementary Table S1 & S2 Proband and Variant Information:

      Case33: GT36a, Female, 49 years old, Spanish

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Affected brother who is proband 36b and affected sister who is proband 36c in this study

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000421, HP:0000225

      (Epistaxis, gingival bleeding)

      CaseHPOFreeText: Bleeding at the onset of menses

      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.131G>T (p.Gly44Val) and NM_000419.3:c.1440-13_1440-1de (p.Arg480Serfs*106)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399806881 and CA913184940

      gnomAD: N/A

    2. Supplementary Table S1 & S2 Proband and Variant Information:

      Case26: GT30, Female, age not specified, Caucasian

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Affected brother (See Supplementary Table 1)

      ParentalGenotype: N/A

      CasePresentingHPOs:

      (Epistaxis, GI bleeding)

      CaseHPOFreeText: Diffuse bruising mainly with trauma

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry showed 5-10% 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.777+1G>A

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA8623036

      gnomAD: MAF in the Latino population is 0.0006774 http://gnomad.broadinstitute.org/variant/17-45363789-G-A

    3. Supplementary Table S1 & S2 Proband and Variant Information:

      Case55: GT55, Female, 28, Argentinian/Brazilian

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Has an affected sister (this is all the information we are provided with)

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000225, HP:0000421

      (Gingival bleeding, epistaxis)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry showed 11-22% 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.647C>T (p.Ala216Val)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399805506

      gnomAD: N/A

    4. Supplementary Table S1 & S2 Proband and Variant Information:

      Case35: GT36c, Female, 47 years old, Spanish

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Affected sister who is proband 36 a and affected brother proband 36b

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000132, HP:0011891

      (Menorrhagia, post-partum hemorrhage)

      CaseHPOFreeText: Intra-abdominal hemorrhage and bleeding after trauma

      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.131G>T (p.Gly44Val) and NM_000419.3:c.1440-13_1440-1de (p.Arg480Serfs*106)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399806881 and CA913184940

      gnomAD: N/A

    5. Supplementary Table S1 & S2 Proband and Variant Information:

      Case7: GT8, Male, 82 at death, French

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000978, HP:0000421, HP:0002239

      (Easy bruising, epistaxis, GI bleeding

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry showed 10-15% 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.2348+5G>C (p.Ser756Gly783delInsArg)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA290947484

      gnomAD: N/A

    6. Supplementary Table S1 & S2 Proband and Variant Information:

      Case47: GT47, Male, 11 years old, French

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Severe mucocutaneous 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: ITGA2B

      Variant: NM_000419.3:c.832del (p.Asp278Ilefs*101)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940374

      gnomAD: N/A

    7. Supplementary Table S1 & S2 Proband and Variant Information:

      Case12: GT13, Female, 14, French

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000967 (Petechiae)

      CaseHPOFreeText: Moderate bleeding syndrome

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry showed <5% variant 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.682C>T (p.Gln228Ter) and NM_000419.3:c.1750C>T (p.Arg584Ter)

      LegacyVariant: N/A

      ClinVar: 2892

      CAiD: CA399805421 and CA115834

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

    1. 22

      Case22: Female, Arab, age not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Table 1 mentions family history available for the proband, however no specific details about family provided in paper

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000421, HP:0000225, HP:0031364, HP:0000132)

      (Epistaxis, gingival bleeding, ecchymosis, 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.409-2_419del

      LegacyVariant: N/A

      ClinVar: 2889

      CAiD: CA10575471

      gnomAD: N/A

    2. 11

      Case11: Female, Iraq, age not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Table 1 mentions family history available for the proband, however no specific details about family provided in paper

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000421, HP:0000225, HP:0000132, HP:0031364, HP:0002249

      (Epistaxis, gingival bleeding, menorrhagia, ecchymosis, melena)

      CaseHPOFreeText: Colon angiodysplasia, retroperitoneal, haematuria, haemarthrosis

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: N/A

      PlateletAggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGB3

      Variant: NM_000212.2:c.2031_2041del (p.Asp677Glufs)

      LegacyVariant: (p.Asp651Glufs*3)

      ClinVar: N/A

      CAiD: CA915940605

      gnomAD: N/A

    3. 1

      Case1: Male, Iraq, age not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Table 1 mentions family history available for the proband, however no specific details about family provided in paper

      ParentalGenotype: N/A

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

      (Epistaxis, gingival bleeding, ecchymosis)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: N/A

      PlateletAggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGB3

      Variant: NM_000212.2:c.2031_2041del (p.Asp677Glufs)

      LegacyVariant: (p.Asp651Glufs*3)

      ClinVar: N/A

      CAiD: CA915940605

      gnomAD: N/A

    4. 4

      Case4: Male, Iraq, age not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Table 1 mentions family history available for the proband, however no specific details about family provided in paper

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000421, HP:0002105, HP:0031364

      (Epistaxis, hemoptysis, ecchymosis)

      CaseHPOFreeText: Intracranial at birth, haematemesis, haematuria

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: N/A

      PlateletAggregation:

      CasePreviousTesting: N/A

      Gene: ITGA2B

      Variant: NM_000419.3:c.2473_2478delinsTCACCAGGGCCTTCACCTCAGCATCCACC

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940595

      gnomAD: N/A

      PreviouslyPublished: 7529063

    1. Supplementary Table S1:

      Case19: GT22, 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: NM_000419.3:c.408+11C>A and NM_000419.3:c.1259T>C (p.Va;420Ala)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940333 and CA399803733

      gnomAD: N/A

    2. Supplementary Table S1:

      Case36: GT42, Canadian/Egypt, 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: NM_000419.3:c.2148dup (p.Leu717AlafsTer3)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940304

      gnomAD: N/A

    3. Supplementary Table S1:

      Case42: GT49, French/Spanish, 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: NM_000419.3:c.1440-13_1440-1del (p.Arg480SerfsTer106) and NM_000419.3:c.2113T>C (p.Cys705Arg)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA913184940 and CA8602816

      gnomAD: MAF in the European (non-Finnish) population is 0.000008792 https://gnomad.broadinstitute.org/variant/17-42455140-A-G for the (p.Cys705Arg) variant

    4. Supplementary Table S1:

      Case45: GT53, Argentina/Brazil, 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: ITGB3

      Variant: NM_000212.2:c.356G>A (p.Arg119Gln) and NM_000212.2:c.1697G>A (p.Gly566Asp)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA8622925 and CA400032338

      gnomAD: MAF in the African population is 0.0002470 https://gnomad.broadinstitute.org/variant/17-45360910-G-A

    5. Supplementary Table S1:

      Case24: GT27, French, gender and age were not specified here

      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.1413C>G (p.Tyr471Ter) and NM_000419.3:c.2468G>A (p.Gly823Glu)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA290950376 and CA399795351

      gnomAD: MAF in the European (non-Finnish) population is 0.000008791 for (p.Tyr471Ter) MAF in the African population is 0.000 for p.Gly823Glu) https://gnomad.broadinstitute.org/variant/17-42453334-C-T

    6. Supplementary Table S1:

      Case31: GT38, Sweden/USA, 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: ITGB3

      Variant: NM_000212.2:c.79+1G>A and NM_000212.2:c.940-2A>G

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA400028478 and CA400025605

      gnomAD: N/A

    1. GT17

      Case#: 6 year old, male

      Disease: Glazmann's Thrombasthenia

      CasePresentingHPOs: HP:0000967, HP:0000978, HP:0004406, HP:0000225, HP:0006298, HP:0001892, HP:0002239

      PlateletAgreggation: Defective response to ADP, Adrenaline, Collagen, Arachidonic acid. Normal response to Ristocetin.

      GenotypingMethod: Genomic DNA was extracted from peripheral blood leukocytes for mutational analysis of the αIIb and β3 genes by DNA sequencing

      ClinVar: 2892

      CAID: CA115834

      Variant: NM_000419.5:c.1750C>T

      GnomAD: East Asian Population 0.0002176 (4/18386)

      ExpressionEvidence: Flow Cytometry of platelet integrin: .24% B3 expression, .18% A2B expression

    2. GT3

      Case#: 6 year old female

      Disease: Glazmann's Thrombasthenia

      CasePresentingHPOs: HP:0000967, HP:0000978, HP:0004406, HP:0000225, HP:0006298, HP:0001892

      Petechiae, Bruising susceptibility, Spontaneous, recurrent epistaxis, Gingival bleeding, Prolonged bleeding after dental extraction, Abnormal bleeding

      PlateletAgreggation: Defective response to ADP, Adrenaline, Collagen, Arachidonic acid. Normal response to Ristocetin.

      GenotypingMethod: Genomic DNA was extracted from peripheral blood leukocytes for mutational analysis of the αIIb and β3 genes by DNA sequencing

      Allele 1:

      ClinVar:1330340

      CAID:CA400021329

      Variant: NM_000212.3:c.361+1G>A

      GnomAD: Not Found

      Allele 2

      ClinVar: 1330351

      CAID: CA400030376

      Variant: NM_000212.3:c.1690G>C

      GnomAD: Not Found

      ExpressionEvidence:Flow Cytometry of platelet integrin: .61% B3 expression, 50% A2B expression

    3. GT16

      Case#: 6 year old, male

      Disease: Glazmann's Thrombasthenia

      CasePresentingHPOs: HP:0000967, HP:0000978, HP:0004406, HP:0006298, HP:0001892

      PlateletAgreggation: Defective response to ADP, Adrenaline, Collagen, Arachidonic acid. Normal response to Ristocetin.

      GenotypingMethod: Genomic DNA was extracted from peripheral blood leukocytes for mutational analysis of the αIIb and β3 genes by DNA sequencing

      Allele 1:

      ClinVar: 953019

      CAID: CA8602528

      Variant: NM_000419.5:c.2929C>T

      GnomAD: South Asia at rate of 0.00003266 (1/30616)

      Allele 2:

      ClinVar: 1330319

      CAID:CA923726222

      Variant: NM_000419.5:c.2444_2445del

      GnomAD:Not found

      ExpressionEvidence: Flow Cytometry of platelet integrin: 11.7% B3 expression, .1% A2B expression

    1. 3.Adult woman/Algeria

      Case2: (Patient 3) Female (adult), age not specified, Algeria

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Severe bleeding when she was a child

      CaseNotHPOs: N/A

      ProteinExpression: Absent surface expression of alphaIIbbeta3

      Platelet Aggregation: Absent platelet aggregation (this is all they mentioned)

      CasePreviousTesting: N/A

      Gene: ITGA2B

      Variant: NM_000419.3:c.1063G>A (p.Glu355Lys)

      LegacyVariant: (p.Glu324Lys)

      ClinVar: 2899

      CAiD: CA115844

      gnomAD MAF in the European (non-Finnish) population is 0.00001978 https://gnomad.broadinstitute.org/variant/17-42461008-C-T

      PreviouslyPublished: PMID: 12362239 and 23346430

    2. Elderly man/France

      Case4: Male (elderly), age not specified, France

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      ProteinExpression: N/A

      Platelet Aggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGA2B

      Variant: NM_000419.3:c.2348+5G>C

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA290947484

      gnomAD N/A

      PreviouslyPublished: 25728920

    3. 1.Adult woman/France

      Case1: (Patient 1) Woman (adult), age not specific, France

      DiseaseAssertion: Glanzmann thrombasthenia (also have undergone deep vein thrombosis)

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Moderate bleeding according to Table 1

      CaseNotHPOs: N/A

      ProteinExpression: Trace amounts of residual alphaIIbbeta3 (this is all that was mentioned)

      Platelet Aggregation: Absent platelet aggregation (this is all that was mentioned)

      CasePreviousTesting: N/A

      Gene: ITGB3

      Variant: NM_000212.2:c.1448G>A (p.Cys483Tyr)

      LegacyVariant: (p.Cys457Tyr)

      ClinVar: N/A

      CAiD: CA400029324

      gnomAD N/A

      PreviouslyPublished: 12152649 and 21848888

    1. Sustained engraftment and resolution of bleeding phenotype after unrelated cord blood hematopoietic stem cell transplantation for severe glanzmann thrombasthenia.

      PMID: 19648793

      Genes: ITGA2B and/or ITBG3

      HGNC: 6138 and 6156

      InsufficientEvidence: This article mentions an individual with GT; however, there is no mention of variants in ITGA2B and/or ITGB3 therefore we have insufficient evidence

    1. 59-year-old Japanese man

      Case1: Male, 59 years old, Japanese

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0002239, HP:0025085

      (GI bleeding, bloody stools)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry showed expression of αIIbβ3 on patient platelets was <5% compared to that of normal controls indicating the patient had Type 1 GT

      PlateletAggregation: Transfused platelets showed normal response to ADP stimulation (See Fig. 3B) indicating that transfused platelets can support primary hemostatic plug formation

      CasePreviousTesting: Analyzed whole coding region of αIIb and β3 cDNA, amplified from patient mRNA.

      Gene: ITGB3

      Variant: NM_000212.2:c.892C>T

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA400025098

      gnomAD: N/A

    1. Patient ID 8

      Case#: Patient ID 8, Female, Korean

      Disease: Glazmann's Thrombasthenia

      CasePresentingHPOs: HP:0000967, HP:0000978, HP:0003010

      Bruising susceptibility, Petechiae, Prolonged bleeding time

      PlateletAgreggation: Impaired response to ADP and Epi.

      GenotypingMethod: Targeted Exome sequencing followed by Whole exome sequencing performed. Sanger Sequencing used to confirm pathogenic variants

      Allele 1:

      ClinVar:Not Found

      CAID: CA399804316

      Variant: NM_000419.5:c.1184G>T

      GnomAD: Not Found

      Allele 2

      ClinVar: 2892

      CAID:CA115834

      Variant: NM_000419.5:c.1750C>T

      GnomAD: East Asian population at rate of 0.0002176 (4/18386)

      ExpressionEvidence: Decreased CD41 expression by flow cytometry

    1. 8 mon/M

      Case#: Patient ID 1, Male 8 months. North Indian

      Disease: Glazmann's Thrombasthenia

      CasePresentingHPOs: HP:0031364, HP:0003540

      Ecchymosis, Impaired platelet aggregation

      PlateletAgreggation: LTA with ADP, Epi, Coll, AA, and Ristocetin: Impaired with all except Ristocetin.

      GenotypingMethod: Next generation sequencing. Sanger sequencing used to confirm pathogenic variants

      Allele 1:

      ClinVar: 627093

      CAID: CA626224613

      Variant: NM_000419.5:c.559del

      GnomAD: South Asian at rate of 0.00003507 (1/28512)

      ExpressionEvidence: No flow cytometry

    2. 13/F

      Case#: Patient ID 2, Female 13 years old. North Indian

      Disease: Glazmann's Thrombasthenia

      CasePresentingHPOs: HP:0031364, HP:0003540, HP:0000421, HP:0002239, HP:0000132

      Ecchymosis, Impaired platelet aggregation, Epistaxis, Gastrointestinal hemorrhage, Menorrhagia

      PlateletAgreggation: LTA with ADP, Epi, Coll, AA, and Ristocetin: Impaired with all agonists

      GenotypingMethod: Next generation sequencing. Sanger sequencing used to confirm pathogenic variants

      ClinVar: 953042

      CAID: CA399804619

      Variant: NM_000419.5:c.1028T>C

      GnomAD: Not Found

      ExpressionEvidence: Flow Cytometry for platelet expression of GPIIb/IIIa in CD41a 4.9% and CD61 96%.

    3. 11/F

      Case#: Patient ID 4, Female 11 years old. North Indian

      Disease: Glazmann's Thrombasthenia

      CasePresentingHPOs: HP:0031364, HP:0003540, HP:0000421, HP:0000225

      Ecchymosis, Impaired platelet aggregation, Epistaxis, Gingival bleeding

      PlateletAgreggation: LTA with ADP, Epi, Coll, AA, and Ristocetin: Impaired with all & aggregation–disaggregation pattern with Ristocetin

      GenotypingMethod: Next generation sequencing. Sanger sequencing used to confirm pathogenic variants

      FamilyInfo:Father heterozygous c.1186G > A variant; d Mother carrier for c.3092delT variant

      Allele 1:

      ClinVar: 627218

      CAID: CA399804315

      Variant:NM_000419.5:c.1186G>A

      GnomAD:South Asian at rate of 0.00006622 (2/30202)

      Allele 2:

      ClinVar:1691488

      CAID: CA915940323

      Variant: NM_000419.5:c.3092del

      GnomAD: NA

      ExpressionEvidence: Flow Cytometry for platelet expression of GPIIb/IIIa in CD41a 0% and CD61 15%.

    1. P2

      Case2: P2, 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 (4% in patient 2)

      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.91del (p.Ala31ProsfsX2)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA913203486

      gnomAD: N/A

  2. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    1. Further Characterization of the Thrombasthenia-related Idiotype OG. Antiidiotype Defines a Novel Epitope(s) Shared by Fibrinogen BE Chain, Vitronectin, and yon Willebrand Factor and Required for Binding to/33

      PMID: 7525851

      Gene: ITGA2B and/or ITGB3

      HGNC: 6138 and 6156

      InsufficientEvidence: This article mentions a GT proband; however, no variants in ITGA2B and/or ITGB3 are mentioned therefore there is insufficient evidence

    1. Case2: Female, 65 years old, Iraqi-Jewish origin

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: Her brother is the other proband in this article

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000225, HP:0000225, HP:0031364, HP:0002249

      (Gingival bleeding, epistaxis, ecchymosis, melena)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      ProteinExpression: Surface expression GPIIb/IIIa was 11% of normal

      PlateletAggregation: Platelet aggregation in response to thrombin, collagen, ADP and epinephrine was absent, whereas ristocetin induced aggregation was normal

      CasePreviousTesting: DNA fragments containing exons and flanking intronic regions of the GPIIb gene were amplified by PCR

      Gene: ITGA2B

      Variant: NM_000419.3:c.1947-2A>G

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399801096

      gnomAD: N/A

    1. A 52-year-old male patient

      Case1: Male, 52 years old, ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: One of the patient’s daughters carried the c.2437C>A mutation. The other daughter carried the c.1771_1772insG along with c.339C>G mutation, indicating that these mutations are on the same allele.

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Recurrent hemorrhagic symptoms, bleeding time >20 minutes and PFA-100 closure times were > 300 seconds

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      ProteinExpression: Flow cytometric analysis showed a clearly detectable but strongly reduced amount of surface expressed GPIIb and GPIIIa

      PlateletAggregation: Platelets failed to aggregate in response to ADP, arachidonic acid, epinephrine, and collagen.

      CasePreviousTesting: Sequencing of exons of GPIIb gene was performed

      Gene: ITGA2B

      Variant: NM_000419.3:c.1771dup (p.Asp560GlyfsX16), NM_000419.3:c.2437C>A (p.His782Asn)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940334, CA399795907, CA500624465

      gnomAD: N/A

    1. M/31

      Case8: Male, 31 years old, Tamil Nadu India

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000421, HP:0031364, HP:0000967, HP:0000225, HP:0006298

      (Epistaxis, ecchymosis, petechiae, gingival bleeding, prolonged bleeding after tooth extraction

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: See Table 1 for values

      PlateletAggregation: See Table 1 for values

      CasePreviousTesting: PCR amplification of ITAG2B and ITGB3

      Gene: ITGA2B

      Variant: NM_000419.3:c.2236G>T (p.Glu746Ter)

      LegacyVariant: (p.Glu715Ter)

      ClinVar: N/A

      CAiD: CA399798321

      gnomAD: N/A

    2. F/16

      Case11: Female, 16 years old, Tamil Nadu India

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000225, HP:0006298, HP:0031364

      (Gingival bleeding, prolonged bleeding after dental extraction, ecchymosis)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: See Table 1 for values

      PlateletAggregation: See Table 1 for values

      CasePreviousTesting: PCR amplification of ITAG2B and ITGB3

      Gene: ITGB3

      Variant: NM_000212.2:c.1801T>G (p.Cys601Gly)

      LegacyVariant: (p.Cys575Gly)

      ClinVar: N/A

      CAiD: CA400032570

      gnomAD: N/A

    1. patient 8.

      Case4: Patient 8, Female, 21 years old

      DiseaseAssertion: Glanzmann thrombasthenia type I (Diagnosed at 5 months 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: ITGB3

      Variant: NM_000212.2:c.1986dup (p.Asp663Ter)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940608

      gnomAD: N/A

    1. GT24

      Case15: (GT24) Gender, age and ethnicity 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: ITGB3

      Variant: NM_000212.2:c.953T>C (p.Leu318Ser)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA400025639

      gnomAD MAF in the European Finnish population is 0.00004620 https://gnomad.broadinstitute.org/variant/17-45367060-T-C

  3. pdfs.semanticscholar.org pdfs.semanticscholar.org
    1. A 9-year old female

      Case1: Female, 9 years old, Indian

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: Article mentions parents have the variant (at end of article); however, no details are provided

      CasePresentingHPOs: HP:0000225, HP:0000421

      (Gingival bleeding, recurrent epistaxis)

      CaseHPOFreeText: Prolonged bleeding from cuts

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Flow cytometry showed the presence of normal levels of GPIIb, GPIIIa, GPIIb-IIIa and GPIb-IX on the patients platelet surface

      PlateletAggregation: In spite of the normal levels of GPIIb-IIIa and normal fibrinogen binding the platelets showed complete absence of aggregation in response to ADP (6 mM) and collagen (4 mg/mL).

      CasePreviousTesting: Denaturing gradient gel electrophoresis analysis and DNA sequencing were done to detect abnormalities. DNA sequencing of exon 3 o ITGB3 was performed

      Gene: ITGB3

      Variant: M_000212.2:c.445T>C (p.Ser149Pro)

      LegacyVariant: (p.Ser123Pro)

      ClinVar: N/A

      CAiD: CA400021997

      gnomAD: N/A

    1. 9LMIHomozygote1346G

      Case9: Patient LM (can be found in the GT database) gender and age are not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A Not reported for this proband

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Undetectable for this patient

      PlateletAggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGA2B

      Variant: NM_000419.3:c.1346G>A (p.Gly449Asp)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399803552

      gnomAD: N/A

      PreviouslyPublished: Reference number 20 in this article

    2. AP

      Case22: Patient AP, gender and age are not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000421, HP:0000225, HP:0006298

      (Epistaxis, gingival bleeding, prolonged bleeding after tooth extraction)

      CaseHPOFreeText: Hematoma

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: 12-20% GPIIIa and GPIIb surface expression

      PlateletAggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGA2B

      Variant: NM_000419.3:c.3077G>A (p.Arg1026Gln) other mutation was not found

      LegacyVariant: N/A

      ClinVar: 50232

      CAiD: CA10575572

      gnomAD: MAF in the European (non-Finnish) population is 0.000008801 https://gnomad.broadinstitute.org/variant/17-42449775-C-T

      PreviouslyPublished: References 37 and 38

    3. Gypsy

      Case11: Patient Gypsy (found in the GT database)

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Blood transfusions required

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Decreased surface expression of GPIIIa and GPIIb

      PlateletAggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGA2B

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

      LegacyVariant: N/A

      ClinVar: 2895

      CAiD: CA10575473

      gnomAD: N/A

      PreviouslyPublished: Reference number 22 in this article

    4. I-J21

      Case39: Patient IJ13

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000979 Purpura

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: <2% GPIIIa and GPIIb expression

      PlateletAggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGB3

      Variant: NM_000212.2:c.2031_2041del and another variant

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940605

      gnomAD: N/A

      PreviouslyPublished: Reference 62

    1. GT9

      Case9: GT-9, Caucasian, gender or age not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: Mother: c.1186G>A heterozygous and Father: c.3060_2T>C heterozygous

      CasePresentingHPOs: N/A

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

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

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

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

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

      Gene: ITGA2B

      Variant: NM_000419.3:c.1186G>A and NM_000419.3:c.3060+2T>C

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399804315 and CA290944108

      gnomAD: MAF in the South Asian population is 0.00006622 http://gnomad.broadinstitute.org/variant/17-42460885-C-T and MAF in the European non-Finnish population is 0.00003876 http://gnomad.broadinstitute.org/variant/17-42451720-A-G

    2. GT11

      Case11: GT-11, Arab, gender or age not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: Mother: c.3092delT heterozygous and Father: deceased

      CasePresentingHPOs: N/A

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

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

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

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

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

      Gene: ITGA2B

      Variant: NM_000419.3:c.641T>C and NM_000419.3:c.3092delT

      LegacyVariant: N/A

      ClinVar: 2901

      CAiD: CA115848 and CA915940323

      gnomAD: N/A

    1. M6

      Case6: Patient M6, 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

    1. Study of the Relationship between HPA-1 and HPA-5 Gene Polymorphisms and Refractory to Platelet Therapy and Recombinant Factor VII in Glanzmann Thrombasthenia Patients in Southeast of Iran

      PMID: 29951177

      Gene: ITGA2B and ITGB3

      HGNC: 6138 and 6156

      InsufficientEvidence: Article mentions Glanzmann thrombasthenia probands; however, no variants associated with patients therefore insufficient evidence

    1. 20-yr-old man

      Case#: Male, 20

      DiseaseAssertion: Glanzmann thrombasthenia–like syndrome

      FamilyInfo: Twin brother (shares variant), Mother, Figure 1B

      ParentalGenotype: Maternal inheritence, diagnosed GTLS

      CasePresentingHPOs: thrombocytopenia (HP:0001873), Platelet anisocytosis (HP:0032438), (HP:0003645) activated partial thromboplastin times, (HP:0000967) petechia

      PlateletAggregation: Thrombocytopenia (51×109/L, reference interval (RI): 150–450×109/L), Serum antiplatelet antibody test was negative. Platelet macrocytosis.

      CaseHPOFreeText: Occasional petechia noted. Platelet macrocytosis.

      CaseNotHPOs: (HP:0012200) prothrombin, (HP:0001892) abnormal bleeding

      CaseNotHPOFreeText: Platlets in Figure 1A. No thrombotic symptoms.

      ProteinExpression: this mutation entails the substitution of the hydrophobic leucine with a hydrophilic arginine. This charge reversal in the TMD of β3 may potentially impact helix conformation, integrin assembly, and signaling pathways.Platelet aggregation was severely diminished in response to adenosine 5′-diphosphate, collagen, arachidonic acid, and epinephrine, but not ristocetin, Figure 1E. Flow cytometry showed slightly increased CD41a expression, probably because of increased platelet size, Figure 1F.

      CasePreviousTesting: Exome sequencing via TruSight One expanded panel (Illumina), whole-genome sequencing via the Korean National Project of Bio Big Data, Maternal inheritance was confirmed via Sanger sequencing analysis.

      PreviouslyPublished: NA

      Gene: ITGB3

      Variant: NM_000212.3: c.2192T>G, [NP_000203.2:p.Leu731Arg]

      HGVS: NM_000212.3:c.2192T>G (ITGB3)

      ClinVar: Absent

      CAID: CA400034083

      gnomAD: Absent

    1. Glanzmann thrombasthenia and Bernard–Souliersyndrome in south Iran

      PMID: 16178914

      Gene: ITGA2B and/or ITGB3

      HGNC: 6138 and 6156

      InsufficientEvidence: This article mentions various probands with GT; however, there are no mentioned variants in ITGA2B and/or ITGB3, therefore, we have insufficient evidence

    1. 14

      Case12: No assertion made on age, gender or ethnicity

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: The identified variants were heterozygote in parents.

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: N/A

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

      Gene: ITGA2B

      Variant: NM_000419.3:c.1071dup (p.Arg358AlafsTer47)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940225

      gnomAD: N/A

    1. WC

      Case10: Patient WC, gender, age and ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia type I

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Bleeding symptoms were evaluated by examining available hospital records. Mild bleeders were defined as those who had minor symptoms, such as epistaxis or gum bleeds, and moderate bleeders suffered, in addition, from bleeding complications after surgery and trauma. 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 transfusion. See Table 1.

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: See Table 6

      PlateletAggregation: See Table 6

      CasePreviousTesting: To ascertain the mutations, we sequenced the coding regions of the αIIb and β3 subunits including the exon/intron boundaries

      Gene: ITGA2B

      Variant: c.2232Gins (Noting this as an Unknown Variant as this won't show up in CAR-- I am sure there is a way to retrieve the CAiD; however, will need to discuss with senior biorcurator)

      LegacyVariant: ^

      ClinVar: ^

      CAiD: ^

      gnomAD: ^

    2. SB

      Case19: Patient SB, gender, age and ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia type I

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Bleeding symptoms were evaluated by examining available hospital records. Mild bleeders were defined as those who had minor symptoms, such as epistaxis or gum bleeds, and moderate bleeders suffered, in addition, from bleeding complications after surgery and trauma. 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 transfusion. See Table 1.

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: See Table 6

      PlateletAggregation: See Table 6

      CasePreviousTesting: To ascertain the mutations, we sequenced the coding regions of the αIIb and β3 subunits including the exon/intron boundaries

      Gene: ITGA2B

      Variant: NM_000419.3:c.3062T>C

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA399787956

      gnomAD: N/A

    3. PJ

      Case23: Patient PJ, gender, age and ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia type I

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Bleeding symptoms were evaluated by examining available hospital records. Mild bleeders were defined as those who had minor symptoms, such as epistaxis or gum bleeds, and moderate bleeders suffered, in addition, from bleeding complications after surgery and trauma. 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 transfusion. See Table 1.

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: See Table 6

      PlateletAggregation: See Table 6

      CasePreviousTesting: To ascertain the mutations, we sequenced the coding regions of the αIIb and β3 subunits including the exon/intron boundaries

      Gene: ITGA2B

      Variant: NM_000212.2:c.2068_2069delGT

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA913012619

      gnomAD: N/A

    4. GI

      Case21: Patient GI, gender, age and ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia type I

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Bleeding symptoms were evaluated by examining available hospital records. Mild bleeders were defined as those who had minor symptoms, such as epistaxis or gum bleeds, and moderate bleeders suffered, in addition, from bleeding complications after surgery and trauma. 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 transfusion. See Table 1.

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: See Table 6

      PlateletAggregation: See Table 6

      CasePreviousTesting: To ascertain the mutations, we sequenced the coding regions of the αIIb and β3 subunits including the exon/intron boundaries

      Gene: ITGB3

      Variant: NM_000212.2:c.1129dup

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA915940291

      gnomAD: N/A

    5. HM

      Case5: Patient HM, gender, age and ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia type I

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Bleeding symptoms were evaluated by examining available hospital records. Mild bleeders were defined as those who had minor symptoms, such as epistaxis or gum bleeds, and moderate bleeders suffered, in addition, from bleeding complications after surgery and trauma. 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 transfusion. See Table 1.

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: See Table 6

      PlateletAggregation: See Table 6

      CasePreviousTesting: To ascertain the mutations, we sequenced the coding regions of the αIIb and β3 subunits including the exon/intron boundaries

      Gene: ITGA2B

      Variant: NM_000419.3:c.1878G>C

      LegacyVariant: N/A

      ClinVar: 2903

      CAiD: CA115852

      gnomAD: N/A

  4. watermark.silverchair.com watermark.silverchair.com
    1. F4P1

      Case4: Patient F4P1, Male, 43 years old, Tunisian

      DiseaseAssertion: Glanzmann thrombasthenia type I

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

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0004406 (Recurrent epsitaxis)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: N/A

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

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

      Gene: ITGA2B and ITGB3

      Variant: ITGA2B variants: g.13378A>C, g.14856C>A, g.19021C>T (I am denoting this as Unknown Variants as I need guidance with these-- biocurator curating this paper can also look them up- but I am noting them here) and ITGB3 variants: NM_000212.2:c.176T>C (p.Leu59Pro) and NM_000212.2:c.1143A>C (p.Val381Val) and NM_000212.2:c.1545G>A (p.Arg515Arg)

      LegacyVariant: N/A

      ClinVar: 13558 (p.Leu59Pro), 255535 (p.Val381Val), 255537 (p.Arg515Arg)

      CAiD: CA123235 (p.Leu59Pro), CA8623175 (p.Val381Val), CA8623284 (p.Arg515Arg)

      gnomAD: MAF in the Ashkenazi Jewish population is 0.1565 https://gnomad.broadinstitute.org/variant/17-45360730-T-C for (p.Leu59Pro) and MAF in the East Asian population is 0.5857 https://gnomad.broadinstitute.org/variant/17-45368337-A-C for (p.Val381Val) and MAF in the East Asian population for (p.Arg515Arg) is 0.3455 https://gnomad.broadinstitute.org/variant/17-45369789-G-A

    1. Open aortic valve replacement in a patient with Glanzmann’sthrombasthenia: a multidisciplinary strategy to minimizeperioperative bleeding

      PMID: 23710629

      Genes: ITGA2B and/or ITGB3

      HGNC: 6138 and 6156

      InsufficientEvidence: Mention of proband with Glanzmann thrombasthenia however no variants in the proband are mentioned for ITGA2B and ITGB3

    1. Patient 2

      Case2: Patient 2, diagnosed at 5 years, gender and ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: HP:0000421, HP:0000225, HP:0000790

      (Epistaxis, gingival bleeding, hematuria)

      CaseHPOFreeText: Reduced clot retraction

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Immunoblot analysis of platelet lysates showed no detectable pro-αIIb or mature αIIb in any of the patient samples. Trace amounts of Beta3 were detected in samples from this patient

      PlateletAggregation: Absent in vitro platelet aggregation in response to ADP, epinephrine and collagen but a normal initial phase response to ristocetin

      CasePreviousTesting: Polymerase chain reaction (PCR), single strand conformation polymorphism (SSCP) analysis, and DNA sequencing was performed for ITGA2B

      Gene: ITGA2B

      Variant: NM_000419.3:c.953C>G (p.Ser318Leu)

      LegacyVariant: p.Ser287Leu

      ClinVar: N/A

      CAiD: CA399804788

      gnomAD: N/A

    1. An αIIb mutation in patients with Glanzmann thrombasthenia located in the N‐terminus of blade 1 of the β‐propeller (Asn2Asp) disrupts a calcium binding site in blade 6

      PMID: 21029361

      Gene: ITGA2B

      HGNC: 6138

      Note: Although article mention 4 probands being studied, the caption under Fig 1 with the pedigree states, "Shown are three of the four homozygous patients (lanes 2, 4 and 6), heterozygotes" therefore the 4th proband is not mentioned

    1. Identificationofafunctionallyimportantsequenceinthecytoplasmictailofintegrinf33byusingcell-permeablepeptideanalogs

      PMID: 8876221

      Gene: ITGB3

      HGNC: 6156

      InsufficientEvidence: This article mentions variants in ITGB3; however, there are no Glanzmann thrombasthenia patients mentioned harboring these variants; therefore, there is insufficient evidence

    1. 3 patients with Glanzmann thrombasthenia

      Case#: patient 1

      DiseaseAssertion: Glanzmann thrombasthenia

      **FamilyInfo: **

      ParentalGenotype: If noted by authors, annotate with the carrier status of each parent in regards to the variant(s) identified in the proband.

      CasePresentingHPOs:

      PlateletAggregation: absent platelet integrin αIIbβ3. Monolayer of spread platelets essentially devoid of fibrinogen binding but with high CD62P expression and phosphatidylserine exposure (Figure S1). Figure 5.

      CaseHPOFreeText:

      CaseNotHPOs:

      **CaseNotHPOFreeText: **

      ProteinExpression:

      CasePreviousTesting:

      **PreviouslyPublished: **

      Gene: ITGA2B

      **HGVS: ** NM_000419.4:c.2943G>A

      **ClinVar: **

      CAID: CA500262444

      **gnomAD: **

    1. Labeling of the Internal Pool of GP IIb-IIIa in Platelets by c7E3 Fab Fragments (abciximab): Flow and Endocytic Mechanisms Contribute to the Transport

      PMID: 10029591

      Gene: ITGA2B and/or ITGB3

      HGNC: 6138 and 6156

      InsufficientEvidence: This article mentions a case report of a GT patient in another article; however, this article does not specifically mention any GT case reports

      PreviouslyPublished: PMID: 2180491 and PMID:

    1. M3

      Case11: (M3) Female, 12 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

    2. M12

      Case20: (M12) Female, 39 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

    1. Supplemental Table S1:

      Cases38and39: Females, Italy, age not specified

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Moderate bleeding

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: <5% αIIbβ3 expression

      PlateletAggregation: Absent platelet aggregation (all the information that is provided in Supp. Table S1)

      CasePreviousTesting: Sanger sequencing of exons, splice sites and untranslated regions of the ITGA2B and ITGB3 genes was performed

      Gene: ITGA2B

      Variant: NM_000419.3:c.2254C>G (p.Leu752Val) and NM_000419.3:c.2264G>C (p.Arg755Pro)

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: CA8602773 and CA8602772

      gnomAD: MAF in the European non Finnish population is 0.00001032 https://gnomad.broadinstitute.org/variant/17-42454390-G-C and MAF in the European non Finnish population is 0.00001060 https://gnomad.broadinstitute.org/variant/17-42454380-C-G

      PreviouslyPublished: PMID: 12083483

  5. www.ncbi.nlm.nih.gov www.ncbi.nlm.nih.gov
    1. Integrin-Dependent Phosphorylation and Activation of the Protein Tyrosine Kinase pp125 FAr in Platelets

      PMID: 1385445

      Gene: ITGA2B and ITGB3

      HGNC: 6138 and 6156

      NoEvidence: This article does not mention Glanzmann thrombasthenia patients with variants in ITGA2B and/or ITGB3; therefore, there is no evidence to report

    1. A 33-year-old woman

      Case1: Female, 33 years old, ethnicity not specified

      DiseaseAssertion: Glanzmann thrombasthenia type I

      FamilyInfo: Fetus was heterozygous for this mutation

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: The GPIIb–IIIa complex was not detectable on the platelets’ surface

      PlateletAggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGA2B

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

      LegacyVariant: N/A

      ClinVar: 2895

      CAiD: CA10575473

      gnomAD: N/A

    1. An example fromour work is a patient

      Case1: Gender, age, 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: Patient had less than 20% of the normal surface expression of αIIbβ3

      PlateletAggregation: N/A

      CasePreviousTesting: N/A

      Gene: ITGA2B

      Variant: NM_000419.3:c.3077G>A (p.Arg1026Gln)

      LegacyVariant: N/A

      ClinVar: 50232

      CAiD: CA10575572

      gnomAD: MAF in the European (non-Finnish) population is 0.000008801http://gnomad.broadinstitute.org/variant/17-42449775-C-T

      PreviouslyPublished: PMID: N/A Title: Expanding the Mutation Spectrum affecting αIIbβ3 integrin in Glanzmann Thrombasthenia: Screening of the ITGA2B and ITGB3 genes in a Large International Cohort

    1. HMJ

      Case1: Patient HMJ

      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

    1. Human endoglin as a potential new partner involved in platelet–endothelium interactions

      PMID: 29080903

      Gene: ITGA2B and ITGB3

      HGNC: 6138 and 6156

      NoEvidence: No mention of patients with Glanzmann thrombasthenia or variants in probands. This article is about endoglin, an adhesion molecule involved in the interaction between endothelial cells and platelets through intigren recognition

    1. αIIbβ3 variants defined by next-generation sequencing: Predicting variants likely to cause Glanzmann thrombasthenia

      PMID: 25827233

      Gene: ITGA2B and ITGB3

      HGNC: 6138 and 6156, respectively

      InsufficientEvidence: This article analyzed missense variants in the integrin αIIbβ3 receptor subunit genes ITGA2B and ITGB3 identified by WES comprising around 32,000 alleles from 16,108 individuals. There is no specific tie between variants and probands; therefore, there is insufficient evidence

    1. The patient, a 14-year-old boy

      Case1: Male, 14 years old, Tunisian

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: Parents were heterozygous for the variant of interest

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

      (Epistaxis, gingival bleeding, ecchymosis)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      ProteinExpression: The proband's platelets did not express GPIIb and small amounts of GPIIIa were detected.

      PlateletAggregation: Absence of platelet aggregation after stimulation by ADP, collagen, and thrombin. Ristocetin-induced platelet agglutination was normal

      CasePreviousTesting: Exon 26 of the GPIIb gene was amplified by PCR with primers

      Gene: ITGA2B

      Variant: NM_000419.3:c.2702C>A (p.Ser901Ter)

      LegacyVariant: (p.Ser870Ter)

      ClinVar: N/A

      CAiD: CA399792888

      gnomAD: N/A

    1. A genetic analysis of integrin function: Glanzmannthrombastheniain vitro

      PMID: 9050889

      Gene: ITGA2B and ITGB3

      HGNC: 6138 and 6156

      InsufficientEvidence: This article mentions ITGA2B/ITGB3 variants and has experimental evidence; however, no GT cases reports are mentioned here

      Note: Previously published articles are mentioned here, they have been tagged

    1. Successful unrelated donor cord blood transplantation for Glanzmann’s thrombasthenia Carrie L. Kitko Department of Pediatrics and Internal Medicine, Blood and Marrow Transplant Program, University of Michigan, Ann Arbor, MISearch for more papers by this author John E. Levine Department of Pediatrics and Internal Medicine, Blood and Marrow Transplant Program, University of Michigan, Ann Arbor, MISearch for more papers by this author Dana C. Matthews Department of Pediatrics, University of Washington, Seattle, WASearch for more papers by this author Paul A. Carpenter Department of Pediatrics, University of Washington, Seattle, WA Fred Hutchinson Cancer Research Center, Seattle, WA, USASearch for more papers by this author

      PMID: 19849809

      Gene: ITGA2B and/or ITGB3

      HGNC: 6138 and 6156

      InsufficientEvidence: This article mentions patients with GT however no variants in ITGA2B and/or ITGB3 are mentioned here

    1. 3

      Case3: No gender, age, or ethnicity provided. Patient followed in Germany

      DiseaseAssertion: Glanzmann thrombasthenia

      FamilyInfo: N/A

      ParentalGenotype: N/A

      CasePresentingHPOs: N/A

      CaseHPOFreeText: Mild bleeding

      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: ITGB3

      Variant: Not enough information, all we are told is "premature stop in exon 3"

      LegacyVariant: N/A

      ClinVar: N/A

      CAiD: N/A

      gnomAD: N/A

    1. female infant

      Case#: Female, at birth

      DiseaseAssertion: Glanzmann Thrombasthenia

      FamilyInfo: Figure 1 Consanguinity Mother: 27 yo. Positive for mutation. Epistaxis, hypochromic microcytic anemia, cesarean postoperative vaginal bleeding. Maternal aunt present with GT, Positive for mutation. Maternal cousin present with GT, Positive for mutation. Paternal cousins present with GT, Positive for mutation.

      ParentalGenotype: Both parents heterozygous carriers.

      CasePresentingHPOs: HP:0000978, Bruising susceptibility. HP:0000225, Gingival bleeding. HP:0003265, Neonatal hyperbilirubinemia. HP:0011869, Abnormal platelet function. HP:0004887, Respiratory failure requiring assisted ventilation. HP:0000967, Petechiae.

      PlateletAggregation: Normal coagulation. Reduced platelet function.

      CaseHPOFreeText: APGAR score 9. Spontaneous skin bruising. Started on feeds second day of life.

      ProteinExpression: Platelet function assays showed severely reduced activity.

      Gene: ITGB3

      Variant: p.Asp145Asn

      HGVS: NP_000203.2:p.Asp145Asn

      ClinVar: 627066

      CAID: CA400021939

      gnomAD: Absent

    1. Case 2

      Case2: Male, 9 years old, Japanese

      DiseaseAssertion: Macrothrombocytopenia

      FamilyInfo: Information on mother is given (minimal other family information)

      ParentalGenotype: Mother: ITGA2B (Phe993del heterozygous)

      CasePresentingHPOs: N/A

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOsFreeText: N/A

      ProteinExpression: Surface expression of αIIbβ3 in platelets of the patient and his mother was about 80% compared to control subjects with an increase of CD42b expression

      PlateletAggregation: N/A

      CasePreviousTesting: The entire coding sequence of exons and exon-intron boundaries of ITGA2B and ITGB3 and the whole coding regions of ITGA2B and ITGB3 cDNA obtained from platelets were sequenced as previously described. In the case of ITGA2B p.Phe993del, PCR products obtained from amplification of exon 30 of ITGA2B from the patient's DNA were subcloned to pCR2.1-TOPO and sequence analysis was performed

      Gene: ITGA2B

      Variant: NM_000419.3:c.3070_3072del (p.Phe1024del)

      LegacyVariant: p.Phe993del legacy nomenclature

      ClinVar: N/A

      CAiD: CA8602460

      gnomAD: N/A

    1. 31

      Case31: 2 mo (at biopsy), Indian

      Case 31 (Level 2)


      CasePreviousTesting: same as group. found 0.7 nmol/mg protein/18 h propionate incorporation, 1.9 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.257C>T (p.Pro86Leu)

      ClinVar: 553773

      CAID: CA3847150

      gnomAD: 0.00009799 (South Asian)


      CaseAddInfo: mut- type, homozygous mutations. documented consanguinity.

    2. 30

      Case30: 6 wks (at biopsy), Pakistani

      Case 30 (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 0.7 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.55dupG (p.Val19Glyfs)

      ClinVar: 222906

      CAID: CA10575888

      gnomAD: n/a


      CaseAddInfo: mut0 type, homozygous mutations. novel variant.

    3. 28

      Case28: 1 y 1 mo (at biopsy), European

      Case 28 (Level 2)


      CasePreviousTesting: same as group. found 1.1 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1181dupT (p.Leu394Phefs)

      ClinVar: 222930

      CAID: CA10575868

      gnomAD: n/a


      Variant2: NM_000255.3:c.1975C>T (p.Gln659Ter)

      ClinVar: 222939

      CAID: CA10575859

      gnomAD: n/a


      CaseAddInfo: mut0 type. both novel mutations. heterozygous mutations, unknown cis or trans.

    4. 27

      Case27: no age or ethnicity recorded

      Case 27 (Level 2)


      CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.4 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1061delCinsGGA (p.Ser354TrpfsTer20)

      ClinVar: n/a

      CAID: CA913187308

      gnomAD: n/a


      Variant2: NM_000255.3:c.1065_1068dupATGG (p.Ser357MetfsTer5)

      ClinVar: 280817

      CAID: CA10602989

      gnomAD: n/a


      CaseAddInfo: mut0 type. both novel mutations. heterozygous mutations. Examination of NGS reads determined mutations are in trans

    5. 26

      Case26: 7 y (at biopsy), Hispanic

      Case 26 (Level 2)


      CasePreviousTesting: same as group. found 4.5 nmol/mg protein/18 h propionate incorporation, 7.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.970G>A (p.Ala324Thr)

      ClinVar: 550893

      CAID: CA364400785

      gnomAD: 0.0001632 (Other)


      Variant2: NM_000255.3:c.1846C>T (p.Arg616Cys)

      ClinVar: 551499

      CAID: CA3846722

      gnomAD: 0.00008688 (Latino)


      CaseAddInfo: mut- type, heterozygous mutations, unknown cis or trans. Protein change in paper (p.P649L) is different than protein change indicated by clin var and CAID (p.Arg616Cys).

    6. 29

      Case29: 3 mo (at biopsy), Chinese

      Case 29 (Level 2)


      CasePreviousTesting: same as group. found 0.3 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1280G>A (p.Gly427Asp)

      ClinVar: 218990

      CAID: CA347873

      gnomAD: 0.0004011 (East Asian)


      Variant2: Exon 13 deletion

      ClinVar: n/a

      CAID: n/a

      gnomAD: n/a


      CaseAddInfo: Variant 2 is novel. Heterozygous mutations in MUT, unknown cis or trans. Additional variant found in TCN2 gene (NM_000355.3:c.509G>A, ClinVar: 341197, CAID: CA10184685, gnomAD: 0.007469 (East Asian)). heterozygous Exon 13 deletion confirmed by microarray-based comparative genomic hybridization.

    7. 25

      Case25: 25 y (at biopsy), White

      Case 25 (Level 2)


      CasePreviousTesting: same as group. found 1.3 nmol/mg protein/18 h propionate incorporation, 1.2 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.935G>T (p.Gly312Val)

      ClinVar: 218988

      CAID: CA347874

      gnomAD: n/a


      Variant2: NM_000255.3:c.1909G>A (p.Gly637Arg)

      ClinVar: n/a

      CAID: CA3846712

      gnomAD: [0.000008798] (http://insert-your-link-here.com)(European non-Finnish)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    8. 24

      Case24: no age or ethnicity recorded

      Case 24 (Level 2)


      CasePreviousTesting: same as group. found 0.4 nmol/mg protein/18 h propionate incorporation, 0.4 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.795_796insT or NM_000255.3:c.795dupT (p.Met266TyrfsTer7)

      ClinVar: n/a

      CAID: CA913187322

      gnomAD: n/a


      Variant2: NM_000255.3:c.1207C>T (p.Arg403Ter)

      ClinVar: 167310

      CAID: CA234287

      gnomAD: 0.0001602 (African)


      CaseAddInfo: Variant 1 is novel. Mut0 type, heterozygous mutations, unknown cis or trans.

    9. 23

      Case23: 3 mo (at biopsy), French Canadian

      Case 23 (Level 2)


      CasePreviousTesting: same as group. found 1.4 nmol/mg protein/18 h propionate incorporation, 1.3 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.753+3A>G

      ClinVar: n/a

      CAID: CA3847056

      gnomAD: 0.000008890 (European non-Finnish)


      Variant2: NM_000255.3:c.1332+1delG

      ClinVar: 554656

      CAID: CA3846920

      gnomAD: 0.000008828 (European non-Finnish)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans. Variant 1 is novel.

    10. 22

      Case22: 28 mo (at biopsy), Korean

      Case 22 (Level 2)


      CasePreviousTesting: same as group. found 0.8 nmol/mg protein/18 h propionate incorporation, 0.8 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1481T>A (p.Leu494Ter)

      ClinVar: 551275

      CAID: CA3846864

      gnomAD: 0.0001088 (East Asian)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans

    11. 21

      Case21: 2 mo (at biopsy), White

      Case 21 (Level 2)


      CasePreviousTesting: same as group. found 0.6 nmol/mg protein/18 h propionate incorporation, 0.6 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1287C>G (p.Tyr429Ter)

      ClinVar: 554278

      CAID: CA364398724

      gnomAD: 0.00006483 (European non-Finnish)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    12. 20

      Case20: 5 days (at biopsy), White

      Case 20 (Level 2)


      CasePreviousTesting: same as group. found 2.1 nmol/mg protein/18 h propionate incorporation, 1.9 nmol/mg/protein/18 h propionate incorporation with hydroxocobalamin supplementation

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.682C>T (p.Arg228Ter)

      ClinVar: 203855

      CAID: CA312778

      gnomAD: 0.0002615 (Latino)


      Variant2: NM_000255.3:c.1106G>A (p.Arg369His)

      ClinVar: 203846

      CAID: CA312764

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: mut0 type, heterozygous mutations, unknown cis or trans.

    1. 2

      Patient2: Female, 5.5yo

      CasePresentingHPOs: HP:0002572, HP:0001259, HP:0003648, HP:0002919 (episodic vomiting, coma, lacticaciduria, ketonuria)

      HPOsFreeText: chronic intermittent IVA, treated with a vegetarian diet and L-carnitine supplements, abnormal excretion of isovalerate metabolites, elevation of isovaleryl glycine in urine, C5-carnitine = 16 µmol/l, birth weight = 2kg, hospitalized at 2yo for vomiting and acidosis. At physical exam at 5.5yo, weight = 18kg, height = 103cm, IQ = 92, and unremarkable systemic examination

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 4mo at onset, 13mo at diagnosis via clinical presentation, consanguineous family, full-term delivery via Caesarean section due to failure of propagation

      CasePMIDs:

      CasePreviousTesting: same as group

      CaseGenotypingMethod: same as group

      Variant1: NM_002225.3:c.1207T>A

      CAID: CA391724509, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391724509

      gnomAD: n/a

      Variant2: NC_000015.9:g.40699940T>C (NM_002225.4(IVD):c.234+14C=)

      CAID: CA147572, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NC_000015.9%3Ag.40699940T%3EC

      ClinVar: 94053, https://www.ncbi.nlm.nih.gov/clinvar/variation/94053/

      gnomAD: 0.6830, https://gnomad.broadinstitute.org/variant/15-40699940-T-C

    2. The variant p.Y403N is located in the turn region adjacent to the alpha helix where hydrogen bond formations are more favourable (Fig. 4). The absence of this variant in 200 normal chromosomes, the clinically severe phenotypes in the two patients, the abnormal biochemical and organic acid profiles (Table 1), and the computational prediction (Figs 3 and 4 and Table 3) suggest a potential genotype–phenotype correlation for this variant.

      Variant 1: NM_002225.3:c.1207T>A

      Variant 2: NM_002225.4(IVD):c.863C>T

      VariantEvidence: This variant is located in the turn region next to the alpha helix where hydrogen bonding is favorable, this location along with the presentation of severe phenotypes and biochemical profiles in the patients harboring these variants suggests a genotype-phenotype correlation (fig. 4)

    1. 3

      Patient3: Female, 22yo

      CasePresentingHPOs: HP:0001249 (intellectual disability)

      HPOsFreeText: Blood C5-carnitine (μM) = 14.27, under a protein restricted diet with carnitine and glycine supplementation

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: diagnosed at 3yo after improper treatment

      CasePMIDs:

      CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

      GroupMethod1: PCR (primers in table 2)

      GroupMethod2: Direct sequencing

      CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

      Variant1: NM_002225.4:c.1007G>A (p.Cys309Tyr) listed in paper as (p.Cys307Tyr)

      CAID: CA391722967, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391722967

      gnomAD: n/a

      Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

      ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

      gnomAD: n/a

    2. 5-2

      Patient5-2 Female, 1yo, sibling to patient 5-1

      CasePresentingHPOs:

      HPOsFreeText: Blood C5-carnitine (μM) = 13.47, under a protein restricted diet with carnitine and glycine supplementation, normal development

      CaseNotHPOs:

      NotHPOsFreeText:

      CaseAddInfo: 2mo and asymptomatic at diagnosis

      CasePMIDs:

      CasePreviousTesting: Blood amino acids and acylcarnitine analyzed with ESI-MS/MS, urine organic acid analysis with GC/MS

      GroupMethod1: PCR (primers in table 2)

      GroupMethod2: Direct sequencing

      CaseGenotypingMethod: genomic DNA extracted from peripheral blood leukocytes, IVD exons amplified via PCR, then products were purified and underwent direct sequencing for variant analysis

      Variant1: NM_002225.4:c.347C>T (p.Ser89Phe) listed in paper as (p.Ser87Phe)

      CAID: CA391716394, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA391716394

      gnomAD: n/a

      Variant2: NM_002225.4(IVD):c.1199A>G (p.Tyr400Cys) listed in paper as (p.Tyr371Cys)

      ClinVar: 371390, https://www.ncbi.nlm.nih.gov/clinvar/variation/371390/

      gnomAD: n/a

    1. C

      Case6 14yo diagnosis, Anglo-Celtic

      CasePresentingHPOs HP:0001256, HP:0000098

      (Mild intellectual disability, Tall stature)

      HPOsFreeText Diagnosis was based on tall height and mild intellectual disability. Plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

      CaseNotHPOs HP:0001083

      (Lens dislocation)

      NotHPOsFreeText no other seqeulae

      CasePreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. IVS8+1G>A, compound heterozygous

      ClinVar 1. 120, 2. n/a

      CAID 2. need more info

      gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. n/a

      CaseAddInfo n/a

      CasePMIDs n/a

    2. 28

      FamilyLabel Family 28

      Family28PresentingHPOs n/a

      HPOsFreeText Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid. Affected individuals were not responsive to the treatment, plasma homocysteine levels went unchanged. Patients were given additional oral betaine(3g twice per day) with a low protein diet.

      FamilyNotHPOs n/a

      NotHPOsFreeText no further sequelae

      CountryOrigin n/a

      Ethnicity Lebanese

      Race n/a

      Family28PreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      FamilyMethod1 PCR

      FamilyMethod2 Sanger

      FamilyGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      ProbandLabel Case 34

      Variant NM_000071.2(CBS):c.19dupC (p.Gln7Profs), homozygous

      ClinVar 371345

      gnomAD MAF=0.00005473, no homozygotes

      FamilyAddInfo n/a

      FamilyPMIDs n/a

    3. 1622ins

      the Asn541 from allele registry and mutalyzer confused me.

      However, there cannot be an Asn542 as there is no Asn542 in the refseq. Asn542 is created when you insert TGAA, that is true, but the HGVS tracks the most immediate change on the refeq which is actually the Asn541.

      It was also weird that mutalyzer and allele registry didn't take insTGAA, but only used insA. I wrote out the refseq, the refseq with TGAA inserted and the refseq with just A inserted. Sure enough, Asn541 is the most immediate change and the frameshift is the same "...LRGRP...stop" whether you insert TGAA or just A. Not too surprising since you are still in-frame after adding 3 bases, but cool to check.

      interesting!

    4. 5

      FamilyLabel Family 5

      Family5PresentingHPOs n/a

      HPOsFreeText plasma free homocystine was reduced from >80μmol to <10μmol (nv <60μmol) in response to treatment with folate and pyridoxine. Treatment began with 100-200mg/day for two weeks followed by an addition of 5mg/day folic acid.

      FamilyNotHPOs HP:0001249

      (Intellectual disability)

      NotHPOsFreeText n/a

      CountryOrigin n/a

      Ethnicity Anglo-Celtic

      Race n/a

      Family5PreviousTesting Free homocystine, methionine, cystine, and cysteine-homo-cysteine mixed disulfide levels were measured by amino acid analyzers and total (free plus bound)homocysteine (tHcys) was measured. Exact values were not provided.

      FamilyMethod1 PCR

      FamilyMethod2 Sanger

      FamilyGenotypingMethod PCR amplified then direct sequenced the entire coding region of CBS.

      ProbandLabel Case 7

      Variant 1. NM_000071.2(CBS):c.833T>C (p.Ile278Thr), 2. IVS1+insC, compound heterozygous

      ClinVar 1. 120, 2. n/a

      CAID 2. need more info

      gnomAD 1. MAF=0.001432(European(non-Finnish)), no homozygotes, 2. n/a

      FamilyAddInfo n/a

      FamilyPMIDs n/a

    1. OS-127 II-1

      CaseOS-127_II-1: Male, Birth onset, Germany

      CasePresentingHPOs: HP:0001992, HP:0410145 (Organic aciduria, Decreased biotinidase activity)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001263 (Global developmental delay)

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous and healthy; Proband is confirmed homozygous via parental testing

      CasePreviousTesting: GS-MS analysis identified urinary organic acids dominated by N-aceylated AAs, supported by NMR spectroscopy of urine samples with serum samples being negative; Values of excreted AAs are in Table 1; Biotinidase deficiency treated via 5 mg biotin/d

      CaseGenotypingMethod: Genomic DNA was extracted from blood samples or after EBV transformation of peripheral blood lymphocytes. Exons and exon-intron boundaries were amplified and bidirectionally sequenced.

      Variant: NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys)

      ClinVar: 18110 https://www.ncbi.nlm.nih.gov/clinvar/variation/18110/

      gnomAD: 0.004135 (4 homozygotes), https://gnomad.broadinstitute.org/variant/3-52022837-C-T

    1. K1

      CaseK1 Female, 12yr report, Bosnian

      CasePresentingHPOs HP:0001557, HP:0025116, HP:0001941, HP:0002098, HP:0003270, HP:0002013, HP:0001290, HP:0000750, HP:0011344, HP:0002069, HP:0002305, HP:0001290, HP:0002059, HP:0004881

      (Abnormal intrauterine movements, Fetal distress, Acidosis, Respiratory distress, Abdominal distension, Vomiting, Hypotonia, Speech delay, Severe GDD, Grand mal seizures, Athetosis, Hypotonia, Cerebral atrophy, Episodic hypoventilation)

      HPOsFreeText born at 42wk gestation. (neonatal, pre-treatment:) apgar score at 1min:7, 5min:8, 10min:8, acidosis, respiratory distress, abdominal distension, vomiting, onset of fits at 2d, resistant to ACD's. (18mo:) introduced to pyridoxine therapy, trial dose/route of 60mg oral, complete cessation of seizures, no apnoea or hypotonia/sleepiness, initial maintenance dose of 800mg. (infancy/childhood:) recurrence of seizures with febrile illness, hypotonia, speech delay/difficulties, severe IQ delay. 1wk after withdrawal from pyridoxine trial at 7y, grand mal seizures recurred(definite PDE).

      CaseNotHPOs HP:0000486

      (Squint)

      NotHPOsFreeText (infancy/childhood:) squint

      CasePreviousTesting Administration of pyridoxine relieved patient's seizures. plasma pipecolic acid: 12(nv<2.5μM), plasma AASA: 1.5(nv<0.2μM), urine AASA: 7.5(nv<1 mmol/mol creatinine). Blood lactate: 5.4mM and CSF lactate: 4.4mM (nv <2.5mM). (PMID:17068770:)post treatment testing: Pipecolic acid in plasma 6.7(nv 0.7-2.6mmol/liter), AASA in plasma 0.9(nv<0.2mmol/liter), urine AASA 19(nv<1mmol/molcreatinine).

      Variant NM_001182.4(ALDH7A1):c.328C>T (p.Arg110Ter), homozygous

      ClinVar 17995

      gnomAD MAF=0.0001385(Other), no homozygotes

      CaseAddInfo parental consanguinity

      CasePMIDs 10894227 (Patient 3...), 17068770 (Patient 8)

    2. family S

      FamilyLabel Family S

      FamilySPresentingHPOs HP:0002098, HP:0010818, HP:0002280

      (Respiratory distress, Generalized tonic seizures, Mega cisterna magna)

      HPOsFreeText (neonatal, pre-treatment:) respiratory distress, generalised tonic seizures. (infancy/childhood:) mega cisterna magna

      FamilyNotHPOs n/a

      CountryOrigin n/a

      Ethnicity Arabic

      Race n/a

      FamilySPreviousTesting Cessation of seizures during pyridoxine therapy

      ProbandLabel S1, Female, 15yr report

      Variant NM_001182.4(ALDH7A1):c.312+2T>A, homozygous

      ClinVar 17997

      gnomAD not in gnomAD

      FamilyAddInfo parental consanguinity

      FamilyPMIDs n/a

    1. 3

      Case# Pat3, F, Chinese, 12day onset

      CasePresentingHPOs HP:0008344, HP:0002013, HP:0011968, HP:0001250, HP:0001263

      CaseNotHPOs HP:0001276, HP:0001279,

      CasePreviousTesting tested for serum BCAAs

      CaseMethod1 PCR

      CaseMethod2 Direct

      CaseGenotypingMethod exons and flanking intronic regions of the BCKDHA, BCKDHB and DBT genes were amplified using PCR and sequenced

      Variant NM_000709.3:c.178G>T, NM_000709.3:c.1214_1219dup

      CAID CA406004676(c.178), CA658820662(c.1214)

      CaseAddInfo mutations confirmed in parents by Sanger sequencing, Her elder brother was healthy. She exhibited feeding difficulties and vomiting at 12 days of age. Severe psychomotor retardation was found at the age of 3 months. Cerebral MRI showed bilateral damage to the globus pallidus, basal ganglia, capsula interna and capsula externa. After treatment, clinical improvement was observed. Currently, she is 4 years old and has moderate psychomotor retardation.

    2. 1

      Case# Pat1, M, Chinese, 3day onset

      CasePresentingHPOs HP:0008344, HP:0008872, HP:0001250, HP:0001276, HP:0001279, HP:0001263

      CaseNotHPOs HP:0002013

      CaseMethod1 PCR

      CaseMethod2 Direct

      CaseGenotypingMethod exons and flanking intronic regions of the BCKDHA, BCKDHB and DBT genes were amplified using PCR and sequenced

      Variant NM_000709.3:c.853+1delG ?

    1. The splice-site deletion of exon 3, found in one Indian patient, probably results in the skipping of exon 3, leading to a frame shift p.(Gly114Alafs*53)

      Case# P2, 5mon onset, Indian

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

      CasePreviousTesting Of the negative samples, we include here only those negative for NAGS and CPS1 genes. NAGS testing was done by single-exon amplification and DNA sequencing.24 CPS1 testing was done by RNA sequencing, in most cases using stimulated lymphocytes

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

      Variant NM_001739.1:c.458_459+22del (p.Gly114Alafs*53)

      CAID CA658820625

      CaseAddInfo consanguineous

    1. Patient 6

      Case6: Male, White

      CasePresentingHPOs: HP:0012072, HP:0002194, HP:0002788, HP:0001256, HP:0000722, HP:0000750, HP:0002360, HP:0005487, HP:0002057, HP:0000664, HP:0000286, HP:0000494, HP:0000368, HP:0000322, HP:0009778, HP:0004209 (Aciduria, Delayed gross motor development, Recurrent upper respiratory tract infections, Mild intellectual disability, Obsessive-compulsive behavior, Delayed speech and language development, Sleep disturbance, Prominent metopic ridge, Prominent glabella, Synophrys, Epicanthus, Downslanted palpebral fissures, Low-set posteriorly rotated ears, Short philtrum, Short thumb, Clinodactyly of the 5th finger)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous

      CasePreviousTesting: Extensive metabolic screening revealed elevated urine AAA (618 mmol/mol creatinine; ref <49) and KAA (348 mmol/mol creatinine; ref not detected) as well as plasma AAA (53 umol/L; ref <12)

      CaseGenotypingMethod: All 17 exons and flanking intronic sequences of DHTKD1 were Sanger sequenced.

      Variant1: NM_018706.6:c.2185G>A (p.Arg455Gln)

      CAID: CA5407838 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA5407838

      gnomAD: 0.0002538, https://gnomad.broadinstitute.org/variant/10-12139688-G-A

      Variant2: NM_018706.6:c.1159+5G>A

      CAID: CA5407761 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA5407761

      gnomAD: 0.0001170, https://gnomad.broadinstitute.org/variant/10-12133688-G-A

    2. Patient 10

      Case10: Male, Mixed, 6 yrs died

      CasePresentingHPOs: HP:0002240, HP:0006579, HP:0003560, HP:0001263, HP:0002376 (Hepatomegaly, Prolonged neonatal jaundice, Muscular dystrophy, Global developmental delay, Developmental regression)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Proband is homozygous

      CasePreviousTesting: Patient fibroblasts were analyzed for mutations in SLC25A21 and activities of KATII with no abnormalities; Niemann-Pick type C disease was diagnosed via bone marrow investigations; Metabolic screening suggested a defect in lysine metabolism with urine values of AAA and KAA increasing following a lysine challenge (200 mg/kg p.o.)

      CaseGenotypingMethod: All 17 exons and flanking intronic sequences of DHTKD1 were Sanger sequenced.

      Variant: NM_018706.6:c.700_701delinsGG (p.Leu234Gly)

      CAID: CA915940679 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA915940679

      gnomAD: Not in gnomAD

  6. www.nature.com www.nature.com
    1. Patient KM03

      Case#: KM03, F, neonatal (onset), Japanese

      CasePresentingHPOs: HP:0001254, HP:0002179, HP:0001276, HP:0001263 (Lethargy, Opisthotonus, Hypertonia, Global developmental delay)

      HPOsFreeText: Diagnosed at the time of newborn screening. Originally presented as classical form, but later determined to be the intermittent form.

      CaseNotHPOs:

      CasePreviousTesting: Lymphoblastoid cells from the patient showed reduced decarboxylation activity: 0.12 nmol/h per mg of protein (~9% of control). The authors previously showed by immunoblot analysis that the level of E2 protein was significantly reduced (PMID 3417306).

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: Total RNA and genomic DNA prepared from lymphoblastoid cells or peripheral leukocytes. RT-PCR was performed with primers in exons 8 and 9 identified an insertion. Gnomic DNA was isolated and sequenced. Confirmed by restriction enzyme digestion.

      Variant: NM_001918.3:c.1018-550A>G (homozygous)

      ClinVar: 11946

      gnomAD: Not in gnomAD

      VariantEvidence: The predicted mRNA encoded a truncated protein with 282 amino acids, including 4 novel amino acids at the carboxyl terminus. 265bp fragment that included the 126 bp intronic region was subcloned into an exon trapping vector and transfected into COS-1 cells to confirm the splicing defect.

      CaseAddInfo: Consanguineous, parents were heterozygous.

      CasePMIDs: 3417306

    1. Case Report

      CaseAD: Male, 5 yrs onset

      CasePresentingHPOs: HP:0000750, HP:0002572, HP:0012537, HP:0001944, HP:0001649, HP:0002789, HP:0001252, HP:0001942, HP:0001987, HP:0002919, HP:0012120 (Delayed speech and language development, Episodic vomiting, Food intolerance, Dehydration, Tachycardia, Tachypnea, Muscular hypotonia, Metabolic acidosis, Hyperammonemia, Ketonuria, Methylmalonic aciduria)

      HPOsFreeText: Frequent catabolism episodes with vomiting were noticed without decompensation

      CaseNotHPOs: HP:0001270, HP:0001919, HP:0011015 (Motor delay, Acute kidney injury, Abnormal blood glucose concentration)

      NotHPOsFreeText: Propionyl-CoA carboxylase activity was within normal ranges in fibroblasts

      CaseAddInfo: Parents are non-consanguineous with no family history, Dietary restriction and supplementation showed amelioration of symptoms

      CasePreviousTesting: Normal ECG and MRI results; Metabolic acidosis (pH = 7.08, bicarbonates = 7.3 mmol/L, normal lactic acid, PCO2 = 25 mmHg) and hyperammmoniemia (100 µmol/L) present; Large increase in plasmatic propionylcarnitine (17.5 µmol/L; N < 0.75), undetectable methylmalonylcarnitine, and high urinary excretion of 3-hydroxypropionate and methylcitrate

      CaseGenotypingMethod: Next-generation sequencing in the proband revealed a homozygous nonsense founder variant in the MCEE gene.

      Variant: NM_032601.4(MCEE):c.139C>T (p.Arg47Ter)

      ClinVar: 2343, http://www.ncbi.nlm.nih.gov/clinvar/variation/2343

      gnomAD: 0.0004884, https://gnomad.broadinstitute.org/variant/2-71351575-G-A

    1. Patient 3

      Case3: Newborn, Hmong (China)

      CasePresentingHPOs:

      HPOFreeText: Born after normal pregnancy, postnatal course normal except for moderately elevated C5-acylcarnitine found during NBS. Treatment with L-carnitine supplementation.

      CaseNotHPOs:

      CasePreviousTesting: Urine 2-MBG 55.7 ug/mg creatinine (ref 0.3-7.5); urine IVG 1.2 ug/mg creatinine (ref 0.3-14.3).

      CaseGenotypingMethod: PCR and sequencing of entire gene.

      Variant: NM_001609.3:c.1165A>G (p.Met389Val) (homozygous)

      CAID: CA5730948

      gnomAD: East Asian 0.0005513

      VariantEvidence: PCR of cDNA using primers in exon 9 and exon 11 showed that exon 10 was missing. Analysis of intron exon junctions flanking exon 10 did not reveal any changes.

      CaseAddInfo: Diagnosis confirmed by Western blot of fibroblasts which showed no SBCAD protein.

      CasePMIDs:

    1. Results

      NonPatientCell: E-Coli (DH5α)

      GeneFunction: GO:0006559

      GeneAlteration: PAH cDNA was cloned into a pMAL-c2E expression vector encoding an N-terminal MBP tag and an enterokinase cleavage site. PAH mutants were constructed using site-directed mutagenesis and confirmed using DNA sequencing. Both the wild-type and the 10 mutant vectors were transformed into E. coli DH5α via overexpresion of fusion proteins at midexponential phase. The proteins were purified and concentration was determined.

      FunctionalEvidence: Expression of the 10 mutant proteins compared to the wild-type demonstrated that several of these mutants induce protein destabilization and subsequent loss of function. Upon deconvolution analysis, five variants showed significanly distrubed oligomerization and a preponderance to misfold and form high-molecular-weight protein aggregates. Enzyme kinetic parameter analysis demonstrated moderate reduction in PAH activity and severely affected allostery in all but one mutation, indicating the strong possibility of global confirmational changes. Protein confirmation was tested by limited proteolysis with proteinase K with six out of eight tested mutants decreasing the half-life of the protein by >50% and decreased stability in five out of eight. Thermal protein denaturation was analyzed by fluorescence and demonstrated that all of the mutations led to substantial distortion of the protein's confirmation and/or loss of structural integrity compared to the wild-type, especially those in the regulatory domain. Finally, amino acid replacements were shown to disrupt local networks of amino acid interactions and alter the normal oligomeric state and therfore the function of the protein.

      FAVariant1: NM_000277.3(PAH):c.1222C>T (p.Arg408Trp)

      ClinVar: 577 https://www.ncbi.nlm.nih.gov/clinvar/variation/577/

      FAVariant2: NM_000277.3(PAH):c.898G>T (p.Ala300Ser)

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

      FAVariant3: NM_000277.3(PAH):c.165T>G (p.Phe55Leu)

      ClinVar: 92734 https://www.ncbi.nlm.nih.gov/clinvar/variation/92734/

      FAVariant4: NM_000277.3(PAH):c.1249T>C (p.Tyr417His)

      ClinVar: 102579 https://www.ncbi.nlm.nih.gov/clinvar/variation/102579/

      FAVariant5: NM_000277.3(PAH):c.940C>T (p.Pro314Ser)

      ClinVar: 102905 https://www.ncbi.nlm.nih.gov/clinvar/variation/102905/

    1. 12

      Case12(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.481C > T (p.Arg161Ter)

      ClinVar: 95703

      CAID: CA223189

      gnomAD: 0.0001241 (African)


      CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) not a carrier

    2. 7

      Case 7 (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.445_446delTG (p.Cys149Hisfs*32)

      ClinVar: 203834

      CAID: CA312741

      gnomAD: 0.00008509 (Latino)


      CaseAddInfo: proband genotype, unknown cis or trans, no phenotypic info, sibling (fetus) carrier for both variants

    1. 2.1. Subjects

      FamilyGL: N/A

      FamilyPresentingHPOs: HP:0012237 (Urocanic aciduria)

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0001507, HP:0100543, HP:0010904 (Growth abnormality, Cognitive impairment, Abnormal circulating histidine concentration)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Genomic DNA was obtained via peripheral blood from the siblings and both parents. PCR and direct sequencing in both forward and reverse directions was used to amplify and sequence the 21 coding exons of UROC1.

      FamilyPreviousTesting: Plasma samples from both subjects demonstrated significant elevations in cis-urocanate, trans-urocanate and imidazole propionate; Z-scores for compounds in alternative histidine degradation pathways were found to be within normal limits, including 1-methylhisitidine, imidazole lactate, and 1-methylhistamine; Table 1 shows detailed metabolite levels; Family history was negative for metabolic disorders or any other familial diseases

      FamilyAddInfo: Family appears to be asymptomatic, Siblings are confirmed compound heterozygous via parental sequencing (father het for Variant 2, mother het for Variant 1)

      Variant1: NM_144639.3:c.356C>G (p.Pro119Arg)

      CAID: CA2591587, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2591587

      gnomAD: 0.0001596, https://gnomad.broadinstitute.org/variant/3-126227314-G-C

      Variant2: NM_144639.3:c.907G>C (p.Ala303Pro)

      CAID: CA2591263, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2591263

      gnomAD: 0.00009300, https://gnomad.broadinstitute.org/variant/3-126220119-C-G

      Affected: 2

      Unaffected: 3

      AddSegregationInfo: Not enough affected

    1. 43

      Case40 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 84(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 312(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R161Q variant destroys an AciI restriction site. Thus, while the patient's DNA fragments would not be cleaved, control fragments would be cleaved. The 848del variant creates a MspI site. This would lead to cleaved patient fragments and uncleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.482G>A (p.Arg161Gln), 2. NM_000159.3(GCDH):c.848delT (p.Leu283Argfs), compound heterozygous

      ClinVar 1. 188789, 2. 370672

      gnomAD 1. MAF=0.0001384(Other), no homozygotes, 2. MAF= 0.0003331(Other), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    2. 6, 7

      Case6 unknown sex, Spain

      CasePresentingHPOs HP:0000707

      (Neurological abnormality)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes defined as "slight," entailing minimal neurological signs and an otherwise normal life. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 500(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 461(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

      ClinVar 2083

      gnomAD MAF= 0.0004013(African), no homozygotes

      CaseAddInfo Sibling (Case 7) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 3200mmol/mol creatinine and 3-OH-glutarate was 843mmol/mol creatinine.

      CasePMIDs n/a

    3. 4, 5

      Case4 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 4135(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 752(nv 2–14 mm/mol creatinine).In patient fibroblasts, %GCD activity was <0.5.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The A293T variant, with the addition of a mismatch primer, destroys an HgaI restriction site. Thus, while the patient's DNA fragments would not cleave, control fragments would be cleaved.

      Variant NM_000159.3(GCDH):c.877G>A (p.Ala293Thr), homozygous

      ClinVar 2083

      gnomAD MAF= 0.0004013(African), no homozygotes

      CaseAddInfo Sibling(Case 5) presented with same enzyme activity, clinical onset and phenotype. Gluterate was 2166mmol/mol creatinine and 3-OH-glutarate was 420mmol/mol creatinine.

      CasePMIDs see note on previous studies

    4. 20

      Case20 sex unknown, Spain

      CasePresentingHPOs HP:0001332

      (Dystonia)

      HPOsFreeText Clinical onset was "insidious," involving slowly progressive psychomotor delay, dystonic postures, lethargy, or macrocephaly. Phenotypes were "mild," owing to static or improving dystonia, with maintained ability to walk without assistance. Diagnosed by routine GC-MS organic acid analysis in urine. There was high excretion of glutarate and 3-hydroxyglutarate with glutarate excretion being higher than that of 3-hydroxyglutarate.

      CaseNotHPOs HP:0002540

      (Non-ambulatory)

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 3571(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 232(nv 2–14 mm/mol creatinine).

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The R132Q variant destroys an AciI site. This would lead to uncleaved patient DNA fragments and cleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.395G>A (p.Arg132Gln), 2. NM_000159.3(GCDH):c.1173delG (p.Asn392Metfs), compound heterozygous

      ClinVar 1. 377917, 2. 370106

      gnomAD 1. not in gnomAD, 2. MAF= 0.00005646(Latino), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    5. 32

      Case32 sex unknown, Spain

      CasePresentingHPOs HP:0006846, HP:0002540, HP:0001344, HP:0001332

      (Acute encephalopathy, Non-ambulatory, Nonverbal, Dystonia)

      HPOsFreeText Phenotype was classified as "severe," with passive or static dystonia and an inability to stand up, walk, or speak. Patient may have gone undetected by routine screens as glutarate excretion was normal and 3-hydroxyglutarate was only slightly increased.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting GC-MS measured glutarate of 69(nv 2–10 mmol/mol creatinine) and 3-OH-glutarate 429(nv 2–14 mm/mol creatinine). In patient fibroblasts, %GCD activity was 3.

      CaseMethod1 SSCP

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR amplified and SSCP screened 11 exons and intron boundaries of GCDH gene. Confirmed variants with Sanger sequencing and restriction digest. The V400M variant creates an NlaIII restriction site. Thus, while the patient's DNA fragments would cleave, control fragments would not be cleaved. The R402W variant destroys a MspI site. This would lead to uncleaved patient fragments and cleaved control fragments.

      Variant 1. NM_000159.3(GCDH):c.1198G>A (p.Val400Met), 2. NM_000159.3(GCDH):c.1204C>T (p.Arg402Trp), compound heterozygous

      ClinVar 1. 2088, 2. 2085

      gnomAD 1. MAF= 0.0002769(Other), no homozygotes, 2. MAF= 0.0007566(European(Finnish)), no homozygotes

      CaseAddInfo n/a

      CasePMIDs n/a

    1. 5

      Case5 Female, 24yo report, USA, Lumbee

      CasePresentingHPOs HP:0001344, HP:0002540, HP:0003150

      (Nonverbal, Non-ambulatory, Glutaricaciduria)

      HPOsFreeText Urine glutaric acid was highly elevated and 3-hydroxyglutaric acid was elevated. Patient presented with acute metabolic decompensation at 2yo and feeds by mouth. Patient was diet restricted in lysine and tryptophan with per individual adjustments to maintain normal plasma amino acid levels. Treatment also included supplemental carnitine and riboflavin.

      CaseNotHPOs n/a

      NotHPOsFreeText n/a

      CasePreviousTesting n/a

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod PCR and sanger sequencing was performed on exon 10 of the GCDH gene.

      Variant NM_000159.3(GCDH):c.1240G>A (p.Glu414Lys), homozygous

      ClinVar 167133

      gnomAD MAF=0.0002017(African), no homozygotes

      CaseAddInfo nonconsanguineous

      CasePMIDs n/a

    1. Case#: Patient 5, Japanese, 8 years old (report) CaseHPOs: Hyperornithinemia

      CaseHPOsFreeText: (From Hayasaka et al. 1981; PMID 7260021, Patient 2). First noted visual problems at age 5 years, glasses prescribed for myopia. Evaluation for night blindness at age 8. Best corrected visual acuity was RE 04 with correction of myopia (-8 D), LE 04 with correction of myopia (-10 D). Typical chorioretinal atrophy with scallop margins at the peripheral fundus and an abnormal reflex in the macular area. Concentric constriction of visual fields. Dark adaptation curve was monophasic. ERG was subnormal, and the electro-oculogram was flat. The ciliary processes were normal by cycloscopy. Not responsive to Vitamin B6.

      CaseNotHPOsFreeText: Normal lens

      CasePreviousTesting: Serum ornithine 12.95 mg/dl (normal 0-36-1-56). OAT activity was not detectable in cell extracts from skin fibroblasts. CaseAddInfo: No consanguinity reported CaseMethod1: PCR

      CaseMethod2: Sequence analysis

      CaseGenotypingMethod: DGGE and sequence analysis of genomic DNA was carried out to identify the variant on the other allele. Variant: NM_000274.3(OAT):c.1276C>T (p.Arg426Ter)

      ClinVar: 177

      gnomAD: Maximum population minor allele frequency = 0.00002893 (Latino); no homozygotes in any population.

    1. ee

      CaseKLC2: Male, 32 yrs death, Japan, Asian

      CasePresentingHPOs: HP:0001249, HP:0002078, HP:0000651, HP:0008353, HP:0000992 (Intellectual disability, Truncal ataxia, Diplopia, Neutral hyperaminoaciduria, Cutaneous photosensitivity)

      HPOsFreeText: Monoamino-monocarboxylic aciduria

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are first-cousin consanguineous, Max LOD score is 2.1 for family

      CasePreviousTesting: Defects in the intestinal absorption of monoamino-monocarboxylic acids determined by oral loading; Urine analyses confirmed the absence of hyperaminoaciduria in the mother (III-4), father (III-5) and the younger brother (IV-3), Brother of proband

      CaseGenotypingMethod: DNA was isolated from peripheral blood samples and from liver samples collected at autopsy. A genome-wide screen with 343 different markers was carried out and linkage analysis performed using homozygosity mapping. Both SLC6A18 and SLC6A19 were investigated for possible pathogenicity, with SLC6A19's pattern of expression supporting it as a primary candidate. Intronic primers were used to bidirectionally sequence each exon and flanking intronic regions, locating a homozygous frameshift mutation that perfectly segregated with the phenotype.

      CasePMIDs: 2582682, 11394870

      Variant: NM_001003841.3(SLC6A19):c.882_883TG1

      ClinVar: 2018 https://ww.ncbi.nlm.nih.gov/clinvar/variation/2018/

      gnomAD: 0.000008900, https://gnomad.broadinstitute.org/variant/5-1214174-CTG-C?dataset=gnomad_r2_1

    1. Patient 4

      Case4 sex unknown, Netherlands, Dutch

      CasePresentingHPOs HP:0001250, HP:0002194

      (Seizures, Delayed motor skills)

      HPOsFreeText Seizures ceased upon administration of pyridoxine. (PMID:16159904:) 1st seizure at 8do, first administered pyridoxine(and age at trial) 2mo, initial dose:100mg, maintenance dose:100mg/day, mildly affected motor skills. (PMID:17088338:) Definite="recurrent (two or more) seizures of any type that cease within seven days of the administration of oral pyridoxine (usual dose, 30 mg/ kg/day; minimum dose, 15 mg/kg/day; maximum dose, 1000 mg/kg/day) or within 30 minutes of intravenous pyridoxine (usual dose, 100 mg; minimum dose, 50 mg), that recur when pyridoxine supplementation is withdrawn, and that cease again when pyridoxine is given as above"

      CaseNotHPOs n/a

      NotHPOsFreeText intrauterine seizures

      CasePreviousTesting PDS confirmed metabolically: α‐AASA urine 4.0(nv <1mmol/mol cr), α‐AASA plasma 1.1(nv <0.2μmol/l), pipecolic acid urine 0.02(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 7.0(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk)

      Variant NM_001182.4(ALDH7A1):c.834G>A (p.Val278=)

      ClinVar 18002

      gnomAD not in gnomAD(C and not G at that position?)

      CaseAddInfo Metabolic testing of sibling(Patient 6, heterozygous for the p.Val278= variant): α‐AASA urine 0.2(nv <1mmol/mol cr), α‐AASA plasma <0.2(nv <0.2μmol/l), pipecolic acid urine 0.02(nv 0.55-24.1mmol/mol cr <6mo, 0.01–1.54mmol/mol cr >6 mo) pipecolic plasma 2.2(nv 3.75-10.8μmol/l <1wk, 0.7-2.46μmol/l >1wk), but was not metabolically confirmed for PDS, development was also normal

      CasePMIDs 17088338 , 16159904

    1. Proband

      CaseF7P: 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, Father was confirmed heterozygous, Proband is heterozygous for this mutation with no second pathogenic mutation located

      CasePreviousTesting: Blood phenylalanine before treatment was 1105 μmol/l, Blood tyrosine before treatment was 87 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:c.*144A>G

      CAID: CA16020999 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA16020999

      gnomAD: 0.001284, http://gnomad.broadinstitute.org/variant/12-103232809-T-C

    1. 5

      Case5: Female, 10m, Chinese, part of Family 1

      HPOsFreeText: (at 20 days) 1.38 C4 umol/L, 0.19 C4/C2, 1.79 C4/C3, 2.58 (mmol/mol creatinine) urine isobutyrylglycine

      Case5 (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: younger sister of patient 6, trans heterozygous, inherited one allele from each parent

    1. Table 2

      Case11a: Male, Sweden

      CasePresentingHPOs: HP:0001290, HP:0003324, HP:0002093, HP:0011968, HP:0001283, HP:0001561, HP:0002804 (Generalized hypotonia, Generalized muscle weakness, Respiratory insufficiency, Feeding difficulties, Bulbar weakness, Polyhydramnios, Arthrogryposis)

      HPOsFreeText: N/A

      CaseNotHPOs: HP:0001627 (Cardiac abnormality)

      NotHPOsFreeText: N/A

      CaseAddInfo: Severe congenital myopathy, Deceased in 5 months

      CasePreviousTesting: N/A

      CaseGenotypingMethod: After LMOD3 was identified as a potential causal gene, bidirectional Sanger sequencing was performed on DNA in genetically unresolved patients using PCR amplification covering 3 exons.

      Variant: NM_198271.4:c.1069G>T (p.Glu357Ter)

      ClinVar: 162219 https://www.ncbi.nlm.nih.gov/clinvar/variation/162219/

      gnomAD: Not in gnomAD

    1. 18

      Case18 Female, 9.9yo report, Ethnicity: Austrian

      CasePresentingHPOs HP:0003571, HP:0008872, HP:0001531, HP:0001254, HP:0002789, HP:0002045

      (propionicacidemia, feeding difficulties in infancy, failure to thrive in infancy, lethargy, tachypnea, hypothermia)

      HPOsFreeText feeding difficulties, failure to thrive, lethargy, tachypnea, hypothermia, exanthema (5do). Scored 55 on Snijders-Omen Test for IQ

      CaseNotHPOs n/a

      CasePreviousTesting Diagnosed by selective metabolic screening. PCC activity in patient lymphoblasts was 0.4% of control.

      Variant NM_000532.4:c.1199-2A>G (Gly400fs), homozygous

      ClinVar n/a

      CAID CA354648962

      gnomAD not in gnomAD

      CaseAddInfo parents not consanguineous

      CasePMIDs n/a

    1. P17

      FamilyPY: White, United Kingdom

      FamilyPresentingHPOs: HP:0002131, HP:0001260, HP:0008003, HP:0030453 (Episodic ataxia, Dysarthria, Jerky ocular pursuit movements, Abnormal visual electrophysiology)

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0000640, HP:0000648, HP:0003390, HP:0011402, HP:0001272, HP:0002283 (Gaze-evoked nystagmus, Optic atrophy, Sensory axonal neuropathy, Demyelinating sensory neuropathy, Cerebellar atrophy, Global brain atrophy)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Blood genomic DNA was enriched and whole exome sequenced. Alightment to hg19 and variant filtering was performed with putative pathogenic variants being confirmed via Sanger sequencing.

      FamilyPreviousTesting: Underwent brain MRI and CSF examination with oligoclonal band analysis; Negative genetic testing for SCA1, 2, 3, 6, 7, 17 (now known as ATXN1, ATXN2, CACNA1A, ATXN7, and TBP, respectively), DRPLA (now known as ATN1), FA (now known as FXN) and FMR1

      FamilyAddInfo: N/A

      Variant: NM_004172.5(SLC1A3):c.1496G>A (p.Arg499Gln)

      ClinVar: 242994, https://www.ncbi.nlm.nih.gov/clinvar/variation/242994/

      gnomAD: 0.0001471, https://gnomad.broadinstitute.org/variant/5-36686238-G-A

      Affected: 3

      Segregations: 2

      AddSegregationInfo: Pedigree in Sup Data, Not enough info provided

    1. Case 4

      Case# Case 4, F, Chinese, 5day onset

      CasePresentingHPOs HP:0008344, HP:0011968, HP:0001954, HP:0002373

      CasePreviousTesting Tested blood aa levels with liquid chromatography-mass spectrum spectrometry, several branched chain amino acids were overly abundant. Whole exome targeted capture sequencing was applied for the mutation screening of the suspicious patients. A total of 712 genes associated with inherited metabolic diseases were selected and their coding regions were captured.

      CaseMethod1 Whole Exome

      CaseMethod2 Sanger

      CaseGenotypingMethod validated whole exome findings with sanger and qPCR.

      Variant NM_000056.4(BCKDHB):c.93_103dupGGCGCGGGGCT (p.Phe35Trpfs), NM_000056.3:c.550del

      ClinVar 189101 (dup)

      CAID CA658820648 (del)

      gnomAD low quality site (dup)

    1. Patient 11

      Case11: Male, 3 wk at initiation of follow up, African American ancestry

      HPOsFreeText: NBS C4-acylcarnitine 1.4 umol/L, lasma C4 acylcarnitine 1.87 umol/L, in vitro probe isoC4-acylcarnitine 0.053 umol/ g protein

      NotHPOsFreeText: normal in vitro probe C4-aclycarnitine, normal urine isobutyrylglycine, normal urine C4-acylcarnitine, normal urine C4/C3 ratio

      CaseAddInfo: mild biochemical phenotype observed. Suggested to be at minimum a carrier of IBD deficiency- however presence of promoter mutation, large deletion, or splice-site alteration undetectable by direct gene sequencing cannot be ruled out.

      Case11 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant2: NM_014384.2(ACAD8):c.1129G>A (p.Gly377Ser)

      ClinVar: 5356

      CAID: CA117435

      gnomAD: 0.0001551 (European non-Finnish)


      CaseAddInfo: heterozygous for mutation

    1. Subject C

      CaseGuC: Male, 5 days onset

      CasePresentingHPOs: HP:0200134, HP:0011153, HP:0010850, HP:0011199, HP:0001252, HP:0003487, HP:0003423, HP:0010864, HP:0011344, HP:0002188, HP:0002059 (Epileptic encephalopathy, Focal motor seizure, EEG with spike-wave complexes, EEG with generalized sharp slow waves, Muscular hypotonia, Babinski sign, Thoracolumbar kyphoscoliosis, Severe intellectual disability, Severe global developmental delay, Delayed CNS myelination, Cerebral atrophy)

      HPOsFreeText: Multiple seizure types, Bilateral T2 prolongation in caudate heads and putamina

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Variant is confirmed heterozygous de novo

      CasePreviousTesting: Investigations include electroencephalography (EEG), head MRI, neurometabolic testing, and chromosome microarray; Individuals with self-limiting benign electroclinical syndromes, such as childhood absence epilepsy (onset > 4 years), were excluded; Head circumference was 44 cm at 4 months (91st percentile); Partial response to ketogenic diet and phenytoin, no response to other antiseizure medications;

      CaseGenotypingMethod: Variants within co-expressed candidate genes in Table S1 were extracted from exome sequencing data. Variants were annotated and were verified with Sanger sequencing of the proband and parents.

      Variant: NM_004171.4(SLC1A2):c.866C>G (p.Pro289Arg)

      ClinVar: 438737, https://www.ncbi.nlm.nih.gov/clinvar/variation/438737/

      gnomAD: Not in gnomAD

    1. III4/F

      Case# FIII.4, F, 19 day old diagnosis, Cyprus (Greek Cypriot)

      CasePresentingHPOs HP:0010910, HP:0010911, HP:0010913, HP:0001254, HP:0011968, HP:0001290, HP:0001276, HP:0002789, HP:0002353,

      HPOcont: Hypervalinemia, Hyperleucinemia, Hyperisoleucinemia, Lethargy, Poor feeding, Hypotonia, Hypertonia, Tachypnea, Abnormal EEG

      HPOfreetext: Reduced alloisoleucine and grunting

      CasePreviousTesting Tested blood BCAA (AIleu: 0, Ileu: 220 (NR: 26–100), Leu: 3270 (NR: 65–220), Val: 459 (NR: 90–300), urine organic acids (Increased:lactate, 2-keto-glutarate, 2-keto-isocaproic, 2-OH-isovaleric, 2-keto-isovaleric, 2-keto-3-methylvaleric, 4-OH-phenylacetate, 4-OH-phenylpyruvate and BCKD activity (0.03(NR: 0.4–3.4) (Fibroblasts))

      CaseMethod1 PCR

      CaseMethod2 Direct Sequencing

      CaseGenotypingMethod Direct sequencing repeated on proband and father for deletion varaint

      Variant (1) NM_000709.3(BCKDHA):c.632C>T (p.Thr211Met) (2) NM_000709.3:c.718delG

      ClinVar (1) 93365

      CAID (2) register link if I put that in correctly

      gnomAD (1) 0.0001163(East Asian), 0.00002043 (Overall)

      CaseAddInfo nonconsanguineous

    1. Individual 1

      Case1: Female

      CasePresentingHPOs: HP:0011343, HP:0012072, HP:0007018 (Moderate global developmental delay, Aciduria, Attention deficit hyperactivity disorder)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Parents are non-consanguineous, Unremarkable family history, Variants are parentally confirmed with c.2185 G>A apparently de novo

      CasePreviousTesting: At 2 yrs had elevated 2-oxoadipate (range = 10–120 mmol/mol creatinine) and 2-hydroxyadipate (range = 5–40 mmol/mol creatinine) in urine (Reference 0 mmol/mol creatinine); Elevated 2-aminoadipate (120 μmol/l); Moderate protein restriction did not influence disease course and was discontinued, Serial cranial magnetic-resonance-imaging studies showed no morphological abnormalities; Neuropsychological testing at 8 years revealed an IQ of 117; Symptoms improved after implementation of methylphenidate and at 14 is clinically normal; No mutation detected in ODC

      CaseGenotypingMethod: Whole exome sequencing was performed to identify mutations responsible for the biochemical abnormality. Exonic sequences were enriched and sequenced with data analysis being used to filter according to inheritance and low allele frequencies in controls. This narrowed down to eight different genes (ADAMTS10, AIRE, C8orf38, DHTKD1, OVOS2, CAMTA2, LPPR3, and RADIL) of which three had been associated with unrelated phenotypes and only one other had predicted pathogenic variants, DHTKD1.

      Variant1: NM_018706.7(DHTKD1):c.1A>G (p.Met1Val)

      ClinVar: 39563 https://www.ncbi.nlm.nih.gov/clinvar/variation/39563/

      gnomAD: Not in gnomAD

      Variant2: NM_018706.5(DHTKD1):c.2185G>A (p.Gly729Arg)

      ClinVar: 39564 https://www.ncbi.nlm.nih.gov/clinvar/variation/39564/

      gnomAD: 0.002748, https://gnomad.broadinstitute.org/variant/10-12154929-G-A

    1. 3.1.1. Patient 1

      CaseFI1: Female, Tunisia, 18 months report

      CasePresentingHPOs: HP:0001511, HP:0001508, HP:0001263, HP:0001249, HP:0001337, HP:0000325, HP:0000272, HP:0000303, HP:0000411, HP:0007495, HP:0000518, HP:0000963, HP:0000973, HP:0100678, HP:0012785, HP:0004220, HP:0009162, HP:0010107, HP:0002827, HP:0002808, HP:0001252, HP:0008619, HP:0001629, HP:0001684, HP:0001643, HP:0005301, HP:0003572, HP:0005961, HP:0025082, HP:0030774 (Intrauterine growth retardation, Failure to thrive, Global developmental delay, Intellectual disability, Tremor, Triangular face, Malar flattening, Mandibular prognathia, Protruding ear, Prematurely aged appearance, Cataract, Thin skin, Cutis laxa, Premature skin wrinkling, Flexion contracture of finger, Short middle phalanx of the 5th finger, Absent middle phalanx of 5th finger, Short proximal phalanx of hallux, Hip dislocation, Kyphosis, Muscular hypotonia, Bilateral sensorineural hearing impairment, Ventricular septal defect, Secundum atrial septal defect, Patent ductus arteriosus, Persistent left superior vena cava, Low plasma citrulline, Hypoargininemia, Abnormal cutaneous elastic fiber morphology, Mitochondrial swelling)

      HPOsFreeText: Weight: 1770 g (< 3rd percentile); length: 39 cm (< 3rd percentile); OFC: 31 cm (< 3rd percentile); Hand and foot malformations; First metacarpal was bowed bilaterally; Serum Ornithine at 23 μmol/l (ref 21–77), Serum Citrulline at 3 μmol/l (ref 27–43), Serum Arginine at 39 μmol/l (ref 49-129), Serum Proline at 105 μmol/l (ref 71-303), Serum Glutamate at 61 μmol/l (ref 8-64), Serum Aspartate at 8 μmol/l (ref <14)

      CaseNotHPOs: HP:0002305, HP:0012443, HP:0009832 (Athetosis, Abnormality of brain morphology, Abnormal distal phalanx morphology of finger)

      NotHPOsFreeText: Urinary organic acids, oligosaccharides, purines and pyrimidines were normal

      CaseAddInfo: Parents are first-degree cousins, Deletion leads to a frameshift and a premature termination codon

      CasePreviousTesting: A skin biopsy was taken and amino acid profiles were analyzed from plasma according to standard procedures

      CaseGenotypingMethod: Familial DNA was extracted from peripheral blood samples. Direct sequencing of PYCR1 and exons 2-18 of ALDH18A1 was performed in the affected individual with no result for Exon 15. To confirm if a deletion was responsible, copy number analysis by qPRC was performed with Exon 15 showing a dramatic decrease in signal compared to the others in the affected individual suggesting a homozygous deletion. The parents showed a 50% reduction suggesting a heterozygous phase for the deletion. Different primer combinations allowed for confirmation of the breakpoints with a microdeletion of exon 15 and flanking intronic sequence (1522 bp) with a guanosine insertion.

      Variant: NM_002860.4(ALDH18A1):c.1802-2_1924-901del

      ClinVar: 156547 https://www.ncbi.nlm.nih.gov/clinvar/variation/156547/

      gnomAD: Not in gnomAD

    1. ID no. 817

      Case817: Female, 7 years report, Spain

      CasePresentingHPOs: HP:0003153, HP:0002345, HP:0002174 (Cystathioninuria, Action tremor, Postural tremor)

      HPOsFreeText: Elevated urine cystathionine (1916 umol/g creatine; reference <46), Normal plasma tHcys (3.5 umol/l; reference <7.5), Post treatment normal urine cystathionine (24 umol/g creatine)

      CaseNotHPOs: HP:0003345, HP:0001249 (Glutathione synthetase deficiency, Mental retardation)

      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

    1. F-22

      CaseF-22 male, 5do onset, Ethinicity: North Indian, Muslim

      CasePresentingHPOs HP:0006846, HP:0001254, HP:0011968, HP:0001250, HP:0001987, HP:0001946, HP:0045045, HP:0003571

      (Acute encephalopathy, Lethargy, Poor feeding, Seizures, Hyperammonemia, Ketosis, Elevated acylcarnitines, Propionicacidemia)

      HPOsFreeText Serum ammonia 700micromolar

      CaseNotHPOs n/a

      CasePreviousTesting Also screened for variants in PCCA

      Variant NM_000532.4(PCCB):c.183+5G>A

      ClinVar 217896

      gnomAD MAF= 0.00003328(South Asian), no homozygotes

      CaseAddInfo consanguineous, no abnormality in family history noted

      CasePMIDs n/a

    1. The retrieved soluble fraction of mutated GNMT lacked measurable enzymatic activity

      VariantEvidence: Expression of recombinant GMT was performed in E. coli. Firstly, the wild-type protein showed high solubility compared to the mutant of which only a minor fraction was soluble. Furthermore, enzyme activity was measured and the mutant GMNT lacked any activity while the wild-type exibits activity of >200 pmol/min/ug.

      Variant: NM_018960.4:c.296G>A (p.Arg99His)

    1. P43

      Case43: Male, Chinese, 2.3y (end of study)

      HPOsFreeText: 2y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case43 (Level 2)


      CasePreviousTesting: NBS

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.2107G>A (p.Gly703Arg)

      ClinVar: n/a

      CAID: CA364394252

      gnomAD: 0.00006152 (African)


      CaseAddInfo: one variant, not homozygous.

    2. P42

      Case42: Female, Chinese, 2.3y (end of study)

      HPOsFreeText: 10 mo onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case42 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.2080C>T (p.Arg694Trp)

      ClinVar: 218996

      CAID: CA347907

      gnomAD: 0.00006534 (South Asian)


      Variant2: NM_000255.3:c.2179C>T (p.Arg727Ter)

      ClinVar: 218998

      CAID: CA347913

      gnomAD: 0.0001504 (East Asian)


      CaseAddInfo: heterozygous mutations in trans.

    3. P41

      Case41: Male, Chinese, 10.3y (end of study)

      HPOsFreeText: 8.8y onset, poor neurological outcome

      NotHPOsFreeText: not responsive to vitamin B12

      Case41 (Level 2)


      CasePreviousTesting: same as group

      CaseMethod1: same as group

      CaseMethod2: same as group

      CaseGenotypingMethod: same as group


      Variant1: NM_000255.3:c.1790T>G (p.Ille597Arg)

      ClinVar: 551764

      CAID: CA364395663

      gnomAD: n/a


      Variant2: NM_000255.3:c.2106delA (p.VAl704Ter)

      ClinVar: 555523

      CAID: CA658821513

      gnomAD: n/a


      CaseAddInfo: both variants novel. heterozygous mutations in trans.

    1. Patients 2–4

      Family2to4: Maltese

      FamilyPresentingHPOs: N/A

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0001270, HP:0007018, HP:0001252, HP:0000750, HP:0000252 (Motor delay, Attention deficit hyperactivity disorder, Muscular hypotonia, Delayed speech and language development, Microcephaly)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: Whole exome sequencing was performed as a trio with both parents. Identified DHTKD1 mutations were evaluated for possible effects and filtered for frequencies and predicted pathogenicity. No other candidate genes were found during the WES analysis for either patient sequenced. Sanger sequencing confirmed the proband's siblings are homozygous for the variant and that each parent is a carrier.

      FamilyPreviousTesting: Amino acid and organic acid testing showed elevated urinary 2-aminoadipic, 2-ketoadipic, and glutaric acids in the proband as well as in two elder brothers, ages 5 and 7.

      FamilyAddInfo: Parents are consanguineous, All three affected siblings are clinically normal

      Variant: NM_018706.6:c.915G>C (p.Gln305His)

      CAID: CA5407680 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA5407680

      gnomAD: Other 0.0001630, https://gnomad.broadinstitute.org/variant/10-12131182-G-C

      Affected: 3

      Unaffected: 2

      AddSegregationInfo: Candidate gene sequencing

    1. Proband II.1

      CaseII-2: Female, Turkey

      CasePresentingHPOs: HP:0001558, HP:0000337, HP:0045075, HP:0000463, HP:0000343, HP:0000278, HP:0000470, HP:0000767, HP:0002375, HP:0002033, HP:0006829 (Decreased fetal movement, Wide forehead, Sparse eyebrow, Anteverted nares, Long philtrum, Retrognathia, Short neck, Pectus excavatum, Decreased spontaneous movement, Poor suck, Severe muscular hypotonia)

      HPOsFreeText: Birth weight was 2050 g and length was 43 cm, Absent Moro reflex, Required ventilator support from birth

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Born with fractures of the right humerus and left femur

      CasePreviousTesting: N/A

      CaseGenotypingMethod: Whole blood smaples were obtained from the parents and the probands and DNA was extracted. WES was performed on II-2, with the results being sequenced and filtered for pathogenicity. Once the LMOD3 variant was detected, PCR amplification and Sanger sequencing was used to amplify exon 1 and confirm the results.

      Variant: NM_198271.4:c.138dup (p.Ser47Glnfs*13)

      ClinVar: 162215 https://www.ncbi.nlm.nih.gov/clinvar/variation/162215/

      gnomAD: European (Non-Finnish) 8.879e-6, Overall 8.049e-6 https://gnomad.broadinstitute.org/variant/3-69171399-T-TG

    1. Biallelic

      Case#: Patient 2, male, 5 years (report), Turkish

      CaseHPOs: HP:0003235, HP:0002240 (hypermethioninemia, hepatomegaly)

      CaseHPOsFreeText: Identified by newborn screening.

      CaseNotHPOsFreeText: No signs of hepatic failure, no clinical symptoms.

      CasePreviousTesting: On day of life 3, elevated methionine concentration in blood of 390 µmol/L (normal 20–40). Total homocysteine in plasma was 59 µmol/L (normal 5–15). At later age (not specified), plasma methionine ranged from 1000 to 2070 µmol/L, while total homocysteine in plasma ranged from 30 to 55 µmol/L.

      CaseMethod1: PCR

      CaseMethod2: Sequencing

      CaseGenotypingMethod: All 9 exons and intron-exon junctions of MAT1A were amplified by PCR from genomic DNA. This was followed by SSCP analysis and sequence analysis of PCR products with abnormal mobility.

      Variant: c.125T>C (p.Leu42Pro) (homozygous)

      ClinVar: N/A

      CAID: CA377363776

      gnomAD: The highest population minor allele frequency in gnomAD is 0.000008791 (European non-Finnish); no homozygotes in any population.

      VariantEvidence: When expressed in E. Coli, the variant resulted in reduction of methionine adenosyltransferase (MAT) and tripolyphosphatase (PPPase) activities to ~10 and ~20% of wild type respectively (Fernandez-Irigoyn et al, 2010, PMID 20675163; Fig 2).

      Points: 0.5

    1. six

      CaseSA6P: Male, 7 months onset, European

      CasePresentingHPOs: HP:0001988, HP:0000825, HP:0001250, HP:0001987 (Recurrent hypoglycemia, Hyperinsulinemic hypoglycemia, Seizures, Hyperammonemia)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Has father with confirmed variant and similar phenotypes

      CasePreviousTesting: Leucine load test showed leucine sensitivity; Protein/leucine restriction and dioxazide was effective at reducing symptoms

      CaseGenotypingMethod: Genomic DNA was prepared from all patients via peripheral blood leukocytes. The GLUD1 gene exons 1-13 and the flanking intronic regions were PCR-amplified and directly sequenced. All variants were confirmed via restriction enzyme analysis. Additionally, paternity testing was performed by HLA typing and by southern blot analysis of DNA fragments as well as PCR analysis of STRs.

      Variant: NM_005271.5(GLUD1):c.965G>A (p.Arg322His)

      ClinVar: 16129, https://www.ncbi.nlm.nih.gov/clinvar/variation/16129/

      gnomAD: Not in gnomAD

    1. Lo

      Case# Lo, M, 10mo diagnosis---originally 1985

      CasePresentingHPOs HP:0011968, HP:0001531, HP:0000737, HP:0007281, HP:0002013, HP:0001259, HP:0005979, HP:0001943

      CaseMethod1 PCR

      CaseMethod2 Sanger

      CaseGenotypingMethod

      Variant NM_000709.3:c.1265A>G(p.Lys422Arg), NM_000709.3:c.137dup(p.Ser47IlefsTer4)

      CAID CA406015486(miss), CA658820686(dup)

      VariantEvidence 3978850: in patient fibroblasts-rate of decarboxylation of alpha-ketoacids: alpha ketoisovalerate[0<0.31], Pyruvate[0.40>.34], alpha-ketoglutarate[0.14>0.10] (Table 1), BCKDH activity[0.0003<0.107] (Table 2), E1 subunit activity[0.6<5.9] (Table 3)--[ProbandvsNormal]

      CaseAddInfo 3978850( a positive dinitrophenylhydrazine test and elevated urinary a-ketoisocaproate, a-methyl-P-OH-valerate and a-OH-isoval- erate,

      CasePMIDs 3978850, 2914958

    1. Patient1

      Case1: female, 2.3y (initial referral), Italian, Family 1

      CasePresentingHPOs: HP:0001508, (failure to thrive)

      HPOsFreeText: birthweight 3060 g, SGOT 11 mo 150 U/L, SGPT 11 mo 160 U/L, 1.8y elevated plasma lactic acid 2.9 mmol/L. 3.9 y alkaline phosphatase 928 U/L, 4.7 y serum tricglycerides 184 mg/dl, fasting plasma methionine 644 umol/L. increased urinary methionine excretion 40 umol/mmol. increased lactic acid excretiom 107 umol/mmol. mild centrilobular fibrosis in liver. some eosinophils present in liver.

      CaseNotHPOs: HP:0001404, HP:0001397, HP:0012465, HP:0001396, (hepatocellular necrosis, hepatic steatosis, elevated hepatic iron concentration, cholestasis)

      NotHPOsFreeText: hepatic dysfunction. normal tHcy.

      CaseAddInfo: proband, second child, low methionine diet (300 mg/day) at 2.4 y decreased plasma methionine to normal.

      Case (Level 2)


      Variant1: NM_018960.5(GNMT):c.149T>C (p.Leu50Pro)

      ClinVar: 4169

      CAID: CA248600

      gnomAD: 0.0002319 (East Asian)


      Variant2: NM_018960.5(GNMT):c.529C>A (p.His177Asn)

      ClinVar: 4170

      CAID: CA248601

      gnomAD: 0.0006993 (European non-Finnish)


      CaseAddInfo: compound heterozygote, Leu50Pro maternal mutation, His177Asn paternal mutation. The amino acid shifts are one # different than those predicted in the paper (Leu49Pro and His176Asn).

    1. d

      CaseST-11: Male, 1 day onset, Turkey

      CasePresentingHPOs: HP:0001319, HP:0000316, HP:0008070, HP:0001410, HP:0001987, HP:0004322, HP:0004482 (Neonatal hypotonia, Hypertelorism, Sparse hair, Liver dysfunction, Hyperammonemia, Short stature, Relative macrocephaly)

      HPOsFreeText: N/A

      CaseNotHPOs: N/A

      NotHPOsFreeText: N/A

      CaseAddInfo: Family is consanguineous, Proband is homozygous for this variant

      CasePreviousTesting: See Group

      CaseGenotypingMethod: See Group

      Variant: NM_001123.3:c.905T>C (p.Phe302Ser)

      CAID: CA377399030, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA377399030

      gnomAD: Not in gnomAD

    2. l

      FamilyST-VII: Iran

      FamilyPresentingHPOs: HP:0002197, HP:0000316, HP:0001889 (Generalized-onset seizure, Hypertelorism, Megaloblastic anemia)

      HPOsFreeText: N/A

      FamilyNotHPOs: HP:0002904, HP:0001410, HP:0001943, HP:0001257, HP:0001347, HP:0001251, HP:0001276 (Hyperbilirubinemia, Decreased liver function, Hypoglycemia, Spasticity, Hyperreflexia, Ataxia, Hypertonia)

      NotHPOsFreeText: N/A

      FamilyGenotypingMethod: See Group

      FamilyPreviousTesting: See Supp Info for methionine/transaminase values; Normal height, weight and head circumference at birth

      FamilyAddInfo: Family is consanguineous, Family is homozygous for this variant

      Variant: NM_006721.4(ADK):c.1022A>G (p.His341Arg)

      ClinVar: 265772, https://www.ncbi.nlm.nih.gov/clinvar/variation/265772/

      gnomAD: Not in gnomAD

      Affected: 2

      Unaffected: 0

      Segregations: 1

      AddSegregationInfo: Not enough info

    1. Mutations in RAB39B in individuals with intellectual disability, autism spectrum disorder, and macrocephaly

      PMID: 28851564

      Gene: RAB39B

      Disease: early-onset parkinsonism-intellectual disability syndrome

      MonDO: MONDO:0010709

      Notes: The family reported has a phenotype of ID and autism. Parkinson disease or clinical features of Parkinsonism are not noted in any patients. Proband may be scored upon expert review.

    1. Foveal Hypoplasia Grading in 95 Cases of Congenital Aniridia: Correlation to Phenotype and PAX6 Genotype

      PMID: 34942114

      Variant NM_001368894.2:c.136C>G(p.Leu46Val)

      Gene: PAX6

      Disease: Ocular dysgenesis

      InheritancePattern: AD

      Notes Pub presents a variant with a diff AA change at position 46, p.L46Q vs the variant being curated which is p.L46V