Variant 9 of 11

Variant1:NM_000203.3: c.494-1G>C

Variant1CAID:CA275298

PMID:35614200

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

A list of 11 IDUA variants identified in cases with MPS is included in Supplemental Table 6, but the variants are not linked to specific patients and are listed individually (not as genotypes). A page note has been added for each variant.

Variant 8 of 11

Variant1:NM_000203.3: c.395T>C p.(Leu132Pro)

Variant1CAID:CA355961295

Case#:Subject 10 : 23 years male, age of onset unknown DiseaseAssertion:MPS1 FamilyInfo:NA CasePresentingHPOs:NA CaseHPOFreeText:recieved Zinc-finger nuclease(ZFN) based in vivo genome editing as part of Study SB-318-1502, one time IV administration.Monitored by Iduronidase enzyme levels and Urine Heparan sulfate levels durinng enzyme withdrawal. ERt recommenced later. CaseNotHPOs:NA CaseNotHPOFreeText:NA CaseEnzymeAssay:Iduronidase 1.20 nmol/mL/h (normal: 6–71.4 nmol/h/mg) CaseUrineGAGs: CaseERT: <br /> CaseBMT:NA Variant1: IDUA c.386-2A>G Variant1ClinVarID: 222994 Variant1CAID: CA356991 Variant2: IDUA c.1898C>T Variant2ClinVarID: 556406 Variant2CAID: AdditionalVariants:NA ParentalGenotype:NA PreviouslyPublishedNA

Case#: 21, Female, 0.8 years (diagnosed), 2.8 years (report), 7.5 kg (weight), 80 cm (height), Iranian

DiseaseAssertion: Hurler Syndrome

FamilyInfo: Parents are consanguineous

CasePresentingHPOs:HP:0001249, HP:0001999, HP:0000943, HP:0001387, HP:0100790, HP:0000365, HP:0007957, HP:0000238 (Mental Retardation, Facial Dysmorphic Features, Multiple Dysostosis, Joint Stiffness, Hernia, Deafness, Corneal Capacity, Hydrocephalus)

CaseHPOFreeText: HM/HSM, Chronic Rhinorrhea, Cardiac Manifestations (mitral stenosis)

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: IDUA activity 0.98 (μmol/spot.20h)

CaseUrineGAGs: Quantitative urinary GAG 10.5 (mg/gCr)

CaseERT: N/A

CaseBMT: N/A

GenotypingMethod: Sanger Sequencing

Variant1: Not Provided

Variant2: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: 7, Female, 0.7 years (diagnosed), 12.9 years (report), 14.2 kg (weight), 97 cm (height), Iranian

DiseaseAssertion: Hurler-Scheie Syndrome

FamilyInfo: Parents are consanguineous

CasePresentingHPOs: HP:0001249, HP:0001999, HP:0000943, HP:0001387, HP:0100790, HP:0000365, HP:0000238 (Mental Retardation, Facial Dysmorphic Features, Multiple Dysostosis, Joint Stiffness, Hernia, Deafness, Hydrocephalus)

CaseHPOFreeText: HM/HSM, Chronic Rhinorrhea

CaseNotHPOs: HP:0007957 (Corneal Capacity)

CaseNotHPOFreeText: Cardiac Manifestations

CaseEnzymeAssay: IDUA activity 0.86 (μmol/spot.20h)

CaseUrineGAGs: Quantitative urinary GAG 10.11 (mg/gCr)

CaseERT: N/A

CaseBMT: N/A

GenotypingMethod: Sanger Sequencing

Variant1: p.G84R

Variant2: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Patient is from The Netherlands

DiseaseAssertion: MPSI-H

FamilyInfo: Patient has consanguinity between parents.

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.653T>C (p.L218P)

Variant1ClinVarID: 222995

Variant1CAID: CA356986

Variant2: c.653T>C (p.L218P)

Variant2ClinVarID: 222995

Variant2CAID: CA356986

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: MPS I_Case 01, male newborn

DiseaseAssertion: MPS type I, MPS I, MPS-I, attenuated MPS I

FamilyInfo: MPS I_Case 01 and MPS I_Case 05 are siblings

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText: This proband is believed to be an affected MPS-patient however, the proband did not have any obvious clinical symptoms to date (up to two years of age). The paper states that this attenuated MPS I case will need a long term follow up.

CaseEnzymeAssay: Proband identified by newborn screening. alpha-L-iduronidase activity in dried blood spot sample is 0.42 umole/L/Hr; this is below the study’s DBS enzyme activity cutoff value of 3 umol/L/h

CaseUrineGAGs: Urine DMB GAG ratio is 107 mg/mmol creatinine. 10.9 ug/ml dermatan sulfate in urine (<0.41 ug/ml is the reference cutoff for dermatan sulfate in this study). 2.67 ug/ml heparan sulfate in urine (<0.8 ug/ml is the reference cutoff for heparan sulfate in this study). 7/75 ug/ml keratan sulfate in urine.

CaseERT: Don’t know (would assume no since the proband is a newborn)

CaseBMT: Don’t know (would assume no since the proband is a new born)

Variant1: c.300–3C>G

Variant1ClinVarID: 551563

Variant1CAID: CA549265042

Variant2: c.1874A>C, p.Y625S

Variant2ClinVarID: 2910181

Variant2CAID: CA355965961

AdditionalVariants: No additional variants are mentioned

ParentalGenotype: No parental testing results are available

PreviouslyPublished No statement from the author indicating the proband is previously published. Since this is a newborn study, I strongly believe this is the proband’s first time being published.

Case#:Patient Sample unique ID 31, Infant screened positive at birth (specimens with activity ≤15% of the DMA for enzyme activity and a CLIR screening algorithm result of indeterminate or MPS I)

DiseaseAssertion:None

FamilyInfo:None

CasePresentingHPOs:None

CaseHPOFreeText:None

CaseNotHPOs:None

CaseNotHPOFreeText: Normal examination at follow up after screening positive at birth (specimens with activity ≤15% of the DMA for enzyme activity and a CLIR screening algorithm result of indeterminate or MPS I)

CaseEnzymeAssay: IDUA activity 0.423 (7.9) umol/L/h (%DMA) during new born screening through dried blood spot (plasma) and 7.9 pmol/punch/h Confirmatory IDUA enzyme

CaseUrineGAGs: DS 2.7 g/mol creatinine and HS 2.5 g/mol creatinine (Normal)

CaseERT:No

CaseBMT:No

Variant1:homozygous PD: c.235G>A; p.A79T (Normal examination)

Variant1ClinVarID:41682

Variant1CAID: CA000358

Variant2: homozygous PD: c.296C>T; p.T99I

Variant2ClinVarID:53610

Variant2CAID:CA326991

AdditionalVariants:None

ParentalGenotype:None provided

PreviouslyPublished:N/A

Case#:Patient Sample unique ID 58, Infant screened positive at birth (specimens with activity ≤15% of the DMA for enzyme activity and a CLIR screening algorithm result of indeterminate or MPS I)

DiseaseAssertion:None

FamilyInfo:None

CasePresentingHPOs:None

CaseHPOFreeText:None

CaseNotHPOs:None

CaseNotHPOFreeText: Normal examination at follow up after screening positive at birth (specimens with activity ≤15% of the DMA for enzyme activity and a CLIR screening algorithm result of indeterminate or MPS I)

CaseEnzymeAssay: IDUA activity 0.413 (8.7) umol/L/h (%DMA) during new born screening through dried blood spot (plasma) and 8.7 pmol/punch/h Confirmatory IDUA enzyme

CaseUrineGAGs: N/A (Family refused to collect additional urine specimen.)

CaseERT:No

CaseBMT:No

Variant1:homozygous PD: c.235G>A; p.A79T (Normal examination)

Variant1ClinVarID:41682

Variant1CAID: CA000358

Variant2: homozygous PD: c.296C>T; p.T99I

Variant2ClinVarID:53610

Variant2CAID:CA326991

AdditionalVariants: heterozygous PD: c.667G>A; p.D223N (ClinVarID: 2220838, CAID: CA363422841)

ParentalGenotype:None provided

PreviouslyPublished:N/A

Case#: MPS 1 patient

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.208C>T (p.Q70X)

Variant1ClinVarID: 11909

Variant1CAID: CA204563

Variant2: c.943G>T (p.D315Y)

Variant2ClinVarID: 4539822

Variant2CAID: CA355962740

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: YS1 of sibship 5 (see Table 1), male, 0.1 years old (age at diagnosis), 0.3 years old (age at ERT enrollment), 7.6 years (duration of ERT)

DiseaseAssertion: MPS1-HS

FamilyInfo: Two affected siblings (OS and YS2 of sibship 5)

CasePresentingHPOs: HP:0007957 (Corneal opacity)

CaseHPOFreeText: Cardiac disease

CaseNotHPOs: HP:0000943, HP:0002828 (Dysostosis, joint contractures)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: Yes - Remained healthy, with the exception of mild ocular and cardiac symptoms. Psychomotor development remained normal and there were no limitations in ADL. Pulmonary function was between 70 and 94 % of normal at T2.

CaseBMT: N/A

Variant1: c.1469T>C (p.L490P)

Variant1ClinVarID: 11919

Variant1CAID: CA220503

Variant2: c.1469T>C (p.L490P)

Variant2ClinVarID: 11919

Variant2CAID: CA220503

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: YS of sibship 6 (see Table 1), male, 0.6 years old (age at diagnosis), 3 years old (age at ERT enrollment), 7 years (duration of ERT)

DiseaseAssertion: MPS-HS

FamilyInfo: Two affected siblings (OS1 and OS2 of sibship 6)

CasePresentingHPOs: HP:0007957, HP:0000943, HP:0002828 (Corneal opacity, dysostosis, joint contractures)

CaseHPOFreeText: Cardiac disease, musculoskeletal symptoms

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: Yes - Pulmonary function was 70–80 % of normal and had no restrictions in ADL.

CaseBMT: N/A

Variant1: N/A

Variant1ClinVarID: N/A

Variant1CAID: N/A

Variant2: N/A

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

PMID: 26446585

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

Case#: 1, Male, Han Chinese

DiseaseAssertion: Hurler Syndrome

FamilyInfo: Not Provided

CasePresentingHPOs: HP:0001249, HP:0007957, HP:0001433 (Mental Retardation (severe), Corneal Clouding, Hepatosplenomegaly)

CaseHPOFreeText: Skeletal Deformities

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 0 Leukocyte IDUA activity (nmol/h/mg protein) (isolated leukocytes in the latter)

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

GenotypingMethod: Using the artificial substrate 4-methyl-umbelliferyl α-L-iduronide (Sigma)

Variant1: c.1190-1G>A

Variant1ClinVarID: 1204494

Variant1CAID: CA355963511

Variant2: Not Identified

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: 8, Male, Han Chinese

DiseaseAssertion: Hurler Syndrome

FamilyInfo: Not Provided

CasePresentingHPOs: HP:0001249, HP:0007957, HP:0001433 (Mental Retardation (severe), Corneal Clouding, Hepatosplenomegaly)

CaseHPOFreeText: Skeletal Deformities

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 0 Leukocyte IDUA activity (nmol/h/mg protein) (isolated leukocytes in the latter)

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

GenotypingMethod: Using the artificial substrate 4-methyl-umbelliferyl α-L-iduronide (Sigma)

Variant1: c.792+1G>T

Variant1ClinVarID: N/A

Variant1CAID: CA355962278

Variant2: Not identified

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 47, 2 years old (age at report), female, Indian

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 1.8% (Range of residual enzyme activity: 0.0%-4.8%)

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.(792+1_793-1)_(972+1_973-1)del in the paper, unsure how to write this in current nomenclature.

Variant1ClinVarID: N/A

Variant1CAID: N/A

Variant2: c.(792+1_793-1)_(972+1_973-1)del in the paper, unsure how to write this in current nomenclature.

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 46, 9 years old (age at report), female, Indian

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: Coarse facial features, hepatosplenomegaly, joint contractures (HP:0000280, HP:0001433, HP:0002828)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 0.0% (Range of residual enzyme activity: 0.0%-4.8%)

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.1898C>T (p.Ser633Leu)

Variant1ClinVarID: 556406

Variant1CAID: CA355966010

Variant2: c.1898C>T (p.Ser633Leu)

Variant2ClinVarID: 556406

Variant2CAID: CA355966010

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 36, 6 years old (age at report), male, Indian

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: Coarse facial features, hepatosplenomegaly, joint contractures, corneal clouding, recurrent infections, dysostosis multiplex, intellectual disability, hernia (HP:0000280, HP:0001433, HP:0002828, HP:0007957, HP:0002719, HP:0000943, HP:0001249, HP:0100790)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 2.5% (Range of residual enzyme activity: 0.0%-4.8%)

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.1373T>C (p.Leu458Pro)

Variant1ClinVarID: N/A

Variant1CAID: CA355964255

Variant2: c.1373T>C (p.Leu458Pro)

Variant2ClinVarID: N/A

Variant2CAID: CA355964255

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 9, female, 1 year (age at presentation).

DiseaseAssertion: MPS1-H

FamilyInfo: Consanguinity in the family present for this patient.

CasePresentingHPOs: Corneal clouding, coarse facial features, dysostosis multiplex, global developmental delay, hepatomegaly, joint stiffness, splenomegaly, recurrent respiratory infections, umbilical hernia (HP:0007957, HP:0000256, HP:0000943, HP:0001263, HP:0002240, HP:0001387, HP:0001744, HP:0002205, HP:0001537)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.362T>C (p.L121P)

Variant1ClinVarID: 1343382

Variant1CAID: CA355961174

Variant2: c.362T>C (p.L121P)

Variant2ClinVarID: 1343382

Variant2CAID: CA355961174

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 7, male, 1 month (age at presentation).

DiseaseAssertion: MPS1-H

FamilyInfo: Consanguinity in the family not present for this patient. Family conducted a prenatal diagnosis on the next pregnancy and CVS to be unaffected

CasePresentingHPOs: Corneal clouding, coarse facial features, dysostosis multiplex, global developmental delay, hepatomegaly, joint stiffness, splenomegaly, umbilical hernia (HP:0007957, HP:0000256, HP:0000943, HP:0001263, HP:0002240, HP:0001387, HP:0001744, HP:0001537)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.362T>C (p.L121P)

Variant1ClinVarID: 1343382

Variant1CAID: CA355961174

Variant2: c.362T>C (p.L121P)

Variant2ClinVarID: 1343382

Variant2CAID: CA355961174

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 21 (see Table 2), 41 weeks, 2 days (Gestational age)

DiseaseAssertion: MPS1-H/S

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: Inguinal hernia (HP:0000023)

CaseNotHPOFreeText: Upper respiratory tract involvement

CaseEnzymeAssay: 0.35 nmol x mg-1 × hr-1

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.653T>C (p.L218P)

Variant1ClinVarID: 222995

Variant1CAID: CA356986

Variant2: c.943G>T (p.D315Y)

Variant2ClinVarID: N/A

Variant2CAID: CA:355962740

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 18 (see Table 2), 40 weeks (Gestational age)

DiseaseAssertion: MPS1-H/S

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Upper respiratory tract involvement

CaseNotHPOs: Inguinal hernia (HP:0000023)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 0.77 nmol x mg-1 × hr-1

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

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

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.1513C>G (p.R505G)

Variant2ClinVarID: 1482722

Variant2CAID: CA:355964784

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 28 (see Table 2), 40 weeks, 5 days (Gestational age)

DiseaseAssertion: MPS1-S

FamilyInfo: Sibling of Patient 29 (see Table 2)

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: Inguinal hernia (HP:0000023)

CaseNotHPOFreeText: Upper respiratory tract involvement

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.474-2A>G (new nomenclature:c.386-2A>G)

Variant1ClinVarID: 222994

Variant1CAID: CA356991

Variant2: c.1148G>A (p.R383H)

Variant2ClinVarID: 558189

Variant2CAID: CA:2802205

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 13 (see Table 2), 38 weeks, 3 days (Gestational age)

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Upper respiratory tract involvement

CaseNotHPOs: Inguinal hernia (HP:0000023)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 0.43 nmol x mg-1 × hr-1

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

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

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.653T>C (p.L218P)

Variant2ClinVarID: 222995

Variant2CAID: CA:356986

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Pt 4, age is 12 months (proband can be found in Table 1)

DiseaseAssertion: Hurler syndrome, mucopolysaccharidosis type IH, MPS IH, MPS type I

FamilyInfo: No family information provided

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CaseEnzymeAssay: In methods it is stated that an IDUA activity assay was conducted on cartilaginous pellets generated from patient-derived bone marrow stromal cells at 5 weeks. However, results of the IDUA activity assays are not stated.

CaseUrineGAGs: "Significantly higher levels of GAGs in MPS IH compared with HD pellets at.1 week of chondrogenic differentiation, thus indicating that GAG accumulation in MPS IH can be seen during cell condensation and early differentiation stages." Total GAG content for each sample in ug GAG/ug DNA shown in Figure 4 graphs.

CaseERT: Don't know

CaseBMT: Don't know

Variant1: p.P496R

Variant1ClinVarID: 496861

Variant1CAID: CA2802275

Variant2: p.P496R

Variant2ClinVarID: 496861

Variant2CAID: CA2802275

AdditionalVariants: No additional variants mentioned

ParentalGenotype: No parental information provided

PreviouslyPublished: No mention of previously being published

Case#: PKMPS1P1, 4 years old (age at presentation), female

DiseaseAssertion: MPS-I

FamilyInfo: Born to a consanguineous couple

CasePresentingHPOs: Joint stiffness, coarse facial features, dysostosis multiplex, hernia (HP:0001387, HP:0000256, HP:0000943, HP:0100790)

CaseHPOFreeText: Difficulty walking, limitation in the range of movements of joints. Failure to gain height and weight.

CaseNotHPOs: Developmental delay (HP:0001263)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.1598C>G (p.P533R)

Variant1ClinVarID: 11910

Variant1CAID: CA256112

Variant2: c.1598C>G (p.P533R)

Variant2ClinVarID: 11910

Variant2CAID: CA256112

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 11 (see Table 1), 6 years old (age at report), 1 year old (age at onset), female, height of 120 cm, weight of 20 kg, located in Tunis: Industrial region

DiseaseAssertion: MPS1 - mild

FamilyInfo: Parents were 2nd cousins (see Table 2), aged 37 yrs (M) and 44 yrs (F).

CasePresentingHPOs: HP:0004322, HP:0001999, HP:0030799, HP:0001537 (Short stature, facial dysmorphia, scaphocephaly, umbilical hernia)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 0.09 μKat/kg

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.1733T>A (p.L578Q)

Variant1ClinVarID: N/A

Variant1CAID: CA355965319

Variant2: c.1598C>G (p.P533R)

Variant2ClinVarID: 11910

Variant2CAID: CA256112

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Family 6, UK

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: The paper states that "Hurler form is characterized by skeletal abnormalities, hepatosplenomegaly and severe mental retardation" but is not specific to this patient.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: The α-L-iduronidase enzyme activities in leucocytes from all patients in the study was measured using the artificial substrate 4-methylumbelliferyl α-L iduronide (Sigma). Values ranged from 0 to 2.47 nmol/h/mg protein (reference range: 28–92 nmol/h/mg protein) and did not correlate to the clinical phenotype.

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

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

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.46_57del (p.Ser16_Ala19del); in the paper it is listed as c.134del12 (old nomenclature)

Variant2ClinVarID: 92643

Variant2CAID: CA220509

AdditionalVariants: N/A

ParentalGenotype: Parental testing conducted, each parent was shown to carry one of the sequence changes found in their affected child.

PreviouslyPublished N/A

Case#: Family 8, UK

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: The paper states that "Hurler form is characterized by skeletal abnormalities, hepatosplenomegaly and severe mental retardation" but is not specific to this patient.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: The α-L-iduronidase enzyme activities in leucocytes from all patients in the study was measured using the artificial substrate 4-methylumbelliferyl α-L iduronide (Sigma). Values ranged from 0 to 2.47 nmol/h/mg protein (reference range: 28–92 nmol/h/mg protein) and did not correlate to the clinical phenotype.

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

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

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.1855C>T (p.R619X)

Variant2ClinVarID: 280976

Variant2CAID: CA2802455

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

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

DiseaseAssertion: Mucopolysaccharidosis type I, MPS I

FamilyInfo: N/A

CasePresentingHPOs:

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: S633L

Variant1ClinVarID: 556406

Variant1CAID: CA355966010

Variant2: N/A

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Functional assay variant with a clinical significance of being a VUS.

DiseaseAssertion: MPS-I

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.298A>G (p.R100G)

Variant1ClinVarID: 2058952

Variant1CAID: CA2801159

Variant2: N/A

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Functional assay variant with a clinical significance of having conflicting interpretations.

DiseaseAssertion: MPS-I

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.757G>T (p.G253C)

Variant1ClinVarID: 554213

Variant1CAID: CA2802076

Variant2: N/A

Variant2ClinVarID: N/A

Variant2CAID: N/A

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

PMID: 25116402

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

PMID: 39132856

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

Case#: Patient 2, 12 years old, Iranian

DiseaseAssertion: MPS1-S (Attenuated)

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 0.3 µmol/g.h (Normal ranges: 10-50 µmol/g.h)

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.401G>T (p.G134V)

Variant1ClinVarID: N/A

Variant1CAID: CA355961317

Variant2: c.401G>T (p.G134V)

Variant2ClinVarID: N/A

Variant2CAID: CA355961317

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 8, born in 1994 (paper published in 2017), 9 months (age at first treatment), 2 years 3 months (age at last treatment)

DiseaseAssertion: MPSI-H

FamilyInfo: N/A

CasePresentingHPOs: Corneal clouding, retinopathy, cataract (HP:0007957, HP:0000488, HP:0000518)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 7.14 ng/mol (56.53 weight matched enzyme reference assay)

CaseUrineGAGs: 1.24 DS/CS

CaseERT: No

CaseBMT: Yes, Sib

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

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.1205G>A (p.W402X)

Variant2ClinVarID: 11908

Variant2CAID: CA220498

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 9, born in 2008 (paper published in 2017), 8 months (age at first treatment)

DiseaseAssertion: MPSI-H

FamilyInfo: N/A

CasePresentingHPOs: Corneal clouding (HP:0007957)

CaseHPOFreeText: N/A

CaseNotHPOs: Retinopathy, cataract (HP:0000488, HP:0000518)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 47 ng/mol (32 weight matched enzyme reference assay)

CaseUrineGAGs: 0.34 DS/CS

CaseERT: Yes

CaseBMT: Yes, Cord

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

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.208C>T (p.Q70X)

Variant2ClinVarID: 11909

Variant2CAID: CA204563

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 3, born in 2005 (paper published in 2017), 2 years and 7 months (age at first treatment)

DiseaseAssertion: MPSI-H

FamilyInfo: N/A

CasePresentingHPOs: Corneal clouding (HP:0007957)

CaseHPOFreeText: N/A

CaseNotHPOs: Retinopathy, cataract (HP:0000488, HP:0000518)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 86 ng/mol (60 weight matched enzyme reference assay)

CaseUrineGAGs: 0.43 DS/CS

CaseERT: Yes

CaseBMT: Yes, Sib

Variant1: c.17_24CCCGCGCC (Found to be c.17_24dup) (p.Ala9ProfsTer?)

Variant1ClinVarID: N/A

Variant1CAID: CA645372294

Variant2: c.1871A>T (p.Asp624Val)

Variant2ClinVarID: N/A

Variant2CAID: CA355965955

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 11, born in 2003 (paper published in 2017), 1 year (age at first treatment)

DiseaseAssertion: MPSI-H

FamilyInfo: N/A

CasePresentingHPOs: Corneal clouding (HP:0007957)

CaseHPOFreeText: N/A

CaseNotHPOs: Retinopathy, cataract (HP:0000488, HP:0000518)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 71.98 ng/mol (10.86 weight matched enzyme reference assay)

CaseUrineGAGs: 0.38 DS/CS

CaseERT: Yes

CaseBMT: Yes, Cord

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

Variant1ClinVarID: 11908

Variant1CAID: CA220498

Variant2: c.208C>T (p.Q70X)

Variant2ClinVarID: 11909

Variant2CAID: CA204563

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: No additional case information provided

DiseaseAssertion: Not specified

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: Not performed

CaseUrineGAGs: Normal

CaseERT: N/A

CaseBMT: N/A

Variant1: c.53T>C (p.L18P)

Variant1ClinVarID: 193062

Variant1CAID: CA238566

Variant2: c.1651G>C (p.V551L)

Variant2ClinVarID: 1410776

Variant2CAID: CA2802341

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 2, Italy

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.979G>C (p.A327P)

Variant1ClinVarID: 167190

Variant1CAID: CA234128

Variant2: c.979G>C (p.A327P)

Variant2ClinVarID: 167190

Variant2CAID: CA234128

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Case#: Patient 7, female, Han origin, 7 years old (age at diagnosis)

DiseaseAssertion: MPS1-H/S

FamilyInfo: N/A

CasePresentingHPOs: Global Developmental Delay, Macrocephaly, Joint stiffness, Hepatosplenomegaly (HP:0001263, HP:0000256, HP:0001387, HP:0001433)

CaseHPOFreeText: Cardiac disease

CaseNotHPOs: Mongolian macula, Hernia, Airway obstruction (HP:0011369, HP:0100790, HP:0006536)

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: IDUA activity 0.3 nmol/h/mg protein. The normal range in Chinese controls was found to be 27.2–52 nmol/h/mg protein.

CaseUrineGAGs: Diagnosis was confirmed biochemically by the demonstration of an increased excretion of urinary dermatan sulfate and heparan sulfate.

CaseERT: N/A

CaseBMT: N/A

Variant1: c.1227dupG (paper says c.1225dupC but according to the variant sequence this should be c.1227dupG - a known variant)

Variant1ClinVarID: 929237

Variant1CAID: CA1139658406

Variant2: c.236C>T (p.A79V)

Variant2ClinVarID: 1458769

Variant2CAID: CA356987

AdditionalVariants: N/A

ParentalGenotype: The transmission of sequence variations found in each patient was inferred by sequencing the corresponding exons of the patient's parents - confirmed in trans by parental testing.

PreviouslyPublished N/A

Case#: Patient 34, male, Han origin, 10 months old (age at diagnosis)

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: Global Developmental Delay, Macrocephaly, Joint stiffness, Mongolian macula, Hepatosplenomegaly, Hernia, Airway obstruction (HP:0001263, HP:0000256, HP:0001387, HP:0011369, HP:0001433, HP:0100790, HP:0006536)

CaseHPOFreeText: Cardiac disease

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: IDUA activity 1.2 nmol/h/mg protein. The normal range in Chinese controls was found to be 27.2–52 nmol/h/mg protein.

CaseUrineGAGs: Diagnosis was confirmed biochemically by the demonstration of an increased excretion of urinary dermatan sulfate and heparan sulfate.

CaseERT: N/A

CaseBMT: N/A

Variant1: c.656dupG (Paper refers to the variant as c.657dupG, there is a typo in the article where all duplication variants are one base pair off)

Variant1ClinVarID: N/A

Variant1CAID: CA2586965940

Variant2: c.623G>A (p.G208D)

Variant2ClinVarID: 554590

Variant2CAID: CA355961948

AdditionalVariants: N/A

ParentalGenotype: The transmission of sequence variations found in each patient was inferred by sequencing the corresponding exons of the patient's parents - confirmed in trans by parental testing.

PreviouslyPublished N/A

Case#: Patient 44, male, Han origin, 21 years old (age at diagnosis)

DiseaseAssertion: MPS1-S

FamilyInfo: N/A

CasePresentingHPOs: Joint stiffness (HP:0001387)

CaseHPOFreeText: N/A

CaseNotHPOs: Global Developmental Delay, Macrocephaly, Mongolian macula, Hepatosplenomegaly, Hernia, Airway obstruction (HP:0001263, HP:0000256, HP:0011369, HP:0001433, HP:0100790, HP:0006536)

CaseNotHPOFreeText: Cardiac disease

CaseEnzymeAssay: IDUA activity 1.5 nmol/h/mg protein. The normal range in Chinese controls was found to be 27.2–52 nmol/h/mg protein.

CaseUrineGAGs: Diagnosis was confirmed biochemically by the demonstration of an increased excretion of urinary dermatan sulfate and heparan sulfate.

CaseERT: N/A

CaseBMT: N/A

Variant1: c.2T>C (p.Met1Thr)

Variant1ClinVarID: 639529

Variant1CAID: CA2801095

Variant2: c.1037T>G (p.L346R)

Variant2ClinVarID: 11927

Variant2CAID: CA256128

AdditionalVariants: N/A

ParentalGenotype: The transmission of sequence variations found in each patient was inferred by sequencing the corresponding exons of the patient's parents - confirmed in trans by parental testing.

PreviouslyPublished N/A

Case#: Pt 105 , Age 30 years, Female, DiseaseAssertion: MPS1 Scheie syndrome. FamilyInfo: NA CasePresentingHPOs: NA CaseHPOFreeText: NA CaseNotHPOs: NA CaseNotHPOFreeText: NA

CaseEnzymeAssay: Low leukocyte IDUA enzyme activity CaseUrineGAGs: NA CaseERT: No CaseBMT: No Variant1: p.R383H Variant1ClinVarID: 558189 Variant1CAID: Variant2:p.W402X Variant2ClinVarID: 11908 Variant2CAID: CA220498 AdditionalVariants: NA ParentalGenotype: NA PreviouslyPublished:NA

PMID: 34360653

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

Case#: Patient 2, Turkish

DiseaseAssertion: MPS1-H

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.192C>A (p.Y64X)

Variant1ClinVarID: 11914

Variant1CAID: CA256113

Variant2: c.979G>C (p.A327P); Table states c.1067G>C instead of c.979G>C. This variant is not in ClinVar or has a CAID. Assuming there is a typo and this is c.979G>C

Variant2ClinVarID: 167190

Variant2CAID: CA234128

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

PMID: 31758674

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

PMID: 25558755

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

Case#: Infant 1

DiseaseAssertion: N/A

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: 5.1 nmol/h/mg; normal range, 15.1-50.9 nmol/h/mg

CaseUrineGAGs: 22.6 mg/mmol creatinine; normal ranges, 0-53 mg/mmol creatinine

CaseERT: N/A

CaseBMT: N/A

Variant1: c.298A>G (p.R100G)

Variant1ClinVarID: 2058952

Variant1CAID: CA2801159

Variant2: c.300-20C>T

Variant2ClinVarID: 1415135

Variant2CAID: CA2801857

AdditionalVariants: c.1345C>A (p.H449N)

ParentalGenotype: c.298A>G (maternal); c.300-20C>T (paternal); c.1345C>A (paternal)

PreviouslyPublished N/A

Case#: Infant (Pregnancy was terminated at 35 gestational weeks due to severe MPS I diagnosis, weight of 3140 g (94th percentile), length of 48 cm (80th percentile), occipitofrontal circumference of 34 cm (83rd percentile).

DiseaseAssertion: MPS1

FamilyInfo: Proband 1's mother and father were not consanguineous, their phenotype was normal, and they had no significant personal or family histories. Mother had previously had given birth to a healthy infant.

CasePresentingHPOs: Single umbilical artery, hepatosplenomegaly, hepatomegaly, coarse facial features, broad nasal tip, micrognathia, thin upper lip vermilion, hypertelorism, plagiocephaly (HP:0001195, HP:0001433, HP:0002240, HP:0000280, HP:0000455, HP:0000347, HP:0000219, HP:0000316, HP:0001357)

CaseHPOFreeText: Dysmorphic features (including a long and broad philtrum), a few echogenic spots in the liver, spleen, peritoneum, and thymus, hepatic overhang of 4 cm, microretrognatism, full and drooping cheeks, large, badly hemmed ears with bulky lobes, bulging eyes, marked suborbital folds, and micro vacuolized appearance of Hofbauer cells.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: Deficiency in α-L-iduronidase activity. Measure value was 0.3 µkat/kg with a laboratory control of 33.8 µkat/kg.

CaseUrineGAGs: N/A

CaseERT: N/A

CaseBMT: N/A

Variant1: c.590G>A (p.G197D)

Variant1ClinVarID: 554670

Variant1CAID: CA91167598

Variant2: c.1139dup (p.L381Afs*18)

Variant2ClinVarID: 3340107

Variant2CAID: CA3046517234

AdditionalVariants: N/A

ParentalGenotype: c.590G>A (inherited from the mother), c.1139dup (inherited from the father)

PreviouslyPublished N/A

Case#: Patient 1, 1-year old at the start of ERT

DiseaseAssertion: MPS1-H - confirmed diagnosis of MPS 1 by enzymatic and mutation analysis

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: N/A

CaseUrineGAGs: Urine GAGs are displayed in a figure and show the level at the start of ERT to 24-months later. At the start, urine GAGs appear to be slightly above 100 mg/mmol creatinine. After 24-months they decreased to be slightly below 50 mg/mmol creatinine. Normal values for >2-year olds are 8-20 mg/mmol creatinine.

CaseERT: Yes - started at 1-year old and was given once every week

CaseBMT: No

Variant1: c.494-1G>A (in the paper, the variant is labeled as IVS4-1G>A)

Variant1ClinVarID: 557942

Variant1CAID: CA355961634

Variant2: c.494-1G>A (in the paper, the variant is labeled as IVS4-1G>A)

Variant2ClinVarID: 557942

Variant2CAID: CA355961634

AdditionalVariants: N/A

ParentalGenotype: N/A

PreviouslyPublished N/A

Supplementary Data, Table 2

Variant noted to be present in 2 individuals

Variant: NM_000257.3(MYH7):c.2609G>A (p.Arg870His)

ClinVar: 14120, https://www.ncbi.nlm.nih.gov/clinvar/variation/14120/

gnomAD: 0.000007072, https://gnomad.broadinstitute.org/variant/14-23894048-C-T

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

PMID: 28491642

Gene: ACTC1

HGNC ID: 143

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

Four MYH7 variants mentioned using reference transcript NM_000257.2

c.464_466delTCT

c.745C>G

c.1106G>A

c.2785G>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)

Case#: A 36-year-old Italian female

DiseaseAssertion: Restrictive cardiomyopathy (RCM), associated with a homozygous TPM1 p.Asn279His variant.

FamilyInfo: The patient’s parents are first cousins and confirmed heterozygotes for p.Asn279His (Fig 2).The patient’s 75-year-old father was diagnosed with HCM at 42 years of age. He reportedly has a history of heart failure but is currently asymptomatic. The patient’s 67-year-old mother had her first echocardiogram after the patient’s diagnosis.(Table I).

ParentalTesting: Father and mother

CasePresentingHPOs: HP:0100749, HP:0002875, HP:0002094, HP:0012764, HP:0003270, HP:0000131, HP:0001635

CaseHPOFreeText: She was diagnosed with RCM and is being evaluated for heart transplantation. was referred for chest pain, lightheadedness, shortness of breath, significant fatigue, dyspnea on exertion, three-pillow orthopnea and abdominal bloating. Eighteen months previously, she had been diagnosed with an unspecified form of cardiomyopathy after developing volume overload while hospitalized for a right oophorectomy and uterine fibroid removal. Her symptoms were consistent with NYHA III–IV heart failure. She has continued to have significant heart failure symptoms that have been difficult to control with medical therapy. Freedom from arrhythmias, however, has been notable. She is currently being considered for orthotopic heart transplantation but her evaluation has been complicated by psychiatric issues.

CaseNotHPOs: HP:0001279, HP:0010741

CaseNotHPOFreeText: She denied syncope and lower extremity edema

CasePreviousTesting: The patients father and mother were tested.

Genotyping Method: Sarcomere gene sequencing

FunctionalAnalysis: used computational analysis and evolutionary conservation to assess the variant of TPM1 p.Asn279His.

Variant: NM_001018005.2:c.835A>C

ClinVar: 43446

CAID: CA018397

gnomAD: NR

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

PMID: 41550885 Gene: MYBPC3 HGNC: 7551

PMID: 24502034

Gene: MYH7

HGNC: 7577

General overview of Ebstein's Anomaly

PMID: 32369506

Gene: MYH7

HGNC: 7577

Of 16 patients presenting with clinical VHL features that underwent genetic testing, patient 1 presented with the c.203C>G mutation of the VHL gene (stated in the paper as c.416C>G which used the Latif sequence as reference). Peripheral blood lymphocytes were collected and products of the polymerase chain reaction performed on this sample were analyzed with single-stranded conformational polymorphism analysis (SSCP), PCR sequencing and Southern analysis. This missense mutation was confirmed using restriction fragment length polymorphism or allele-specific oligonucleotide analysis. This patient has a family history of multiple tumor types indicative of VHL disease but the family did not undergo genetic testing. This patient presented with a pheochromocytoma.

PatientID: 3

KindredID: K-V7/V6

Case: M, Age Unknown, Korean

DiseaseAssertion: VHL

FamilyInfo: The proband (ID 1) was affected with retinal hemangioblastoma, bilateral pheochromocytoma, and pancreatic tumor. The daughter (ID 2) was affected with retinal hemangioblastoma and bilateral pheochromocytoma. The son (ID 3) was affected with retinal hemangioblastoma. All three were positive for the D121N (c.361G>A) germline variant of the VHL gene.

CasePresentingHPOs: HP:0009711 (Retinal capillary hemangioma)

CaseHPOFreeText: Retinal hemangioblastomas, pancreatic tumor and bilateral pheochromocytoma. Diagnosed with VHL type 2.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.D121N (c.361G>A)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA351753750, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA351753750

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: D121N (c.361G>A)

MultipleGeneVariants: N/A

PatientID: 1

KindredID: 1

Case: F, 32Y0M, Ethnicity Unknown

DiseaseAssertion: assumed VHL

FamilyInfo: No family history: Father and brother were tested and no VHL mutation was found; Her mother died at the age of 51 years of a lung carcinoma, prior to any genetic testing. Therefore impossible to confirm de novo.

CasePresentingHPOs: HP:0002666; HP:0008256 (pheochromocytoma; adrenocortical adenoma)

CaseHPOFreeText: presented a right adrenal mass at sonography performed for gallbladder’s stones. An abdominal computed tomography (CT) confirmed the presence of a solid hypodense lesion of the right adrenal gland, 3 × 2·5 cm in size

CaseNotHPOs: N/A

CaseNotHPOFreeText: Ophthalmoscopy as well as brain, thoracic and abdominal Nuclear Magnetic Resonance (NMR) did not show any of the typically VHL associated lesions (retinal or CNS angiomas; endolymphatic sac tumours; pancreatic or renal cysts; renal carcinoma; cystoadenoma of the broad ligament).

CasePreviousTesting: RET/ SDHB/ SDHC/ SDHD

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: unknown - see CaseProblemVariantFreeText

LegacyVariant: N/A

CaseProblemVariantFreeText: Paper states: p.L198V (c.594C>G). The base at cDNA position 561 is actually a ‘G’. Could be c.592C>G as this gives a p.L198V change, however cannot justify this assumption with the evidence given, and authors were not able to confirm.

ClinVarID: N/A

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant

CivicName: None

MultipleGeneVariants: N/A

PatientID: 7

KindredID: 7

Case: M, 48Y0M, Chinese

DiseaseAssertion: VHL

FamilyInfo: N/A

CasePresentingHPOs: HP:0009726; HP:0005562; HP:0010797; HP:0001737; HP:0006770 (Renal neoplasm, Multiple renal cysts, Hemangioblastoma, Pancreatic cysts, Clear cell renal cell carcinoma)

CaseHPOFreeText: Patient 7 had a medical history of a left solid renal tumor and multiple renal cysts. They also had central nervous system hemangioblastomas and pancreatic cysts.

CaseNotHPOs:None

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.N150Ifs*9 (c.447del)

LegacyVariant: c.661delA

CaseProblemVariantFreeText: N/A

ClinVar: N/A

CAID: CA432421904, http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.447del

gnomAD: N/A

VariantEvidence: N/A

MutationType: minus_1_frameshift_variant

CivicName: N150fs (c.447del)

MultipleGeneVariants: N/A

PatientID: 249

KindredID: 95

Case: F, Age Unknown, Chinese

DiseaseAssertion: Asymptomatic

FamilyInfo: The proband (patient 244) has a daughter with the variant (patient 245) who was asymptomatic at the time of assessment.

CasePresentingHPOs: N/A

CaseHPOFreeText: The proband's nephew (son of sister) was asymptomatic at the time of assessment

CaseNotHPOs: HP:0001737; HP:0001732; HP:0005584; HP:0009711; HP:0002666; HP:0010797 (Pancreatic cysts, Abnormality of the pancreas, Renal cell carcinoma, Retinal capillary hemangioma, Pheochromocytoma, Hemangioblastoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: This cohort was also published in an earlier paper by Wang et al., 2014 (PMID 24581539) as well as a later paper by Wang et al., 2018 (PMID: 29330336).

SupplementalData: Patient and family genotype-phenotype information is listed in Supplementary Table 1.

Variant: Exon 1 Deletion (c.1-?_340+?del)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: exon_loss_variant

CivicName: Exon 1 Deletion

MultipleGeneVariants: N/A

PatientID: 200

KindredID: 77

Case: F, 25Y0M, Chinese

DiseaseAssertion: VHL

FamilyInfo: The proband (patient 200) has six family members who passed away before diagnosis/ had no DNA sample available. Of the family who passed away before diagnosis: the proband's aunt 1 (patient 202) had a CNS hemangioblastoma at 27; the daughter of aunt 1 (patient 203) had a pheochromocytoma at 31; aunt 2 (patient 205) had a CNS hemangioblastoma at 43, renal cell carcinoma at 36, and multiple pancreatic cysts/tumors at 48. Of the family for whom no DNA sample was available: the proband's mother (patient 201) had a CNS hemangioblastoma at 51, multiple pancreatic cysts/tumors at 46, and a pheochromocytoma at 25; the grandson of aunt 1 (patient 204) had a pheochromocytoma at age 9; and the son of aunt 2 (patient 206) had a pheochromocytoma at 16 and renal cell carcinoma + multiple pancreatic cysts/tumors at 21.

CasePresentingHPOs: HP:0010797 (Hemangioblastoma)

CaseHPOFreeText: The patient presented with a pheochromocytoma and renal cell carcinoma at 36.

CaseNotHPOs: HP:0009711; HP:0001737; HP:0001732; HP:0002666; HP:0005584 (Retinal capillary hemangioma, Pancreatic cysts, Abnormality of the pancreas, Pheochromocytoma, Renal cell carcinoma )

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: This patient was also published in a later paper by Wang et al., 2018 (PMID: 29330336).

SupplementalData: Patient and family genotype-phenotype information is listed in Supplementary Table 1.

Variant: p.R167W (c.499C>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 2218; https://www.ncbi.nlm.nih.gov/clinvar/variation/2218/