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

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

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

NM_002203:c.780-11A>T

Unable to identify variant for following reasons: 1) NM_002203 is for ITGA2 not ITGA2B -- though ITGA2 is listed as the gene for this one so maybe that was intentional 2) c.780 is not at an exon boundary in ITGA2B Mane transcript

NM_000419:c.2613delG

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

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

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

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

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

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

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

PMID: 9235918

Gene: ITGA2B and/or ITGB3

HGNC: 6138 and 6156, respectively

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

PMID: 12840847

Gene: ITGA2B and/or ITGB3

HGNC: 6138 and 6156

InsufficientEvidence: This article mentions two probands with GT; however, no variants in ITGA2B and/or ITGB3 were mentioned

PMID: 23929305

Gene: ITGA2B and ITGB3

HGNC: 6138 and 6156

InsufficientEvidence: This article is a review on GT; there are several previously published probands; however, there are no new case reports in this article.

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

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

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

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

PMID: 32237906

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

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

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

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

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

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

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

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

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

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

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

PMID: 22513797

Gene: ITGA2B

HGNC: 6138

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

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.

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.

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.

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

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).

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.

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.

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.

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.

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

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.

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.

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

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)

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

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

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

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

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!

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

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

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)

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

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.

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 ?

Case#: 2, female 4 days (onset), 4 y 3 mo (current), Chinese

CasePresentingHPOs: HP: 0008344, HP: 0012088, HP: 0011968, HP: 0001276, HP: 0001941, HP: 0002543, HP: 0011342 (elevated A keto acids in urine, abnormal urinary odor, feeding difficulties, hypertonia, acidosis, abnormal globus pallidus MRI signals, mild global developmental delay)

HPOsFreeText: Poor response to light and sound, abnormal MRI signals in frontal lobes, Blood ammonia: 95 uM, Hemoglobin: 117 g/L, Leucin: 745.01 uM, Valine: 526.40 uM, Isoleucine: 181.06 uM, Alloisoleucine: 69.45 uM

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo:

CasePreviousTesting: n/a

CaseMethod1: same as group

CaseMethod2: same as group

CaseGenotypingMethod: same as group

Variant: NM_000709.3(BCKDHA): c.659C>T (p.Ala220Val)

ClinVar: 93367

CAID: n/a (because this doesn't need to be included if it is in ClinVar right?)

gnomAD: not in gnomAD

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

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

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

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

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

Case#: DBT-6

CasePresentingHPOs: Clinical information not available

Variant: NM_001918.3:c.1281+3A>G

CAID: CA658820827

gnomAD: Not in gnomAD

VariantEvidence: Non-canonical splice variant

CaseAddInfo:

CasePMIDs:

Case#: DBT-5

CasePresentingHPOs: Classic form of MSUD

Variant: NM_001918.3:c.1195T>C

CAID: CA341330334

gnomAD: Not in gnomAD

VariantEvidence: No functional evidence

CaseAddInfo:

CasePMIDs:

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:

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/

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

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

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

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

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

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

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

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

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

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.

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

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

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

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

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

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.