Case: T3-1, female, 21yo

DiseaseAssertion: VWD3

FamilyInfo:

ParentalGenotype(s):

CasePresentingHPOs:

CaseHPOFreeText: Blood type: O+, bleeding score = 24, VWF:Ag (IU/mL) = 0.01; VWF:RCo (IU/mL) = 0.00; FVIII:C (IU/mL) = 0.01

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting:

GenotypingMethod: qRT-PCR

PreviouslyPublished:

Gene: VWF

Variant 1: c.876delC (p.Pro293Glnfs*164)

HGVS: n/a

ClinVarID: n/a

CAID: n/a

gnomAD: n/a

Variant 2: c.1255C>T (p.Gln419Ter)

HGVS: NM_000552.5:c.1255C>T (p.Gln419Ter)

ClinVarID: n/a

CAID: CA232314778; https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA232314778

gnomAD: absent

Case: T3-4, male, 16yo

DiseaseAssertion: VWD3

FamilyInfo:

ParentalGenotype(s):

CasePresentingHPOs:

CaseHPOFreeText: Blood type: A+, bleeding score = 24, VWF:Ag (IU/mL) = 0.01; VWF:RCo (IU/mL) = 0.03; FVIII:C (IU/mL) = 0.01

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting:

GenotypingMethod: qRT-PCR

PreviouslyPublished:

Gene: VWF

Variant 1: c.1657dupT (p.Trp553Leufs*97)

HGVS: n/a

ClinVarID: n/a

CAID: n/a

gnomAD: n/a

Variant 2: c.8419_8422dupTCCC (p.Pro2808Leufs*24)

HGVS: n/a

ClinVarID: n/a

CAID: n/a

gnomAD: n/a

Case: Proband, female, 27 years old at report; ethnicity not reported.

DiseaseAssertion: VWD2A. The authors confirmed type 2A VWD based on VWF:Ac/VWF:Ag ratio <0.7 (excluding types 1C, 2N, and 3), RIPA negative for increased platelet affinity (excluding type 2B), and multimer analysis showing HMWM deletion with IMWM reduction (excluding type 2M).

FamilyInfo: The patient denied a family history of abnormal bleeding. The father carried VWF c.2281+1G>A and was not diagnosed with VWD (VWF:Ag 61%, VWF:Ac 60.6%, FVIII activity 82%, VWF:Ac/VWF:Ag ratio 0.9). The mother carried VWF c.4654T>A and was diagnosed by the authors as having low VWF per British Committee for Standards in Haematology criteria (VWF:Ag 40%, VWF:Ac 26.6%, FVIII activity 66%, VWF:Ac/VWF:Ag ratio 0.6). Neither parent had a history of abnormal bleeding. Parental laboratory results and genotypes are reported in Table 2.

ParentalGenotype: Both parents were genotyped. The father was heterozygous for c.2281+1G>A and the mother was heterozygous for c.4654T>A (Table 2). The authors report that the two variants were inherited separately from each parent, establishing compound heterozygosity. Note: Figure 2 shows Sanger sequencing validation for c.2281+1G>A only, confirming the variant in the patient and father and a normal genotype at that locus in the mother. No confirmatory sequencing trace is shown for the maternal c.4654T>A variant; that genotype is reported only in Table 2.

CasePresentingHPOs: HP:0000421, HP:0000132, HP:0004846, HP:0012147, HP:0030132, HP:0011871 (Epistaxis, Menorrhagia, Prolonged bleeding after surgery, Reduced quantity of VWF, Absence of large von Willebrand factor multimers, Impaired RIPA)

CaseHPOFreeText: Gingival bleeding persisted for two days after tooth extraction. History of frequent epistaxis and one episode of heavy menorrhagia in 2007 treated with plasma transfusion. ISTH-BAT bleeding score 7 (epistaxis score 1, bleeding after tooth extraction score 2, heavy menorrhagia with plasma transfusion score 4). VWF:Ag 26.2%, VWF:Ac 5.7%, FVIII activity 43%, VWF:Ac/VWF:Ag ratio 0.21. Low-concentration RIPA 23.7% (reference 30.0-70.0%). VWF multimer analysis demonstrated deletion of high-molecular-weight multimers and reduction of intermediate-molecular-weight multimers (Figure 1). Arachidonic acid-induced platelet aggregation was impaired, with a maximal aggregation rate of 14.3%.

CaseNotHPOs: HP:0003645, HP:0001873 (Prolonged partial thromboplastin time, Thrombocytopenia)

CaseNotHPOFreeText: APTT 39.2 s (reference 32.0-45.0), platelets 183x10^9/L (reference 125-350), PT 13.6 s (reference 11.0-15.0), and fibrinogen 2.71 g/L (reference 2.0-4.0) were all within reference ranges, as was thrombin time. High-concentration RIPA 52.9% (reference 40.0-80.0), normal. Systemic physical examination unremarkable with no active bleeding on admission. Prior laparoscopic surgery for luteal rupture without a remarkable increase in bleeding. Hemoglobin 125 g/L was marginally below the stated reference range (130-175), although the authors described the complete blood count as normal.

CasePreviousTesting: Whole-exome sequencing was performed, which is a genome-wide method. No genes other than VWF were reported as tested or implicated. No earlier molecular genetic testing was reported.

GenotypingMethod: Whole-exome sequencing followed by one-generation (Sanger) sequencing validation, performed on the proband and both parents.

Variant 1

Gene: VWF

Variant: c.2281+1G>A, heterozygous, inherited from the father. Intron 17 canonical splice donor site; the authors describe the affected region as lying between the D2 and D' domains. Classified as pathogenic by the authors per ACMG guidelines.

HGVS: NM_000552.5:c.2281+1G>A

ClinVar: NA

CAID: CA383523243

gnomAD: Absent (gnomAD v4.1.1; variant not found, region adequately covered)

Variant 2

Gene: VWF

Variant: c.4654T>A (p.Phe1552Ile), heterozygous, inherited from the mother. Exon 28, A2 domain; missense. Classified as a variant of uncertain significance by the authors per ACMG guidelines. Note: the article gives the protein consequence as p.Phe1152Ile in the Case Presentation and p.Phe1552Ile in the Discussion; these are internally inconsistent. p.Phe1552Ile is correct, as confirmed by HGVS validation and by the ClinGen Allele Registry record (NP_000543.3:p.Phe1552Ile), and is consistent with the stated exon 28 location.

HGVS: NM_000552.5:c.4654T>A (p.Phe1552Ile)

ClinVar: NA

CAID: CA383500446

gnomAD: Absent (gnomAD v4.1.1; variant not found, region adequately covered)

Case: Patient 51, Family Y (Table 1.), F/33, Afro-Caribbean

DiseaseAssertion: VWD1

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs:

CaseHPOFreeRext: BAT = 5, FVIII:C (IU/dL) = NA, VWF:Ag (IU/dL) = 30, VWF:Act (IU/dL) = 31

CaseNOTHPOs:

CaseNOTHPOFreeText: Blood group O+

CasePreviousTesting:

GenotypingMethod: All samples were analyzed by captured-based high throughput sequencing which was performed with a custom-design of the VWF gene provided by Twist BioScience (San Francisco, USA). It comprised all 52 exons, intronic flanking regions, promoter and 3’UTR region of the VWF gene. Libraries were prepared by using the Twist NGS target enrichment solution (Twist BioScience) according to the manufacturer protocol. Samples were analyzed on a NovaSeq 6000 sequencer (Illumina) with a median read depth of 2500X by using the 300-cycle S1 NovaSeq 6000seq reagent kit with 150-bp paired-end reads. The raw data were analyzed with Mutect21 and Vardict2 tools. The inhouse NGSreport software (CHU Lille) was used for data visualization, sequences check and conservation of variants with high quality metrics. In some cases, patients genomic DNA was screened for sequence variations (large deletions, insertions and duplications) by Multiplex Ligation-dependent Probe Amplification (MCR Holland).

PreviouslyPublished: NA

Gene: VWF

Variant: c.4751A > G, p.(Tyr1584Cys)

HGVS: NM_000552.5:c.4751A>G (p.Tyr1584Cys)

ClinVarID: 310

CAID: CA114162

gnomAD: MAF of 0.004105 (483/1179782 alleles) in European/Non-Finnish population https://gnomad.broadinstitute.org/variant/chr12-6018667-T-C?dataset=gnomad_r4

Case: Patient 48, Family U (Table 1.), M/43, Afro-Caribbean

DiseaseAssertion: VWD2M

FamilyInfo: Patient 43 (M/10, Afro-Caribbean), Patient 44 (M/15, Afro-Caribbean), Patient 46 (M/47, Afro-Caribbean) and Patient 47 (M/78, Afro Caribbean) also from Family U. (Table 1.)

ParentalGenotype(s): NA

CasePresentingHPOs:

CaseHPOFreeRext: BAT = 4, FVIII:C (IU/dL) = 32, VWF:Ag (IU/dL) = 25, VWF:Act (IU/dL) = 21

CaseNOTHPOs:

CaseNOTHPOFreeText: Blood group AB+

CasePreviousTesting:

GenotypingMethod: All samples were analyzed by captured-based high throughput sequencing which was performed with a custom-design of the VWF gene provided by Twist BioScience (San Francisco, USA). It comprised all 52 exons, intronic flanking regions, promoter and 3’UTR region of the VWF gene. Libraries were prepared by using the Twist NGS target enrichment solution (Twist BioScience) according to the manufacturer protocol. Samples were analyzed on a NovaSeq 6000 sequencer (Illumina) with a median read depth of 2500X by using the 300-cycle S1 NovaSeq 6000seq reagent kit with 150-bp paired-end reads. The raw data were analyzed with Mutect21 and Vardict2 tools. The inhouse NGSreport software (CHU Lille) was used for data visualization, sequences check and conservation of variants with high quality metrics. In some cases, patients genomic DNA was screened for sequence variations (large deletions, insertions and duplications) by Multiplex Ligation-dependent Probe Amplification (MCR Holland).

PreviouslyPublished: NA

Gene: VWF

Variant: c.3943C > T p.(Arg1315Cys)

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

ClinVarID: 100310

CAID: CA228502

gnomAD: MAF of 8.476e-7 (1/ 1179850 alleles) in European population https://gnomad.broadinstitute.org/variant/chr12-6019161-A-C?dataset=gnomad_r4

Case: Patient 47, Family U (Table 1.), M/78, Afro-Caribbean

DiseaseAssertion: VWD2M

FamilyInfo: Patient 43 (M/10, Afro-Caribbean), Patient 44 (M/15, Afro-Caribbean), Patient 46 (M/47, Afro-Caribbean) and Patient 48 (M/43, Afro Caribbean) also from Family U. (Table 1.)

ParentalGenotype(s): NA

CasePresentingHPOs:

CaseHPOFreeRext: BAT = 4, FVIII:C (IU/dL) = 11, VWF:Ag (IU/dL) = 20, VWF:Act (IU/dL) = 12.6

CaseNOTHPOs:

CaseNOTHPOFreeText: Blood group B+

CasePreviousTesting:

GenotypingMethod: All samples were analyzed by captured-based high throughput sequencing which was performed with a custom-design of the VWF gene provided by Twist BioScience (San Francisco, USA). It comprised all 52 exons, intronic flanking regions, promoter and 3’UTR region of the VWF gene. Libraries were prepared by using the Twist NGS target enrichment solution (Twist BioScience) according to the manufacturer protocol. Samples were analyzed on a NovaSeq 6000 sequencer (Illumina) with a median read depth of 2500X by using the 300-cycle S1 NovaSeq 6000seq reagent kit with 150-bp paired-end reads. The raw data were analyzed with Mutect21 and Vardict2 tools. The inhouse NGSreport software (CHU Lille) was used for data visualization, sequences check and conservation of variants with high quality metrics. In some cases, patients genomic DNA was screened for sequence variations (large deletions, insertions and duplications) by Multiplex Ligation-dependent Probe Amplification (MCR Holland).

PreviouslyPublished: NA

Gene: VWF

Variant: c.3943C > T p.(Arg1315Cys)

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

ClinVarID: 100310

CAID: CA228502

gnomAD: MAF of 8.476e-7 (1/ 1179850 alleles) in European population https://gnomad.broadinstitute.org/variant/chr12-6019161-A-C?dataset=gnomad_r4

Variant: c.4196G > A, p.(Arg1399His)

HGVS: NM_000552.5:c.4196G>A (p.Arg1399His)

ClinVarID: 293

CAID: CA114133

gnomAD: MAF of 0.01540 (456/29604 alleles) in Ashkenazi Jewish population https://gnomad.broadinstitute.org/variant/chr12-6019222-C-T?dataset=gnomad_r4

Case: Patient 62, Family M (Table 1.), F/42, Afro-Caribbean

DiseaseAssertion: VWD3

FamilyInfo: Patient 20 (M/80, Afro-Caribbean) also in Family M. (Table 1.)

ParentalGenotype(s): NA

CasePresentingHPOs:

CaseHPOFreeRext: BAT =32, FVIII:C (IU/dL) = 2, VWF:Ag (IU/dL) = 5, VWF:Act (IU/dL) = 5

CaseNOTHPOs:

CaseNOTHPOFreeText: Blood group O+

CasePreviousTesting:

GenotypingMethod: All samples were analyzed by captured-based high throughput sequencing which was performed with a custom-design of the VWF gene provided by Twist BioScience (San Francisco, USA). It comprised all 52 exons, intronic flanking regions, promoter and 3’UTR region of the VWF gene. Libraries were prepared by using the Twist NGS target enrichment solution (Twist BioScience) according to the manufacturer protocol. Samples were analyzed on a NovaSeq 6000 sequencer (Illumina) with a median read depth of 2500X by using the 300-cycle S1 NovaSeq 6000seq reagent kit with 150-bp paired-end reads. The raw data were analyzed with Mutect21 and Vardict2 tools. The inhouse NGSreport software (CHU Lille) was used for data visualization, sequences check and conservation of variants with high quality metrics. In some cases, patients genomic DNA was screened for sequence variations (large deletions, insertions and duplications) by Multiplex Ligation-dependent Probe Amplification (MCR Holland).

PreviouslyPublished: NA

Gene: VWF

Variant: c.1530G > A, p.(Val510 =)

HGVS: NM_000552.5:c.1530G>A (p.Val510=)

ClinVarID:

CAID: CA6403368

gnomAD: MAF of 0.00002198 (2/91004 alleles) in South Asian population https://gnomad.broadinstitute.org/variant/chr12-6062957-C-T?dataset=gnomad_r4

Variant: c.1892C > T, p.(Ala631Val)

HGVS: NM_000552.5:c.1892C>T (p.Ala631Val)

ClinVarID: 422844

CAID: CA6403245

gnomAD: MAF of 0.001908 (137/71810 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6056910-G-A?dataset=gnomad_r4

Variant: c.2220G > A, p.(Met740Ile)

HGVS: NM_000552.5:c.2220G>A (p.Met740Ile)

ClinVarID: 100206

CAID: CA201316

gnomAD: MAF of 0.1816 (13626/75022 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6046784-C-T?dataset=gnomad_r4

Variant: c.2451T > A, p.(His817Gln)

HGVS: NM_000552.5:c.2451T>A (p.His817Gln)

ClinVarID: 100224

CAID: CA228345

gnomAD: MAF of 0.1150 (8626/75016 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6036483-A-T?dataset=gnomad_r4

Variant: c.3445T > C, p.(Cys1149Arg)

HGVS: NM_000552.5:c.3445T>C (p.Cys1149Arg)

ClinVarID: 309

CAID: CA228410

gnomAD: MAF of 0.000003160 (1/316464 alleles) in European (non-Finnish) population https://gnomad.broadinstitute.org/variant/chr12-6022833-A-G?dataset=gnomad_r4

Variant: c.4414G > C p.(Asp1472His)

HGVS: NM_000552.5:c.4414G>C (p.Asp1472His)

ClinVarID: 256679

CAID: CA6402534

gnomAD: MAF of 0.5076 (38011/74882 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6019004-C-G?dataset=gnomad_r4

Variant: c.6554G > A, p.(Arg2185Gln)

HGVS: NM_000552.5:c.6554G>A (p.Arg2185Gln)

ClinVarID: 100443

CAID: CA228748

gnomAD: MAF of 0.1927 (14427/74878 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-5993906-C-T?dataset=gnomad_r4

Variant: c.6432dupA, (Pro2145Thrfs*5)

HGVS: NM_000552.5:c.6432dup (p.Pro2145Thrfs*5)

ClinVarID:

CAID: CA603482896

gnomAD: MAF of 0.00001333 (1/75038 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-5994027-G-GT?dataset=gnomad_r4

Case: Patient 22, Family I (Table 1.), F/67, Afro-Caribbean

DiseaseAssertion: VWD2A (IIE)

FamilyInfo: Patient 13 (F/65, Afro-Caribbean), Patient 21 (F/97, Afro-Caribbean), Patient 23 (F/86, Afro-Caribbean), Patient 24 (F/92, Afro-Caribbean), Patient 25 (F/62, Afro-Carribean) also from Family I. (Table 1.)

ParentalGenotype(s): NA

CasePresentingHPOs:

CaseHPOFreeRext: BAT =2, FVIII:C (IU/dL) = 33, VWF:Ag (IU/dL) = 20, VWF:Act (IU/dL) = 17

CaseNOTHPOs:

CaseNOTHPOFreeText: Blood group B+

CasePreviousTesting:

GenotypingMethod: All samples were analyzed by captured-based high throughput sequencing which was performed with a custom-design of the VWF gene provided by Twist BioScience (San Francisco, USA). It comprised all 52 exons, intronic flanking regions, promoter and 3’UTR region of the VWF gene. Libraries were prepared by using the Twist NGS target enrichment solution (Twist BioScience) according to the manufacturer protocol. Samples were analyzed on a NovaSeq 6000 sequencer (Illumina) with a median read depth of 2500X by using the 300-cycle S1 NovaSeq 6000seq reagent kit with 150-bp paired-end reads. The raw data were analyzed with Mutect21 and Vardict2 tools. The inhouse NGSreport software (CHU Lille) was used for data visualization, sequences check and conservation of variants with high quality metrics. In some cases, patients genomic DNA was screened for sequence variations (large deletions, insertions and duplications) by Multiplex Ligation-dependent Probe Amplification (MCR Holland).

PreviouslyPublished: NA

Gene: VWF

Variant: c.1530G > A, p.(Val510 =) p.

HGVS: NM_000552.5:c.1530G>A (p.Val510=)

ClinVarID:

CAID: CA6403368

gnomAD: MAF of 0.00002198 (2/91004 alleles) in South Asian population https://gnomad.broadinstitute.org/variant/chr12-6062957-C-T?dataset=gnomad_r4

Variant: c.1892C > T, p.(Ala631Val)

HGVS: NM_000552.5:c.1892C>T (p.Ala631Val)

ClinVarID: 422844

CAID: CA6403245

gnomAD: MAF of 0.001908 (137/71810 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6056910-G-A?dataset=gnomad_r4

Variant: c.2220G > A, p.(Met740Ile)

HGVS: NM_000552.5:c.2220G>A (p.Met740Ile)

ClinVarID: 100206

CAID: CA201316

gnomAD: MAF of 0.1816 (13626/75022 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6046784-C-T?dataset=gnomad_r4

Variant: c.2451T > A, p.(His817Gln)

HGVS: NM_000552.5:c.2451T>A (p.His817Gln)

ClinVarID: 100224

CAID: CA228345

gnomAD: MAF of 0.1150 (8626/75016 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6036483-A-T?dataset=gnomad_r4

Variant: c.3258C > T, p.(Tyr1086 =)

HGVS: NM_000552.5:c.3258C>T (p.Tyr1086=)

ClinVarID: 256664

CAID: CA6402788

gnomAD: MAF of 0.1284 (9131/71128 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6023752-G-A?dataset=gnomad_r4

Variant: c.3445T > C, p.(Cys1149Arg)

HGVS: NM_000552.5:c.3445T>C (p.Cys1149Arg)

ClinVarID: 309

CAID: CA228410

gnomAD: MAF of 0.000003160 (1/316464 alleles) in European (non-Finnish) population https://gnomad.broadinstitute.org/variant/chr12-6022833-A-G?dataset=gnomad_r4

Variant: c.4414G > C p.(Asp1472His)

HGVS: NM_000552.5:c.4414G>C (p.Asp1472His)

ClinVarID: 256679

CAID: CA6402534

gnomAD: MAF of 0.5076 (38011/74882 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-6019004-C-G?dataset=gnomad_r4

Variant: c.6554G > A, p.(Arg2185Gln)

HGVS: NM_000552.5:c.6554G>A (p.Arg2185Gln)

ClinVarID: 100443

CAID: CA228748

gnomAD: MAF of 0.1927 (14427/74878 alleles) in African/African American population https://gnomad.broadinstitute.org/variant/chr12-5993906-C-T?dataset=gnomad_r4

Case: Patient 46, Family U (Table 1.), M/47, Afro-Caribbean

DiseaseAssertion: VWD2M

FamilyInfo: Patient 43 (M/10, Afro-Caribbean), Patient 44 (M/15, Afro-Caribbean), Patient 47(M/78, Afro-Caribbean) and Patient 48 (M/43, Afro Caribbean) also from Family U. (Table 1.)

ParentalGenotype(s): NA

CasePresentingHPOs:

CaseHPOFreeRext: BAT = 11, FVIII:C (IU/dL) = 35.2, VWF:Ag (IU/dL) = 22, VWF:Act (IU/dL) = 8

CaseNOTHPOs:

CaseNOTHPOFreeText: Blood group A+

CasePreviousTesting:

GenotypingMethod: All samples were analyzed by captured-based high throughput sequencing which was performed with a custom-design of the VWF gene provided by Twist BioScience (San Francisco, USA). It comprised all 52 exons, intronic flanking regions, promoter and 3’UTR region of the VWF gene. Libraries were prepared by using the Twist NGS target enrichment solution (Twist BioScience) according to the manufacturer protocol. Samples were analyzed on a NovaSeq 6000 sequencer (Illumina) with a median read depth of 2500X by using the 300-cycle S1 NovaSeq 6000seq reagent kit with 150-bp paired-end reads. The raw data were analyzed with Mutect21 and Vardict2 tools. The inhouse NGSreport software (CHU Lille) was used for data visualization, sequences check and conservation of variants with high quality metrics. In some cases, patients genomic DNA was screened for sequence variations (large deletions, insertions and duplications) by Multiplex Ligation-dependent Probe Amplification (MCR Holland).

PreviouslyPublished: NA

Gene: VWF

Variant: c.3943C > T p.(Arg1315Cys)

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

ClinVarID: 100310

CAID: CA228502

gnomAD: MAF of 8.476e-7 (1/ 1179850 alleles) in European population https://gnomad.broadinstitute.org/variant/chr12-6019161-A-C?dataset=gnomad_r4

Case: P4 Female, Korean, 64 years at report

DiseaseAssertion: VWD1

FamilyInfo: Positive family history, no details provided.

ParentalGenotype: NA

CasePresentingHPOs: HP:0030129, HP:0012147, HP:0030132, HP:0011871

(Impaired ristocetin cofactor assay activity, Reduced quantity of VWF, Absence of large von Willebrand factor multimers, Impaired RIPA)

CaseHPOFreeText: bleeding score 11, FVII:C 40%, VWF:Rco 23 IU/dL, VWF:Ag 26 IU/Dl, VWF:Rco/VWF:Ag 0.9, RIPA NT

CaseNotHPOs: HP:0003645, HP:0001873

(Prolonged partial thromboplastin time, Thrombocytopenia)

CaseNotHPOFreeText: aPTT 36s, platelets 270x10^9/L

CasePreviousTesting: NA

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

Gene: VWF

Variant: c.3389G>A p.C1130Y

HGVS: NM_000552.4:c.2574C>G (p.Cys858Trp)

ClinVar: NA

CAID: CA232299278

gnomAD: MAF of 0.0001002 (2/19954 alleles) in the East Asian population

https://gnomad.broadinstitute.org/variant/12-6143965-G-C

Case: Rotz Proband, female, reported at birth

DiseaseAssertion: VWD2b

FamilyInfo: Mother was 30yo reported with new onset thrombocytopenia during labor, diagnosed with maternal ITP; mother also had history of menorrhagia and excessive bleeding with minor trauma; VWF profile revealed a Factor VIII activity=49 IU/dL, VWF antigen=32 IU/dL, and undetectable RCo

ParentalGenotype(s): mother also carried c.3964G>A unregistered variant

CasePresentingHPOs: HP:0001873, HP:0030132, HP:0000967, HP:0000421, HP:0001892, HP:0001903, HP:0001981

(thrombocytopenia, Absence of large von Willebrand factor multimers, Petechiae, epistaxis, abnormal bleeding, anemia, schistocyte)

CaseHPOFreeText: small hematoma at IV puncture site, platelet count was 9×109/L, ultrasound showed no hemorrhage, hemoglobin=7.6 g/dL

CaseNOTHPOs: HP:0012147, HP:0030129

(Reduced quantity of VWF, impaired ristocetin cofactor assay activity)

CaseNOTHPOFreeText: no unusual findings on physical exam

CasePreviousTesting: NA

GenotypingMethod: Sequencing of VWF exon 28

PreviouslyPublished: NA

Gene: VWF

Variant: c.3964G>A unregistered variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Case: Patient 7 (Family B), male, 81yo

DiseaseAssertion: VWD2B

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0030132, HP:0030129, HP:0030130, HP:0011871

(Absence of large von Willebrand factor multimers, impaired ristocetin cofactor assay activity, Impaired von Willebrand factor collagen binding activity, Impaired RIPA)

CaseHPOFreeText: blood group A, Platelet count x103/μl = 165, PFA 100 sec = >300, SPA % = NA, MADR mg/mL = 0.6, VWF:Ag U/dL = 166.4, VWF:CB U/dL = 30.0, VWF:CB ratio = 0.18, VWF:RCo U/dL = 112.0, VWF:RCo ratio = 0.67, Platelet VWF U/dL = NA, FVIII U/dL = 136.0, BAT F/M = NA

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: Sequencing of exon 28 of VWF

PreviouslyPublished: NA

Gene: VWF

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

HGVS: NM_000552.4(VWF):c.3922C>T (p.Arg1308Cys)

ClinVarID: 289; https://www.ncbi.nlm.nih.gov/clinvar/variation/289/

CAID: NA

gnomAD: absent

Case: Patient 17 (Family E), female, 24yo

DiseaseAssertion: VWD2B

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0030132, HP:0030129, HP:0030130, HP:0011871, HP:0012147

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

CaseHPOFreeText: blood group O, Platelet count x103/μl = 65, PFA 100 sec = >300, SPA % = 22.5, MADR mg/mL = 0.15, VWF:Ag U/dL = 35.9, VWF:CB U/dL = 15.6, VWF:CB ratio = 0.44, VWF:RCo U/dL = 14.4, VWF:RCo ratio = 0.40, Platelet VWF U/dL = 140.3, FVIII U/dL = 35.9, BAT F/M = 13

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: Sequencing of exon 28 of VWF

PreviouslyPublished: NA

Gene: VWF

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

HGVS: NM_000552.4(VWF):c.3946G>A (p.Val1316Met)

ClinVarID: 290; https://www.ncbi.nlm.nih.gov/clinvar/variation/290/

CAID: NA

gnomAD: absent

Case: Patient 4 (Family A), male, 43yo

DiseaseAssertion: VWD2B

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0030132, HP:0030129, HP:0030130, HP:0011871, HP:0012147

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

CaseHPOFreeText: blood group A, Platelet count x103/μl = 163, PFA 100 sec = >300, SPA % = 0, MADR mg/mL = 0.6, VWF:Ag U/dL = 42.8, VWF:CB U/dL = 10.6, VWF:CB ratio = 0.25, VWF:RCo U/dL = 25.2, VWF:RCo ratio = 0.58, Platelet VWF U/dL = 132.7, FVIII U/dL = 47.1, BAT F/M = 10

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: Sequencing of exon 28 of VWF

PreviouslyPublished: NA

Gene: VWF

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

HGVS: NM_000552.4(VWF):c.3922C>T (p.Arg1308Cys)

ClinVarID: 289; https://www.ncbi.nlm.nih.gov/clinvar/variation/289/

CAID: NA

gnomAD: absent

Case: Patient ID 051 (green color code), 11 year old Black female, not Hispanic

DiseaseAssertion: Type 3 Von Willebrand Disease

CasePresentingHPOs: HP:6000676

(Anti-von Willebrand factor antibody positivity)

CaseHPOFreeRext: ISTH-BAT bleeding score of 32

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: N/A

GenotypingMethod: Full-length VWF exonic Sanger sequencing and array comparative genomic hybridization to detect deletions or duplications

Gene: VWD

HGVS: NM_000552.5

Variant1: p.Trp1144*

ClinVarID / CAID: None

Variant2: p.Leu1281Cysfs*16

CAID: CA2575053893

gnomAD: MAF of 1.695E-6 in European (non-Finnish), no homozygotes noted; gnomAD Page

Case: P24, Chinese, male, 6yo

DiseaseAssertion: VWD3

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type A blood, bleeding score = 13; VWF:Ag (%) = 0.9, VWF:RCo (%) = 0.7, FVIII:C (%) = 5.0, VWF:CB (%) = 0.7, VWFpp (%) = 0.9, VWF:RCo/VWF:Ag = 0.8, VWF:CB/VWF:Ag = 0.8, VWFpp/VWF:Ag = 1.0, FVIII:C/VWF:Ag = 5.6

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant: c.478G>C (p.Gly160Arg)

HGVS: NM_000552.5:c.478G>C (p.Gly160Arg)

ClinVarID: NA

CAID: CA383518174; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA383518174

gnomAD: absent

Case: P59, Chinese, female, 7yo

DiseaseAssertion: VWD3

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type O blood, bleeding score = 7; VWF:Ag (%) = 1.4, VWF:RCo (%) = 1.0, FVIII:C (%) = 3.9, VWF:CB (%) = 1.3, VWFpp (%) = 1.2, VWF:RCo/VWF:Ag = 0.7, VWF:CB/VWF:Ag = 0.9, VWFpp/VWF:Ag = 0.9, FVIII:C/VWF:Ag = 2.8

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant 1: c.2964C>A (p.Tyr988Ter)

HGVS: NM_000552.5:c.2964C>A (p.Tyr988Ter)

ClinVarID: NA

CAID: CA383516120; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA383516120

gnomAD: absent

Variant 2: c.6540T>G (p.Tyr2180Ter)

HGVS: NM_000552.5:c.6540T>G (p.Tyr2180Ter)

ClinVarID: NA

CAID: CA383490834; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA383490834

gnomAD: absent

Case: P30, Chinese, female, 16yo

DiseaseAssertion: VWD3

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type O blood, bleeding score = 21; VWF:Ag (%) = 0.5, VWF:RCo (%) = <0.5, FVIII:C (%) = 2.0, VWF:CB (%) = 0.6, VWFpp (%) = <0.5`, VWF:RCo/VWF:Ag = NA, VWF:CB/VWF:Ag = 1.2, VWFpp/VWF:Ag = NA, FVIII:C/VWF:Ag = 4.0

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant: Exons 6–16 del - unregistered variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Case: P89, Chinese, female, 51yo

DiseaseAssertion: VWD2N

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type O blood, bleeding score = 7; VWF:Ag (%) = 125.8, VWF:RCo (%) = 119.6, FVIII:C (%) = 9.8, VWF:CB (%) = 127.8, VWFpp (%) = 109.8, VWF:RCo/VWF:Ag = 1.0, VWF:CB/VWF:Ag = 1.0, VWFpp/VWF:Ag = 0.9, FVIII:C/VWF:Ag = 0.1, VWF: FVIIIB (%) = 0.1

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant: c.2446C>T (p.Arg816Trp)

HGVS: NM_000552.4(VWF):c.2446C>T (p.Arg816Trp)

ClinVarID: 295; https://www.ncbi.nlm.nih.gov/clinvar/variation/295/

CAID: NA

gnomAD: MAF = 0.0002541 (9/35418 alleles) in the Latino/Admixed American population; https://gnomad.broadinstitute.org/variant/12-6145654-G-A?dataset=gnomad_r2_1

Case: P28, Chinese, male, 15yo

DiseaseAssertion: VWD2B

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type A blood, bleeding score = 4; VWF:Ag (%) = 17.7, VWF:RCo (%) = 4.9, FVIII:C (%) = 25.5, VWF:CB (%) = 5.1, VWFpp (%) = 45.3, VWF:RCo/VWF:Ag = 0.3, VWF:CB/VWF:Ag = 0.3, VWFpp/VWF:Ag = 2.6, FVIII:C/VWF:Ag = 1.4, RIPA (0.5 mg/ml, %) = 20.5, PLT(×109/l) = 112

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

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

HGVS: NM_000552.4(VWF):c.3922C>T (p.Arg1308Cys)

ClinVarID: 289; https://www.ncbi.nlm.nih.gov/clinvar/variation/289/

CAID: NA

gnomAD: absent

Case: P47, Chinese, female, 23yo

DiseaseAssertion: VWD1

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type O blood, bleeding score = 12; VWF:Ag (%) = 4.5, VWF:RCo (%) = 3.3, FVIII:C (%) = 36.5, VWF:CB (%) = 4.2, VWFpp (%) = 5.3, VWF:RCo/VWF:Ag = 0.7, VWF:CB/VWF:Ag = 0.9, VWFpp/VWF:Ag = 1.2, FVIII:C/VWF:Ag = 8.1, RIPA (1.2 mg/ml, %) = 55.9

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant 1: c.100C>T (p.Arg34Ter)

HGVS: NM_000552.4(VWF):c.100C>T (p.Arg34Ter)

ClinVarID: 100171; https://www.ncbi.nlm.nih.gov/clinvar/variation/100171/

CAID: NA

gnomAD: MAF = 0.00002645 (3/113436 alleles) in the European (non-Finnish) population; https://gnomad.broadinstitute.org/variant/12-6230460-G-A?dataset=gnomad_r2_1

Variant 2: c.6860G>A (p.Arg2287Gln)

HGVS: NM_000552.3:c.6860G>A (p.Arg2287Gln)

ClinVarID: NA

CAID: CA6401877; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA6401877

gnomAD: MAF = 0.005415 (108/19946 alleles) in the East Asian population; https://gnomad.broadinstitute.org/variant/12-6094770-C-T

Case: P8, Chinese, male 3yo

DiseaseAssertion: VWD3

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type A blood, bleeding score = 5; VWF:Ag (%) = 2.1, VWF:RCo (%) = 1.7, FVIII:C (%) = 4.8, VWF:CB (%) = 1.5, VWFpp (%) = 2.3, VWF:RCo/VWF:Ag = 0.8, VWF:CB/VWF:Ag = 0.7, VWFpp/VWF:Ag = 1.1, FVIII:C/VWF:Ag = 2.3

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant 1: c.1025_1032dup - unregistered variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Variant 2: c.7969C>T (p.Gln2657Ter)

HGVS: NM_000552.5:c.7969C>T (p.Gln2657Ter)

ClinVarID: NA

CAID: CA383487678; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA383487678

gnomAD: NA

Case: P81, Chinese, female, 30yo

DiseaseAssertion: VWD1

FamilyInfo: NA

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0012147

(Reduced quantity of VWF)

CaseHPOFreeText: type A blood, bleeding score = 7; VWF:Ag (%) = 5.0, VWF:RCo (%) = 5.3, FVIII:C (%) = 6.1, VWF:CB (%) = 6.8, VWFpp (%) = 46.0, VWF:RCo/VWF:Ag = 1.1, VWF:CB/VWF:Ag = 1.4, VWFpp/VWF:Ag = 9.2, FVIII:C/VWF:Ag = 1.2, RIPA (1.2 mg/ml, %) = 85.4

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant: c.3614G>A (p.Arg1205His)

HGVS: NM_000552.4(VWF):c.3614G>A (p.Arg1205His)

ClinVarID: 308; https://www.ncbi.nlm.nih.gov/clinvar/variation/308/

CAID: NA

gnomAD: absent

Case: P9, female, 28yo

DiseaseAssertion: VWD2M

FamilyInfo: NA

ParentalGenotype(s): NA

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

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

CaseHPOFreeText: bleeding score = 7; VWF:Ag (%) = 35, VWF:RCo(%) = 24, VWF:RCo/VWF:Ag ratio = 0.69, VWF:CIIIB (%) = 11, VWF:CIIIB/VWF:Ag ratio = 0.31, VWF:CVIB (%) = 19.2, VWF:CVIB/VWF:Ag ratio = 0.54

CaseNOTHPOs: HP:0030132

(Absence of large von Willebrand factor multimers)

CaseNOTHPOFreeText: NA

CasePreviousTesting: NA

GenotypingMethod: NGS

PreviouslyPublished: NA

Gene: VWF

Variant: c.5140G>C (p.Ala1714Pro)

HGVS: NM_000552.3:c.5140G>C (p.Ala1714Pro)

ClinVarID: NA

CAID: CA383496428; http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA383496428

gnomAD: absent

Case: 2A-4

DiseaseAssertion: VWD2A

FamilyInfo:

ParentalGenotype(s):

CasePresentingHPOs: AcuStar RCo/Ag = 0.39; AcuStar CB/Ag = 0.17; ELISA CB/Ag = 0.20

CaseHPOFreeText:

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting:

GenotypingMethod: not described

PreviouslyPublished: PMID: 1537829

Gene: VWF

Variant: c.4789C>T (p.Arg1597Trp)

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

ClinVarID: 285; https://www.ncbi.nlm.nih.gov/clinvar/variation/285/?new_evidence=false

CAID:

gnomAD: absent

Case#: 21006, Age 40, Male, Blood Type O+ (Table S3)

Disease Assertion: VWD 1

FamilyInfo: The patient is one of 4 members of Family# 2103. Each patient has the p.Gly2083Asp variant. Some of the patients have a second variant.

Parental Genotype: Not listed

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding Score 8, VWF:Ag: 11, VWF:RCo: 10, FVIII:C:29, VWF:CB: 10.3

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

Protein Expression: N/A

CasePreviousTesting: 48,48 Access-Array amplification. NGS Molecular analysis was performed. Sanger sequencing was used to validate selected mutations

Gene: VWF

Variant: NM_000552.4:c.6248G>A (p.Gly2083Asp)

ClinVar: N/A

CAID: CA383492072 CAID

gnomAD: N/A

Case#: 29002, Age 38, Female, Blood Type O+ (Table S3)

Disease Assertion: VWD 1

FamilyInfo: The patient is the only member of Family#2902.

Parental Genotype: Not listed

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding score 7, VWF:Ag: 22, VWF:RCo: 17, FVIII:C: 54, VWF:CB:17

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

Protein Expression: N/A

CasePreviousTesting: 48,48 Access-Array amplification. NGS Molecular analysis was performed. Sanger sequencing was used to validate selected mutations.

Gene: VWF

Variant: NM_000552.4:c.3223-7_3236dup (p.Pro1079_Tyr1080insLeuGlnValAspProGluPro) and NM_000552.4(VWF):c.5277C>T (p.Asp1759=)

ClinVar: 310061 ClinVar

CAID: CA1139532066 and CA6402333 CAID1 CAID2

gnomAD: MAF of 0.01423 (1837/129090 alleles) in the European (non-Finnish) population (CA6402333). gnomAD

Case#: 30008, Age 24, Female, Blood Type A+ (Table S3)

Disease Assertion: VWD 1

FamilyInfo: The patient is one of two members of Family #3006. Both patients have the same variant.

Parental Genotype: Not listed

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding Score 12, VWF:Ag:18, VWF:RCo:19.3, FVIII:C: 35, VWF:CB: 21

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

Protein Expression: N/A

CasePreviousTesting: 48,48 Access-Array amplification. NGS Molecular analysis was performed. Sanger sequencing was used to validate selected mutations.

Gene: VWF

Variant: NM_000552.4:c.6536C>T (p.Ser2179Phe)

ClinVar: 100442 ClinVar

CAID: CA228746 CAID

gnomAD: N/A

Case#: 35008, Age 64, Male, Blood Type A+ (Table S3)

Disease Assertion: VWD 1

FamilyInfo: The patient is the only member of Family# 3503.

Parental Genotype: Not listed

CasePresentingHPOs: N/A

CaseHPOFreeText: VWF:Ag: 5.3, VWF:RCo:5, FVIII:C: 10, VWF:CB: 4.9

CaseNotHPOs: N/A

CaseNotHPOFreeText: Bleeding Score 2

Protein Expression: N/A

CasePreviousTesting: 48,48 Access-Array amplification. NGS Molecular analysis was performed. Sanger sequencing was used to validate selected mutations.

Gene: VWF

Variant: NM_000552.4:c.1625C>G (p.Ala542Gly), NM_000552.4:c.5198T>C (p.Leu1733Pro), and NM_000552.4:c.6187C>T (p.Pro2063Ser)

ClinVar: 381621 and 100436 ClinVar1 ClinVar2

CAID: CA6403319, CA383496267, and CA202650 CAID1 CAID2 CAID3

gnomAD: MAF of 0.001355 (48/ 35418 alleles) in the Latino population (CA6403319). gnomAD

MAF of 0.04854 (1486/30616 alleles) in the South Asian population (CA202650). gnomAD

Case#: 37005, Age 39, Female, Blood Type O+ (Table S3)

Disease Assertion: VWD 1

FamilyInfo: The patient is the only member of Family#3705.

Parental Genotype: Not listed

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding Score 9, VWF:Ag:26, VWF:RCo: 18, FVIII:C: 44, VWF:CB: 18

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

Protein Expression: N/A

CasePreviousTesting: 48,48 Access-Array amplification. NGS Molecular analysis was performed. Sanger sequencing was used to validate selected mutations.

Gene: VWF

Variant: NM_000552.4:c.2878C>T (p.Arg960Trp)

ClinVar: N/A

CAID: CA6402916 CAID

gnomAD: MAF of 0.0004900 (50/ 30612 alleles) in the South Asian population. gnomAD

Case#: 30006, Age 70, Female, Blood Type A- (Table S3)

Disease Assertion: VWD 1

FamilyInfo: The patient is the only member of Family#3005.

Parental Genotype: Not listed

CasePresentingHPOs: N/A

CaseHPOFreeText: Bleeding Score 17, VWF:Ag: 24, VWF:RCo: 29.4, FVIII:C:30, VWF:CB: 28

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

Protein Expression: N/A

CasePreviousTesting: 48,48 Access-Array amplification. NGS Molecular analysis was performed. Sanger sequencing was used to validate selected mutations.

Gene: VWF

Variant: NM_000552.4:c.5336G>T(p.Arg1779Leu)

ClinVar: N/A

CAID: CA383495656 CAID

gnomAD: MAF of 0.00002891 ( 1/ 34592 alleles) in the Latino population. gnomAD

Case: IC-T105, Canadian, female

DiseaseAssertion: VWD3

FamilyInfo: Pedigree in Fig 1A, 4 homozygotes, 3 heterozygotes

ParentalGenotype(s): not reported

CasePresentingHPOs:

CaseHPOFreeText: VWF:Ag = 0.02 IU/mL, VWF:RCo = 0.00 IU/mL, FVIII:C = 0.03, bleeding score = 18

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: NA

GenotypingMethod: sequencing of VWF gene

PreviouslyPublished: PMID:23311757

Gene: VWF

Variant: c.8419_8422dup (p.Pro2808Lysfs*24) - Unregistered Variant

HGVS: NA

ClinVarID: NA

CAID: NA

gnomAD: NA

Case: IP-6

DiseaseAssertion: VWD2

FamilyInfo: Mother is unaffected carrier of F8 Asn2129Ser. The VWF deletion of exons 33-34 segregates in 5 other affected male family members including the father and a full brother of IP-6. The patient’s father displayed a significant decrease in VWF:Ag and VWF:RCo, 13% and 7%, respectively, FVIII: C of 18.5% and the VWF:RCo/VWF:Ag ratio of 0.5 pointing out to type 2 VWD.

ParentalGenotype(s): Mother is heterozygous for F8FAsn2129Ser. Father is heterozygous for VWF deletion of exons 33-34.

CasePresentingHPOs:

CaseHPOFreeRext: VWF:Ag (17%), VWF:RCo (9%) and FVIII:C (1,9%). Bleedings in the oral cavity, ankle joint and hematomas.

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: Direct sequencing of exons 2–52 including exon/intron boundaries of the VWF gene

GenotypingMethod: multiple ligation‐dependent probe amplification (MLPA; using kit P011 and P012; MRC Holland, Amsterdam, the Netherlands) according to the manufacturer’s instructions. The PCR products were run on an ABI PRISM 3130XL sequencer with the GeneScan 500 LIZ size standard and analyzed using GeneMapper Software 5.0 (Applied Biosystems, Darmstadt, Germany). Dosage analysis based on a comparison between deleted and reference wild‐type DNA samples was performed using the Excel‐based software Coffalyser V9.4 (MRC Holland).

PreviouslyPublished: NA

Gene:VWF

Variant: deletion of exons 33-34

HGVS:

ClinVarID:

CAID:

gnomAD:

MultipleGeneVariants:

GeneName: F8

Variant: Asn2129Ser

ClinVarID or CAID:

gnomAD:

Case: Case Report, female, 63yo

DiseaseAssertion: VWD2B

FamilyInfo: sister exhibited thrombocytopenia and mother had suffered from acute subdural hematoma in the context of chronic thrombocytopenia

ParentalGenotype(s): NA

CasePresentingHPOs: HP:0002138, HP:0011854, HP:0001873, HP:0032044, HP:0030132

(Subarachnoid hemorrhage, Hemoperitoneum, thrombocytopenia, Decreased vigilance, Absence of large von Willebrand factor multimers)

CaseHPOFreeText: thrombocytopenia with pregnancy, platelet count fluctuated between 3 and 200 G/l, subarachnoid hemorrhage associated with a subdural hematoma after falling, hemostasis results were normal, meningeal hemorrhage, cephalalgia; FVIII:C: 1.63 IU/ml; VWF:RCo: 0.7 IU/ml; VWF:Ag: 1.8 IU/ml, ratio VWF:Rco/VWF/Ag: 0.39; Ristocetin-induced platelet agglutination could not be performed due to the severe thrombocytopenia

CaseNOTHPOs: NA

CaseNOTHPOFreeText: NA

CasePreviousTesting: tests for autoimmune disease negative

GenotypingMethod: NGS of exon 28 of VWF gene; variant confirmed via Sanger sequencing

PreviouslyPublished: NA

Gene: VWF

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

HGVS: NM_000552.4(VWF):c.3946G>A (p.Val1316Met)

ClinVarID: 290; https://www.ncbi.nlm.nih.gov/clinvar/variation/290/

CAID:

gnomAD: absent

Case#: 5, male, 65yo

DiseaseAssertion: VWD1

FamilyInfo: grandson diagnosed with VWD

ParentalGenotype: N/A

CasePresentingHPOs: HP:0000978, HP:0004846, HP:0012147, HP:0030129, HP:0030130 (Bruising susceptibility, Reduced quantity of VWF, Impaired ristocetin cofactor assay activity, Impaired von Willebrand factor collagen binding activity)

CaseHPOFreeText: Bleeding after oral surgery, ESRD awaiting renal transplantation, Type A blood, VWF:Ag (0·55–2 iu/ml) pre = 0·41, VWF:RCo (0·55–2 iu/ml) pre = 0·29, FVIII:C (0·55–2 iu/ml) pre = 0·31, FVIII:C/VWF:Ag ratio = 0·75, VWF:FVIII binding (>20%) = 12%, VWF:FVIII binding/VWF:Ag (>0·7) = 0·29, Uncomplicated kidney transplant with VWF concentrate replacement

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

ProteinExpression: N/A

CasePreviousTesting: RFLP; confirmatory sequencing

Gene: VWF

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

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

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

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

Case#: 12 yr, female,

DiseaseAssertion: HCM

FamilyInfo: Father and younger brother also diagnosed, same mutation, brother asymptomatic,

CasePresentingHPOs: Syncope, Left bundle branch block, third degree atrioventricular block, amaurosis fugax, vertigo, ventricular septal hypertrophy, mitral regurgitation (HP:0001279, HP:0011713, HP:0001709, HP:0100576, HP:0002321, HP:0005144, HP:0001653)

CaseHPOFreeText: bilateral atrial enlargement to 44mm for left and 40 mm for right, interventricular septum thickened to 23mm, posterior left ventricle thickened to 10 mm, left ventricular ejection fraction of 51.8%, elevated plasma level B-type Natriuretic peptic 1165 pg/ml

CaseNotHPOs: heart murmur (HP:0030148)

CaseNotHPOFreeText: normal liver and spleen size, no edema, pericardial abnormality, no obstruction of left ventricular outflow tract, normal pasma amino acids and urine organic acids

CasePreviousTesting: whole exome sequencing

CaseGenotypingMethod: heart rate of 102/min; respiratory rate of 25/min; blood pressure of 127/74 mmHg; ECG; 175 QRS complex; Holter monitor; MRI; Etiologic investigations; Bioinformatic analysis based on Polymorphism Phenotyping v2, Sorting Intolerant From Tolerant;

Variant: NM_000257.4(MYH7):c.2155C>T (p.Arg719Trp)

ClinVar: 14104 https://www.ncbi.nlm.nih.gov/clinvar/variation/14104/

CAID: N/A

gnomAD: 0.00006481 https://gnomad.broadinstitute.org/variant/14-23895180-G-A

Supplementary Data: Online Table 3

Case:

CasePreviousTesting: Full sarcomere testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1), Additional testing (ABCC9, ACTN2, ANKRD1, BAG3, CALR3, CRYAB, CSRP3, DES, DMD, DSC2, DSG2, DSP, EMD, GLA, JPH2, JUP, LAMA4, LAMP2, LMNA, MYH6, MYPN, MYOZ1, MYOZ2, PKP2, PLN, PRKAG2, RBM20, RYR2, SCN5A, SGCD, TAZ, TCAP, TMEM43, TNNC1, TTN, VCL and LDB3)

CaseGenotypingMethod: DNA isolated from peripheral blood, targeted enrichment, next-gen sequencing with panel of 46 genes

Variant: NM_000257.3:c.2453T>A

CAID: CA389048376, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA389048376

gnomAD: n/a

CaseIII-3: female

DiseaseAssertion: LVNC, Ebstin anomaly, congenital heart disease

FamilyInfo: all mutation carriers have LVNC, with some having Ebstein anomaly and/or other CHD

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting:

GenotypingMethod:

Variant: NM_000257.4:c.847T>G

ClinVar: 66081

CAID: CA016893

gnomAD:

Supplementary Data Table S3

Case: 140

DiseaseEntity: HCM

HPOsFreeText: left ventricular hypertrophy (LVH) ≥15 mm

InheritancePattern: n/a

CasePreviousTesting: MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1 (59 genes total tested)

CaseGenotypingMethod: NGS of 59 genes (Supplemental Table S1), pathogenic and likely pathogenic variants confirmed via Sanger Sequencing

Variant1: NM_000257.4(MYH7):c.1816G>A (p.Val606Met)

ClinVar: 14091 https://www.ncbi.nlm.nih.gov/clinvar/variation/14091/

gnomAD: 0.00001548, https://gnomad.broadinstitute.org/variant/14-23896866-C-T

Variant2: NM_000257.4(MYH7):c.3853+7C>T

ClinVar: 42977 https://www.ncbi.nlm.nih.gov/clinvar/variation/42977/

gnomAD: 0.003956, https://gnomad.broadinstitute.org/variant/14-23888685-G-A

Case1: 17 month onset

DiseaseAssertion: Noncompaction of the ventricular myocardium

FamilyInfo: No known family history of heart disease or sudden cardiac death, Has two sisters with the same MYH7 variant and similar phenotypes, See Fig 3 for pedigree

CasePresentingHPOs: HP:0001279, HP:0001635, HP:0012818, HP:0031295, HP:0030718, HP:0005133, HP:0005180, HP:0001653, HP:0001723, HP:0002092, HP:0004890, HP:0030876, HP:0005168 (Syncope, Heart failure, Biventricular noncompaction cardiomyopathy, Left atrial enlargement, Right atrial enlargement, Right ventricular dilation, Tricuspid regurgitation, Mitral regurgitation, Restrictive cardiomyopathy, Pulmonary arterial hypertension, Elevated pulmonary artery pressure, Increased pulmonary capillary wedge pressure, Elevated right atrial pressure)

HPOsFreeText: Both cardiac ventricles had a coarsely trabeculated and spongy appearance in posterior wall, lateral wall, apical segments, and right ventricle, LVEF at 51%, Short E-wave deceleration time at the transmitral level (85 msec) with a high E/A ratio (2.1), Ratio between the thickness of the noncompacted layer and the myocardial layer was 3.4:1, Underwent cardiac catheterization, Left ventricular systolic pressure and end-diastolic pressure were 95 mmHg and 37 mmHg respectively, Pulmonary vascular resistance was 4.0 Wood Unit m^2

CaseNotHPOs: N/A

NotHPOsFreeText: Normal left ventricle end-diastolic volume (110%), No other congenital heart disease

CaseAddInfo: Died at age 2 yrs of advanced heart failure

CasePreviousTesting: TruSight One sequencing panel was used for testing (Illumina)

CaseGenotypingMethod: Blood samples were collected from the proband and his siblings and genomic DNA was extracted. Target enrichment was performed using the TruSight One sequencing panel (Illumina). Analysis was annotated and filtered, after which the MYH7 pathogenic variant was confirmed using PCR and Sanger sequencing.

Variant: NM_000257.4(MYH7):c.5740G>A (p.Glu1914Lys)

ClinVar: 43088 https://www.ncbi.nlm.nih.gov/clinvar/variation/43088/

gnomAD: Not in gnomAD

MultipleGeneVariants

(1) PLEC Variant

Variant: NM_000445.4:c.3005-8T>C

CAID: CA187619061 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA187619061

gnomAD: Not in gnomAD

Supplementary Material 4

Case M-28: Japanese

DiseaseAssertion: idiopathic cardiomyopathy (HCM and DCM)

CasePreviousTesting: Clinical evaluation, chest radiography, electrocardiography, echocardiography, cardiac catheterization, full testing (MYBPC3, TNNT2, TNNI3, MYL2, MYL3, TPM1, ACTC1)

CaseGenotypingMethod: 8 sarcomeric genes amplified from genomic DNA via PCR then screened using bidirectional direct sequencing

Variant: NM_000257.3(MYH7):c.2770G>A (p.Glu924Lys)

ClinVar: 14092, https://www.ncbi.nlm.nih.gov/clinvar/variation/14092/

gnomAD: n/a

Case#: 45 yr, female, diagnosed at 13 from heart murmur

DiseaseAssertion: HCM

FamilyInfo: sibling with HCM, family history of symptoms and same mutation

CasePresentingHPOs: left ventricular hypertrophy (HP:0001712)

CaseHPOFreeText: abnormal coaptation of the mitral valve, systolic anterior motion of the mitral valve,

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

CaseGenotypingMethod: stem cell derivation and cardiomyocyte differentiation; hiPSC-cardiomyocyte shRNA silencing experiments; qPCR analysis of MYH7 alleles; ECG; Micropatterning; ASO silencing

Variant: NM_000257.4(MYH7):c.1208G>A (p.Arg403Gln)

ClinVar: 14087 https://www.ncbi.nlm.nih.gov/clinvar/variation/14087/

CAID: N/A

gnomAD: absent

CaseCM006

DiseaseAssertion: HCM

GenotypingMethod: NGS

MultipleGeneVariants:

VariantMYH7: NM_000257.4:c.4343A>T

ClinVar: 432912

CAID: CA041680

gnomAD: 0.0001320 European (non Finnish)

https://gnomad.broadinstitute.org/variant/14-23886722-T-A

VariantNEXN: NM_144573.3:c.620A>G

ClinVar: 520305

CAID: CA918690

gnomAD: https://gnomad.broadinstitute.org/variant/1-78392229-A-G

0.00005794 Latino

CaseR858C: 44 year old (text states male, pedigree states female)

DiseaseAssertion: HCM

FamilyInfo: No family members manifested sudden death, lethal arrhythmia, LVOT obstruction, or severe heart failure.

One family member also carried double mutations

CaseHPOFreeText: greater LV hypertrophy than his family members who carried a single mutation

CasePreviousTesting: systematic mutation screening of eight sarcomeric genes: (MYH7), (MYBPC3), (TNNT2), (TNNI3), (MYL2), (MYL3), (TPM1), and (ACTC), using direct DNA sequencing

GenotypingMethod: Genomic DNA was isolated from the leukocytes of the peripheral blood. Polymerase chain reaction was used to amplify the exons and flanking intronic bases of the eight genes, including MYH7, MYBPC3, TNNT2, TNNI3, MYL2, and MYL3. When no mutation was found, analysis of the TPM1 and ACTC genes was performed

MultipleGeneVariants:

VariantMYH7: NM_000257.4:c.2572C>T

ClinVar: 164324

CAID: CA012656

gnomAD: https://gnomad.broadinstitute.org/variant/14-23894085-G-A

0.00006152 African

VariantTNNT2: NM_001001430.3:c.857G>A

ClinVar: 43677

CAID: CA005304

gnomAD: https://gnomad.broadinstitute.org/variant/1-201328348-C-T

0.0008699 East Asian

CaseIII:2: 44 year old male, South Asian

DiseaseAssertion: HCM, septal hypertrophic obstructive cardiomyopathy

FamilyInfo: family history of two sudden cardiac deaths at ages 35 and 19, and three family members with septal hypertrophic obstructive cardiomyopathy

CasePresentingHPOs: HP:0001279, HP:0002094, HP:0001962

"Syncope, Dyspnea, Palpitations"

CasePreviousTesting: screened sarcomeric thin filament protein gene, α-tropomyosin (TPM1), screening of seven other sarcomeric genes: MYH7, MYBPC3, TNNT2, TNNI3, MYL2, MYL3, and ACTC

GenotypingMethod: sequences covering all the exons and exon–intron boundaries of TPM1 and seven other sarcomeric genes (MYH7, MYBPC3, TNNT2, TTN, TNNI3, MYL2, MYL3, and ACTC) were synthesized

MultipleGeneVariants:

VariantMYH7: NM_000257.4:c.2686G>A

ClinVar: 132908

CAID: CA012857

gnomAD: not found

VariantMYH7: NP_000248.2:p.Ile524Lys

ClinVar: not found

CAID: valid allele but not present in the registry

gnomAD: not found

VariantTPM1: NM_000366.6:c.644C>T

ClinVar: 31883

CAID: CA018243

gnomAD: https://gnomad.broadinstitute.org/variant/15-63354418-C-T

0.000008806 European (non-Finnish)

CaseII-9: Male, 38 years diagnosis, China, Asian

DiseaseAssertion: Hypertrophic cardiomyopathy

FamilyInfo: Proband's father (I-1) and mother (I-2) had histories of mild episodes of dizziness, no other symptoms reported in the other family members

CasePresentingHPOs: HP:0001279, HP:0001712, HP:0001639 (Syncope, Left ventricular hypertrophy, Hypertrophic cardiomyopathy)

HPOsFreeText: Heart rate 62 bpm, PR interval 172 ms, QRS complex duration 88 ms, Diffuse repolarization changes with a late-onset inverted T-wave pattern, LVMI 109.55 g/m2, MLVWT 24 mm, Ejection Fraction 70%

CaseNotHPOs: HP:0030148 (Heart murmur)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: See Table 1

CaseGenotypingMethod: Genomic DNA was extracted from blood and amplified. It was then subjected to a sequencing panel with an Illumina sequencer based on the 96 genes related to cardiac function. All readings were aligned, with any variants confirmed by Sanger sequencing and filtered for pathogenicity.

Variant: NM_000257.3:c.5151T>A (p.His1717Gln)

CAID: CA389036862 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000257.3%3Ac.5151T%3EA

gnomAD: Not in gnomAD

Multiple Gene Variants:

KCNQ1 Variant

Variant: NM_000218.2:c.568C>T (p.Arg190Trp)

ClinVar: 53070 https://www.ncbi.nlm.nih.gov/clinvar/variation/53070/

gnomAD: Latino 2.896e-5, Overall 4.011e-6 https://gnomad.broadinstitute.org/variant/11-2591948-C-T

MYLK2 Variant

Variant: NM_033118.3:c.970A>G (p.Lys324Glu)

ClinVar: CA408526793 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_033118.3%3Ac.970A%3EG

gnomAD: African 6.453e-5, Overall 4.087e-6 https://gnomad.broadinstitute.org/variant/20-30412153-A-G

TMEM70 Variant

Variant: NM_017866.5:c.440T>C (p.Ile147Thr)

ClinVar: 571761 https://www.ncbi.nlm.nih.gov/clinvar/variation/571761/

gnomAD: East Asian 4.893e-4, Overall 3.579e-5 https://gnomad.broadinstitute.org/variant/8-74893513-T-C

CaseHCM006: 15 yrs report, Vietnam, Asian

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: Family history of sudden cardiac death

CasePresentingHPOs: HP:0002875, HP:0001712, HP:0031295, HP:0011103, HP:0001653 (Exertional dyspnea, Left ventricular hypertrophy, Left atrial enlargement, Abnormality of the left ventricular outflow tract, Mitral regurgitation)

HPOsFreeText: Maximal LV thickness 33 mm

CaseNotHPOs: HP:0005110, HP:0001297, HP:0004756 (Atrial fibrillation, Stroke, Ventricular tachycardia)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: The gene panel included 10 sarcomeric genes (MYH7, MYBPC3, TNNT2, TNNI3, TPM1, MYL2, MYL3, ACTC1, TNNC1, MYH6), 9 genes encoding Z-disk components and Ca2+ homeostasis factors (LDB3, CSRP3, TCAP, VCL, ACTN2, MYOZ2, NEXN, JPH2, PLN), and 4 genes involved in HCM phenocopies (GLA, LAMP2, PRKAG2, TTR), All probands had left ventricular wall thickness >= 15 mm and no other diseases that can cause secondary hypertrophy

CaseGenotypingMethod: The coding region, flanking sequences, and untranslated regions of each gene were enriched by LC-PCR, amplified, and sequenced on the Illumina MiSeq or MiniSeq platform. Identified variants were then filtered for pathogenicity and confirmed by Sanger sequencing.

Variant: NM_000257.4(MYH7):c.2207T>C (p.Ile736Thr)

ClinVar: 164342 https://www.ncbi.nlm.nih.gov/clinvar/variation/164342/

gnomAD: Not in gnomAD

Multiple Gene Variants

(1) NEXN Variant

Variant: NM_144573.3(NEXN):c.835C>T (p.Arg279Cys)

ClinVar: 30994 https://www.ncbi.nlm.nih.gov/clinvar/variation/30994/

gnomAD: 0.006303, http://gnomad.broadinstitute.org/variant/1-78392548-C-T

Case9: Male, 46 years onset, 48 years diagnosis, Italy

HPOsFreeText: See Group Phenotypes, ERT started at 48, GAA Activity at ~7.5 pmol/min/mg before ERT and ~11 after

GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4:c.525delT (p.Glu176Argfs*45)

ClinVar: 4033 https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

gnomAD: European (Non-Finnish) 1.880e-4, Overall 9.959e-5 http://gnomad.broadinstitute.org/variant/17-78078909-CT-C

CaseAddInfo: Late Onset Pompe Disease

Case8: Male, 16 years onset, 36 years diagnosis, Italy

HPOsFreeText: See Group Phenotypes, ERT started at 36, GAA Activity at ~5 pmol/min/mg before ERT and ~13 after

GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4:c.525delT (p.Glu176Argfs*45)

ClinVar: 4033 https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

gnomAD: European (Non-Finnish) 1.880e-4, Overall 9.959e-5 http://gnomad.broadinstitute.org/variant/17-78078909-CT-C

CaseAddInfo: Late Onset Pompe Disease

Case18: Female, 50 years onset, 53 years diagnosis, Italy

HPOsFreeText: See Group Phenotypes, ERT started at 56, GAA Activity at ~6 pmol/min/mg before ERT and ~9 after

GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4:c.1465G>A (p.Asp489Asn)

ClinVar: 92465 https://www.ncbi.nlm.nih.gov/clinvar/variation/92465/

gnomAD: European (Finnish) 4.621e-5, Overall 1.195e-5 http://gnomad.broadinstitute.org/variant/17-78084553-G-A

CaseAddInfo: Late Onset Pompe Disease

Case3: Male, 30 years onset, 66 years diagnosis, Italy

HPOsFreeText: See Group Phenotypes, ERT started at 67, GAA Activity at ~8 pmol/min/mg before ERT and ~10 after

GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4:c.1927G>A (p.Gly643Arg)

ClinVar: 4023 https://www.ncbi.nlm.nih.gov/clinvar/variation/4023/

gnomAD: European (Non-Finnish) 3.667e-5, Overall 2.479e-5 http://gnomad.broadinstitute.org/variant/17-78086713-G-A

CaseAddInfo: Late Onset Pompe Disease

Case1: Male, 21 years onset, 31 years diagnosis, Italy

HPOsFreeText: See Group Phenotypes, ERT started at 31, GAA Activity at ~7.5 pmol/min/mg before ERT and ~8 after

GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4:c.1927G>A (p.Gly643Arg)

ClinVar: 4023 https://www.ncbi.nlm.nih.gov/clinvar/variation/4023/

gnomAD: European (Non-Finnish) 3.667e-5, Overall 2.479e-5 http://gnomad.broadinstitute.org/variant/17-78086713-G-A

CaseAddInfo: Late Onset Pompe Disease

Case13: Male, 34 years onset, 45 years diagnosis, Italy

HPOsFreeText: See Group Phenotypes, ERT started at 45, GAA Activity at ~10 pmol/min/mg before ERT and ~10.5 after

GroupGenotypingMethod: PCR Amplification and GAA Gene Sequencing

Variant1: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.4:c.525delT (p.Glu176Argfs*45)

ClinVar: 4033 https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

gnomAD: European (Non-Finnish) 1.880e-4, Overall 9.959e-5 http://gnomad.broadinstitute.org/variant/17-78078909-CT-C

CaseAddInfo: Late Onset Pompe Disease

Patient7: 71yo

CasePresentingHPOs: HP:0003325, HP:0002093, HP:0002315, HP:0004887, HP:0000822, HP:0003141, HP:0002870, HP:0020038

HPOsFreeText: morning headache, GAA = 7%, BMI = 28.3, temporo-insular lacunes

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 18yr disease duration, variants in trans

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000152.4(GAA):c.-32-13T>G

Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.3:c.2530_2541del

CAID: CA658795292, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA658795292

gnomAD: n/a

Patient5: 36yo

CasePresentingHPOs: HP:0003325, HP:0002093, HP:0001513, HP:0002637

HPOsFreeText: GAA = 4.6%, BMI = 35.1, normal CTA, right temporal pole ischaemia

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: 4yr disease duration, variants in trans

CasePMIDs:

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant1: NM_000152.4(GAA):c.-32-13T>G

Clinvar: 4027, https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: 0.003582, http://exac.broadinstitute.org/variant/17-78078341-T-G

Variant2: NM_000152.3:c.2530_2541del

CAID: CA658795292, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA658795292

gnomAD: n/a

Case#: Subject number 4, female, 11 years (report)

DiseaseAssertion: Pompe disease

FamilyInfo: No known family member with PD

CasePresentingHPOs: HP:0001638 (cardiomyopathy), HP:0002153 (hyperkalemia), HP:0001324 (muscle weakness)

CaseHPOFreeText:

CaseNotHPOs: HP:0003546 (Exercise intolerance), HP:0001252 (Hypotonia), HP:0003326 (Myalgia), HP:0002015 (dysphagia), HP:0002098 (respiratory distress), HP:0002094 (dyspnoea)

CaseNotHPOFreeText: no biopsy, not asymptomatic

CasePreviousTesting: "Enzymatic activity was detected by fluorometric techniques" "The GAA sequence was performed in all patients whose enzyme activity measured in DBS and lymphocytes was decreased."

glucosidase activity: GAA activity was 0.16 mol/Lh in dried blood spots (normal range >0.75).

Variant 1: NM_000152.5(GAA):c.-32-13T>C

Variant 1 ClinVarID: 4027

Variant 1 CAid: CA116606

Variant 2: NM_000152.5(GAA):c.1831G>A (p.Gly611Ser)

Variant 2 ClinVarID: 935199

Variant 2 CAid: CA401369553

Zygosity: Compound heterozygous

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Patient (case report), male, 1 month old, ethnicity unknown

DiseaseAssertion: Pompe disease

FamilyInfo: No history of consanguinity in parents. The patient has a 15 months old sibling that is healthy.

Family medical history was notable for tuberous sclerosis in the patient’s father’s first cousin.

CasePresentingHPOs: HP:0200128, HP:0001639, HP:0002240

(Biventricular hypertrophy, Hypertrophic cardiomyopathy, Hepatomegaly,

CaseHPOFreeText: Echogenic mass within the left ventricle.

Short-axis images revealed the possibility of an additional mass within the left ventricle adjacent to the papillary muscles

Right axis deviation

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

Normal results were noted for levels of plasma amino acids, lactate and pyruvate, total and free carnitine, and acylcarnitine compounds. Urine organic acid quantitation was normal.

PR interval was normal

CasePreviousTesting: The serum creatine kinase was elevated (478 U/L; normal 60–305 U/L).

GAA activity in whole blood from a blood spot was 1.8 pmol/punch/hour (control 10–49 pmol/punch/hour)

The GAA gene was sequenced.

Variant 1: NM_000152.5(GAA):c.525del (p.Glu176fs)

ClinVar: 4033

CAID: CA220406

gnomAD: N/A

Variant 2: NM_000152.5(GAA):c.1927G>A (p.Gly643Arg)

ClinVar: 4023

CAID: CA116596

gnomAD: Highest population MAF=0.00003667 (Euroean (non-Finnish))

ParentalGenotype:N/A

PreviouslyPublished:N/A

Case#: Subject number 6(L)

DiseaseAssertion: Late Onset Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: CK testing: 176 U/L (28-300 U/L is normal), AST: 61 U/L (24-72 U/L is normal), ALT: 39 U/L (17-63 U/L is normal), Hex4: 5.9 mmol/mol Creatinine (≤20 mmol/mol Creatinine is normal)

glucosidase activity: GAA activity #1 was 1.32 micromole/L/h and GAA activity #2 (NBS) 0.88 in dried blood spots (>2.10 micromole/L/h is normal). 0.7 in confirmatory testing (>6.7 is normal).

Variant 1: NM_000152.5(GAA):c.-32-13T>G

Variant 1 ClinVarID: 4027

Variant 1 CAid: CA116606

Variant 2: NM_000152.5(GAA):c.-32-13T>G

Variant 2 ClinVarID: 4027

Variant 2 CAid: CA116606

Zygosity: homozygous

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Subject number 2(L)

DiseaseAssertion: Late Onset Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: CK testing: 72 U/L (28-300 U/L is normal), AST: 21 U/L (24-72 U/L is normal), ALT: 23 U/L (17-63 U/L is normal), Hex4: 4.2 mmol/mol Creatinine (≤20 mmol/mol Creatinine is normal)

glucosidase activity: GAA activity #1 was 1.86 micromole/L/h and GAA activity #2 (NBS) 1.44 in dried blood spots (>2.10 micromole/L/h is normal). 5.3 in confirmatory testing (>6.7 is normal).

Variant 1: NM_000152.5(GAA):c.2238G>C

Variant 1 ClinVarID: 265160

Variant 1 CAid: CA8815665

Variant 2: NM_000152.5(GAA):c.1552-3C>G

Variant 2 ClinVarID: 419722

Variant 2 CAid: CA8815383

Zygosity: compound heterozygous

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Subject number 17(L)

DiseaseAssertion: Late Onset Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: CK testing: 275 U/L (60-305 U/L is normal), AST: 150 U/L (22-71 U/L is normal), ALT: 42 U/L (7-50 U/L is normal), Hex4: 5.2 mmol/mol Creatinine (≤20 mmol/mol Creatinine is normal), BNP 44.5 pg/mL (0.0–100.0 pg/mL is normal)

glucosidase activity: GAA activity #1 was 1.04 micromole/L/h and GAA activity #2 (NBS) 0.77 in dried blood spots (>2.10 micromole/L/h is normal). 1.80 in confirmatory testing (>3.88 is normal).

Variant 1: NM_000152.5(GAA):c.-32-13T>G

Variant 1 ClinVarID: 4027

Variant 1 CAid: CA116606

Variant 2: NM_000152.5(GAA):c.-32-13T>G

Variant 2 ClinVarID: 4027

Variant 2 CAid: CA116606

Zygosity: homozygous

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Subject number 29(L)

DiseaseAssertion: Late Onset Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

glucosidase activity: GAA activity #2 (NBS) 0.48 in dried blood spots (>2.10 micromole/L/h is normal).

Variant 1: NM_000152.5(GAA):c.-32-13T>G

Variant 1 ClinVarID: 4027

Variant 1 CAid: CA116606

Variant 2: NM_000152.5(GAA):c.1547G>A

Variant 2 ClinVarID: 983721

Variant 2 CAid: CA401367155

Zygosity: compound heterozygous

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Subject number 28(L)

DiseaseAssertion: Late Onset Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

glucosidase activity: GAA activity #2 (NBS) 1.06 in dried blood spots (>2.10 micromole/L/h is normal).

Variant 1: NM_000152.5(GAA):c.-32-13T>G

Variant 1 ClinVarID: 4027

Variant 1 CAid: CA116606

Variant 2: NM_000152.5(GAA):c.2238G>C

Variant 2 ClinVarID: 265160

Variant 2 CAid: CA8815665

Variant 3: NM_000152.5(GAA):c.2065G>A

Variant 3 ClinVarID: 4030

Variant 3 CAid: CA116612

Zygosity: compound heterozygous

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case84

HPOsFreeText: See Group Phenotypes

CasePreviousTesting: Sanger sequencing

CaseMethod1: Sanger sequencing and PCR Amplification

CaseMethod2: Whole Exome Sequencing (WES)

CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.

Variant1: NM_000152.4:c.743T>C (p.Leu248Pro)

CAID: CA401363263 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.4%3Ac.743T%3EC

gnomAD: European (Non-Finnish) 1.551e-5, Overall 7.079e-6 http://gnomad.broadinstitute.org/variant/17-78081406-T-C

Variant2: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

CaseAddInfo: Adult Late Onset Pompe Disease

Case46

HPOsFreeText: See Group Phenotypes

CasePreviousTesting: Sanger sequencing

CaseMethod1: Sanger sequencing and PCR Amplification

CaseMethod2: Whole Exome Sequencing (WES)

CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.

Variant1: NM_000152.4:c.525delT (p.Glu176Argfs*45)

ClinVar: 4033 https://www.ncbi.nlm.nih.gov/clinvar/variation/4033/

gnomAD: European (Non-Finnish) 1.880e-4, Overall 9.959e-5 http://gnomad.broadinstitute.org/variant/17-78078909-CT-C

Variant2: NM_000152.4:c.1655T>C (p.Leu552Pro)

ClinVar: 279811 https://www.ncbi.nlm.nih.gov/clinvar/variation/279811/

gnomAD: European (Non-Finnish) 7.053e-5, Overall 3.188e-5 http://gnomad.broadinstitute.org/variant/17-78085800-T-C

CaseAddInfo: Infantile Onset Pompe Disease

Case8

HPOsFreeText: See Group Phenotypes

CasePreviousTesting: Sanger sequencing

CaseMethod1: Sanger sequencing and PCR Amplification

CaseMethod2: Whole Exome Sequencing (WES)

CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.

Variant1: NM_000152.4:c.1754+1G>A

ClinVar: 286458 https://www.ncbi.nlm.nih.gov/clinvar/variation/286458/

gnomAD: Not in gnomAD

Variant2: NM_000152.4:c.722_723delTT (p.Phe241Cysfs*88)

CAID: CA658795235 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.4%3Ac.722_723delTT

gnomAD: Not in gnomAD

CaseAddInfo: Infantile Onset Pompe Disease

Case55

HPOsFreeText: See Group Phenotypes

CasePreviousTesting: Sanger sequencing

CaseMethod1: Sanger sequencing and PCR Amplification

CaseMethod2: Whole Exome Sequencing (WES)

CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.

Variant1: NM_000152.4:c.953T>C (p.Met318Thr)

ClinVar: 4021 https://www.ncbi.nlm.nih.gov/clinvar/variation/4021/

gnomAD: African 8.608e-5, Overall 4.485e-5 http://gnomad.broadinstitute.org/variant/17-78081693-T-C

Variant2: NM_000152.4:c.-32-13T>G

ClinVar: 4027 https://www.ncbi.nlm.nih.gov/clinvar/variation/4027/

gnomAD: Ashkenazi Jewish 5.541e-3, Overall 3.401e-3 http://gnomad.broadinstitute.org/variant/17-78078341-T-G

CaseAddInfo: Juvenile Late Onset Pompe Disease

Case29

HPOsFreeText: See Group Phenotypes

CasePreviousTesting: Sanger sequencing

CaseMethod1: Sanger sequencing and PCR Amplification

CaseMethod2: Whole Exome Sequencing (WES)

CaseGenotypingMethod: Patients were previously confirmed with Pompe disease by Sanger sequencing to capture the pathogenic variants. The process was repeated as part of the study taking care to amplify the coding regions and exon/intron boundaries to compare with the WES results afterwards.

Variant1: NM_000152.4:c.1293_1312del (p.Gln433Aspfs*66)

CAID: CA658795249 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.4%3Ac.1293_1312del

gnomAD: Not in gnomAD

Variant2: NM_000152.4:c.1716C>G (p.His572Gln)

CAID: CA401369055 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.4%3Ac.1716C%3EG

gnomAD: Not in gnomAD

CaseAddInfo: Infantile Onset Pompe Disease

CaseOPOPD-50: Male, Taiwan, Birth diagnosis

HPOsFreeText: GAA (MS/MS) enzyme activity at 0.68 umol/hr/L

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

Variant1: NM_000152.4:c.1634C>T (p.Pro545Leu)

ClinVar: 4032 https://www.ncbi.nlm.nih.gov/clinvar/variation/4032/

gnomAD: European (Finnish) 1.199e-4, Overall 1.774e-5 http://gnomad.broadinstitute.org/variant/17-78084822-C-T

Variant2: NM_000152.4:c.1726G>A (p.Gly576Ser)

ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A

CaseAddInfo: One Pompe Mutation allele and One Pseudodeficency Mutation allele

CaseOPOPD-40: Female, Taiwan, Birth diagnosis

HPOsFreeText: GAA (MS/MS) enzyme activity at 0.99 umol/hr/L

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

Variant1: NM_000152.4:c.872T>C (p.Leu291Pro)

CAID: CA401363854 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.4%3Ac.872T%3EC

gnomAD: Not in gnomAD

Variant2: NM_000152.4:c.1726G>A (p.Gly576Ser)

ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A

CaseAddInfo: One Pompe Mutation allele and One Pseudodeficency Mutation allele, 2 others have the same genotypes

CaseLP-5: Male, Taiwan, Birth diagnosis

HPOsFreeText: 4MU enzyme activity at 1.08, MS/MS ennzyme activity at 0.46

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

Variant1: NM_000152.4:c.752C>T (p.Ser251Leu)

ClinVar: 325781 https://www.ncbi.nlm.nih.gov/clinvar/variation/325781/

gnomAD: East Asian 2.760e-3, Overall 3.540e-4 http://gnomad.broadinstitute.org/variant/17-78081415-C-T

Variant2: NM_000152.4:c.761C>T (p.Ser254Leu)

ClinVar: 325782 https://www.ncbi.nlm.nih.gov/clinvar/variation/325782/

gnomAD: East Asian 2.759e-3, Overall 1.947e-4 http://gnomad.broadinstitute.org/variant/17-78081424-C-T

Variant3: NM_000152.4:c.1726G>A (p.Gly576Ser)

ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A

Variant4: NM_000152.4:c.1935C>A (p.Asp645Glu)

ClinVar: 4029 https://www.ncbi.nlm.nih.gov/clinvar/variation/4029/

gnomAD: East Asian 1.729e-3, Overall 1.240e-4 http://gnomad.broadinstitute.org/variant/17-78086721-C-A

CaseAddInfo: Suspected Late Onset Pompe Disease, Nomenclature indicates Variants 1 and 2 are in cis and Variants 3 and 4 are also in cis

CasePDC-3: Female, Taiwan, Birth diagnosis

HPOsFreeText: 4MU enzyme activity at 1.26, MS/MS ennzyme activity at 1.21

GenotypingMethod: GAA Gene Sequencing and PCR Amplification

Variant1: NM_000152.4:c.752C>T (p.Ser251Leu)

ClinVar: 325781 https://www.ncbi.nlm.nih.gov/clinvar/variation/325781/

gnomAD: East Asian 2.760e-3, Overall 3.540e-4 http://gnomad.broadinstitute.org/variant/17-78081415-C-T

Variant2: NM_000152.4:c.761C>T (p.Ser254Leu)

ClinVar: 325782 https://www.ncbi.nlm.nih.gov/clinvar/variation/325782/

gnomAD: East Asian 2.759e-3, Overall 1.947e-4 http://gnomad.broadinstitute.org/variant/17-78081424-C-T

Variant3: NM_000152.4:c.1726G>A (p.Gly576Ser)

ClinVar: 92467 https://www.ncbi.nlm.nih.gov/clinvar/variation/92467/

gnomAD: East Asian 0.1427, Overall 0.01700 http://gnomad.broadinstitute.org/variant/17-78085871-G-A

CaseAddInfo: Patient is either a carrier or has a pseudodeficency allele, Nomenclature indicates that Variants 1 and 2 are in cis, PDC-4 and 5 have the exact same allele combination

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

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

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

(Dyspnea, Shortened PR interval, Motor delay, Hepatomegaly

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

CaseNotHPOs:

CaseNotHPOFreeText:

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

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

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

ClinVar: 188874

CAID: CA274067

gnomAD: Highest population MAF = 0.0002513 in East Asian

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

ClinVar: 189013

CAID: CA274256

gnomAD: Highest population MAF = 0.00005534 (East Asian)

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

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

PreviouslyPublished: N/A

Case#: Patient 12, Gender N/A, Onset at 3-4 months old, Southeast Asian

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001252, HP:0002090, HP:0002878, HP:0005165

(Hypotonia, Pneumonia, Respiratory failure, Shortened PR interval)

CaseHPOFreeText: Failed endotracheal extubation, BVH, mild sub-aortic obstruction, SDD, Ejection fraction 13%, creatine kinase levels 966 u/l

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: GAA enzyme activity in leukocytes was 0.10% of normal control value.

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

Variant 1: c.1327-2A>G

ClinVar: N/A

CAID: CA401366177

gnomAD: Highest population MAF = 0.0002297 (African)

Variant 2: c.1437G>C (p.Lys479Asn)

ClinVar: N/A

CAID: CA401366671

gnomAD: N/A

ParentalGenotype: Mother was the carrier of variant 1 c.1327-2A>G

Father was the carrier of variant 2 c.1437G>C (p.Lys479Asn)

PreviouslyPublished:

Case#: Patient 1, gender N/A, Age of onset was 7-8 months (died at 3 years of age), Southeast Asian

DiseaseAssertion: Pompe Disease

FamilyInfo:

CasePresentingHPOs: HP:0001252, HP:0001270, HP:0001638, HP:0005165 (Muscular Hypotonia, Motor delay, Cardiomyopathy, Shortened PR interval)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

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

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

Variant1: NM_000152.5(GAA):c.876C>G (p.Tyr292Ter)

ClinVar: 637958

CAID: CA401363871

gnomAD: N/A

Variant2: NM_000152.5:c.1003G>A (p.Gly335Arg)

ClinVar: 972790

CAID: CA501005

gnomAD: Highest population MAF = 0.00003266 (South Asian).

ParentalGenotype: Patient inherited variant 1 (NM_000152.5(GAA):c.876C>G (p.Tyr292Ter) from father.

Variant 2 (c.1003G>A (p.Gly335Arg)) was inherited from mother PreviouslyPublished:N/A

Case#: Patient 2, Gender N/A, 1-2 months old at onset, Southeast Asian

DiseaseAssertion: Pompe disease

FamilyInfo: Patient has two previously deceased siblings with cardiomyopathy

CasePresentingHPOs: HP:0002789, HP:0002240, HP:0005165, HP:0001639 (Tachypnea, Hepatomegaly, Shortened PR interval, Hypertrophic cardiomyopathy)

CaseHPOFreeText: BVH, EF 30%

CaseNotHPOs: N/A

CaseNotHPOFreeText:N/A

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

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

Variant1: NM_000152.5(GAA):c.1935C>A (p.Asp645Glu)

ClinVar: 4029

CAID: CA116610

gnomAD: Highes population MAF = 0.001729 (East Asian)

Variant2: NM_000152.5(GAA):c.1933G>C (p.Asp645His)

ClinVar:<br /> 189013

CAID: CA274256

gnomAD: Highest population MAF = 0.00005534 (East Asian)

ParentalGenotype: Father was carrier of variant 1 c.1935C>A ( p.Asp645Glu

Mother was carrier of the Variant 2 c.1933G>C (p.Asp645His

PreviouslyPublished:

Patient6: Female

CasePresentingHPOs: HP:0002194, HP:0001522

HPOsFreeText: ERT dosage = 20 mg/kg/2 w, CRIM negative

CaseNotHPOs: HP:0004887

NotHPOsFreeText: No reversal of HCM

CaseAddInfo: Symptom onset at 1mo, diagnosis and ERT at 4mo, ERT lasted for 4mo, died at 11mo

CasePMIDs: 22252923, 27629047

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_000152.3:c.1657C>T

CAID: CA401368835, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000152.3%3Ac.1657C%3ET

gnomAD: n/a

Patient2: female

CasePresentingHPOs: HP:0004887, HP:0002194, HP:0001263, HP:0002463, HP:0002870, HP:0011003, HP:0002289

HPOsFreeText: ERT dosage = 20 mg/kg/2 w, use of BiPAP, could sit independently, HCM reversal, CRIM positive, BiPAP ventilation at night

CaseNotHPOs: HP:0000407

NotHPOsFreeText:

CaseAddInfo: Symptom onset and diagnosis at 1d, ERT at 3w, required BiPAP at 57mo, ERT lasted for 77mo, currently 6.5yo

CasePMIDs: 8401535

CasePreviousTesting: same as group

CaseGenotypingMethod: same as group

Variant: NM_000152.4(GAA):c.1927G>A (p.Gly643Arg)

ClinVar: 4023, https://www.ncbi.nlm.nih.gov/clinvar/variation/4023/

gnomAD: 5.884e-05, http://exac.broadinstitute.org/variant/17-78086713-G-A

Case#: Subject number 7, male, 62 years (diagnosis), 66 years (baseline visit), 67 years (ERT), 67 years (ventilation)

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001324 (Muscle Weakness), HP:0002098 (respiratory distress)

CaseHPOFreeText: mechanical ventilation at last visit

CaseNotHPOs: HP:0003236 (Elevated circulating creatine kinase concentration), HP:0002870 (obstructive sleep apnea)

CaseNotHPOFreeText: no mechanical ventilation at Baseline Visit

CasePreviousTesting: "reduced enzymatic activity on fibroblasts, blood leukocytes or skeletal muscle and/or the presence of two known mutations in the GAA gene"

PreviouslyPublished: N/A

Case#: Subject number 2, female, 20 years (diagnosis), 48 years (baseline visit), 39 years (ERT), 34 years (ventilation)

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001324 (Muscle Weakness), HP:0002098 (respiratory distress)

CaseHPOFreeText: mechanical ventilation at Baseline Visit, mechanical ventilation at last visit

CaseNotHPOs: HP:0003236 (Elevated circulating creatine kinase concentration), HP:0002870 (obstructive sleep apnea)

CaseNotHPOFreeText:

CasePreviousTesting: "reduced enzymatic activity on fibroblasts, blood leukocytes or skeletal muscle and/or the presence of two known mutations in the GAA gene"

PreviouslyPublished: N/A

Case#: Subject number 30, male, 12 years (baseline visit)

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0003236 (Elevated circulating creatine kinase concentration)

CaseHPOFreeText:

CaseNotHPOs: HP:0002870 (obstructive sleep apnea), HP:0002098 (respiratory distress), HP:0001324 (Muscle Weakness)

CaseNotHPOFreeText: no mechanical ventilation at Baseline Visit, no mechanical ventilation at last visit

CasePreviousTesting: "reduced enzymatic activity on fibroblasts, blood leukocytes or skeletal muscle and/or the presence of two known mutations in the GAA gene"

PreviouslyPublished: N/A

Case#: Subject number 5, female, 20 years (diagnosis), 45 years (baseline visit), 42 years (ERT)

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001324 (Muscle Weakness)

CaseHPOFreeText:

CaseNotHPOs: HP:0003236 (Elevated circulating creatine kinase concentration), HP:0002870 (obstructive sleep apnea), HP:0002098 (respiratory distress)

CaseNotHPOFreeText: no mechanical ventilation at Baseline Visit, no mechanical ventilation at last visit

CasePreviousTesting: "reduced enzymatic activity on fibroblasts, blood leukocytes or skeletal muscle and/or the presence of two known mutations in the GAA gene"

PreviouslyPublished: N/A

Case#: Subject number 4, female, 56 years (diagnosis), 63 years (baseline visit), 59 years (ERT)

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001324 (Muscle Weakness)

CaseHPOFreeText:

CaseNotHPOs: HP:0003236 (Elevated circulating creatine kinase concentration), HP:0002870 (obstructive sleep apnea), HP:0002098 (respiratory distress)

CaseNotHPOFreeText: no mechanical ventilation at Baseline Visit, no mechanical ventilation at last visit

CasePreviousTesting: "reduced enzymatic activity on fibroblasts, blood leukocytes or skeletal muscle and/or the presence of two known mutations in the GAA gene"

PreviouslyPublished: N/A

Case#: Subject number 25, male, 41 years (diagnosis), 46 years (baseline visit), 43 years (ERT), 43 (age at ventilation)

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0001324 (Muscle Weakness), HP:0002098 (respiratory distress)

CaseHPOFreeText: mechanical ventilation at Baseline Visit, mechanical ventilation at last visit

CaseNotHPOs: HP:0003236 (Elevated circulating creatine kinase concentration), HP:0002870 (obstructive sleep apnea)

CaseNotHPOFreeText:

CasePreviousTesting: "reduced enzymatic activity on fibroblasts, blood leukocytes or skeletal muscle and/or the presence of two known mutations in the GAA gene"

PreviouslyPublished: N/A

Case#: Subject number 36, male, 44 years (diagnosis), 49 years (baseline visit)

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0003236 (Elevated circulating creatine kinase concentration)

CaseHPOFreeText:

CaseNotHPOs: HP:0002098 (respiratory distress), HP:0002870 (obstructive sleep apnea), HP:0001324 (Muscle Weakness)

CaseNotHPOFreeText: no mechanical ventilation at Baseline Visit, no mechanical ventilation at last visit

CasePreviousTesting: "reduced enzymatic activity on fibroblasts, blood leukocytes or skeletal muscle and/or the presence of two known mutations in the GAA gene"

PreviouslyPublished: N/A

Case#: Subject number 3, female, 26 years (baseline visit)

DiseaseAssertion: Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0003236 (Elevated circulating creatine kinase concentration)

CaseHPOFreeText:

CaseNotHPOs: HP:0002870 (obstructive sleep apnea), HP:0001324 (Muscle Weakness), HP:0002098 (respiratory distress)

CaseNotHPOFreeText: no mechanical ventilation at Baseline Visit, no mechanical ventilation at last visit

CasePreviousTesting: "reduced enzymatic activity on fibroblasts, blood leukocytes or skeletal muscle and/or the presence of two known mutations in the GAA gene"

PreviouslyPublished: N/A