Case#: Patient 2 is a 24-year-old Japanese man. Birth weight was 1900 g (~4.2 lbs) and mental and motor development were both normal. He had graduated from high school. Physical examination demonstrated a height of 157.0 cm, body weight of 45.3 kg.

DiseaseAssertion: MPS1-S

FamilyInfo: He was born from nonconsanguineous, young and healthy parents. He had a healthy elder brother and an affected twin brother (Patient 1).

CasePresentingHPOs: Inguinal hernia, bronchial asthma, systolic ejection heart murmur, umbilical hernia, joint contractures, spastic gait, hypoesthesia, positive Romberg sign, Babinski signs, mild aortic valve stenosis (HP:0000023, HP:0002099, HP:0031664, HP:0001537, HP:0002828, HP:0002064, HP:0033748, HP:0002403, HP:0003487, HP:0001650)

CaseHPOFreeText: Admitted to the hospital due to a 3-month history of progressive gait disturbance, onset was 6 months after the development of gait disturbance in Patient 1. Exaggeration of deep tendon reflexes was slight in the upper extremities, and marked in the lower extremities. Radiographies of chest and cervical spine showed similar findings to those in Patient 1. CSF examinations demonstrated an elevated protein level (342 mg/dL) without pleocytosis. WAIS-III demonstrated an overall IQ of 75, verbal IQ of 67 and performance IQ of 90.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: The patient showed IDUA activity from peripheral leukocytes < 0.9 nmol/mg protein/h (normal range; 29.8–89.8 nmol/mg protein/h), and that of their mother showed 19.9 nmol/mg protein/h.

CaseUrineGAGs: Urine chemistry examination demonstrated increased excretion of uronic acid (51.7 mg/g creatinine).

CaseERT: Yes, with laronidase

CaseBMT: N/A

Variant1: c.164dup (p.Leu56AlafsTer7) (c.252insC - in paper but nomenclature is not current)

Variant1ClinVarID: 855487

Variant1CAID: CA355945969

Variant2: c.1121C>A (p.Thr374Asn) (c.1209C>A - in paper but nomenclature is not current)

Variant2ClinVarID: 4078984

Variant2CAID: CA355963378

AdditionalVariants: N/A

ParentalGenotype: Mother: c.164dup; Father: c.1121C>A

PreviouslyPublished N/A

Case#: Patient 1 is a 24-year-old Japanese man. His birth weight was 2300 g (~5 lbs) and he had graduated from a vocational school. Physical examination demonstrated a height of 156.6 cm (mean height of Japanese male at age 24 is 170.9 ± 6.0 (SD) cm, body weight of 45.8 kg (mean body weight of Japanese male at age 24 is 62.6 ± 9.8 (SD) kg according to the National Health and Nutrition Survey in Japan, 2006). He demonstrated overall intelligence quotient (IQ) of 101, verbal IQ of 93 and performance IQ of 112.

DiseaseAssertion: MPS1-S

FamilyInfo: He was born from nonconsanguineous, young and healthy parents. He had a healthy elder brother and an affected twin brother (Patient 2).

CasePresentingHPOs: Inguinal hernia (treated by surgical repair in childhood and again at age 20), systolic ejection heart murmur, umbilical hernia, scissor gait, Babinski sign, mild aortic valve stenosis, severe cervical cord compression (HP:0000023, HP:0031664, HP:0001537, HP:0012407, HP:0003487, HP:0001650, HP:0002341)

CaseHPOFreeText: Admitted to the hospital due to a 6-month history of progressive gait disturbance. Mental and motor development were normal. Past medical histories included Kawasaki disease at age 6 months. Deep tendon reflexes were mildly exaggerated in the upper extremities, and markedly exaggerated in the lower extremities with bilateral Babinski signs. Radiography of the chest demonstrated mild thoracic deformity and that of cervical spine demonstrated hypoplasia of vertebral body and spinous process. Brain MRI demonstrated enlarged perivascular space and small hyperintense lesions on fluid attenuated inversion recovery image. Cerebrospinal fluid (CSF) examinations demonstrated an elevated protein level (440 mg/dL; normal range 10–40 mg/dL), which would be resulted from CSF circulatory disturbance caused by severe spinal canal stenosis, without pleocytosis.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CaseEnzymeAssay: The patient showed IDUA activity from peripheral leukocytes < 0.9 nmol/mg protein/h (normal range; 29.8–89.8 nmol/mg protein/h), and that of their mother showed 19.9 nmol/mg protein/h.

CaseUrineGAGs: Urine chemistry examination demonstrated increased excretion of uronic acid (63.1 mg/g creatinine; normal range 8.3–12.3 mg/g creatinine).

CaseERT: Yes, with laronidase

CaseBMT: N/A

Variant1: c.164dup (p.Leu56AlafsTer7) (c.252insC - in paper but nomenclature is not current)

Variant1ClinVarID: 855487

Variant1CAID: CA355945969

Variant2: c.1121C>A (p.Thr374Asn) (c.1209C>A - in paper but nomenclature is not current)

Variant2ClinVarID: 4078984

Variant2CAID: CA355963378

AdditionalVariants: N/A

ParentalGenotype: Mother: c.164dup; Father: c.1121C>A

PreviouslyPublished N/A

PMID: 21176924

Gene: IDUA

Disease: MPS1

Inheritance: Autosomal recessive

Case: 16 years diagnosis, Chinese

DiseaseAssertion: Charcot-Marie-Tooth disease

FamilyInfo: Mother（mild Pes Cavus）; Brother（Amyotrophy, Pes Cavus and so forth）

CasePresentingHPOs: HP:0001761, HP:0033526, HP:0001265

GenotypingMethod: Genomic DNA was extracted from the peripheral blood of the family members of a pedigree with autosomal dominant CMT disease, and 65 candidate genes of the proband were screened using target exon capture and the next generation sequencing, and the suspicious genes were verified using Sanger sequencing.

Variant: NM_018972.4:c.371A>G (p.Tyr124Cys)

CAID: CA371548535

gnomAD: NOT in gnomAD

Case#: 55-year-old man

DiseaseAssertion: single coronary artery (SCA) and presented with dilated cardiomyopathy (DCM)

FamilyInfo: Unremarkable

ParentalTesting: NR

CasePresentingHPOs: HP:0002094, HP:0031352, HP:0001638, HP:0001644, HP:0010741

CaseHPOFreeText: chest tightness and dyspnoea after activity lasting for 2 months. CTCA showed congenital absence of the right coronary artery. TTE revealed enlargement of the left heart and cardiomyopathy. CMR revealed DCM. oedema of both lower limbs. Laboratory data in Table 1.

CaseNotHPOs: NR

CaseNotHPOFreeText: Stenosis

CasePreviousTesting: See NGS results in Supplementary Table 1

Genotyping Method: Genetic screening (NGS results in Supplementary Table 1) with confirmation by Sanger

FunctionalAnalysis: NR

Variant: c.1858C>T (p.Arg620Cys)

ClinVar: 67694

CAID: CA015449

gnomAD: v4.1.0 GrpMax FAF: 0.00002033 (European non-Finnish)

AdditionalInfo: The patient also has APOA5:c.990_993delAACA (p. Asp332Valfs*5) (P/LP in ClinVar with 2 stars)

Case#: V3, Pakistan, female, 23 years old (report),

DiseaseAssertion: GAMT deficiency

FamilyInfo: Patient V3 is a sister of V1. Consanguineous family.

CasePresentingHPOs: HP:0010864, HP:0001250, HP:0001257, HP:0003487, HP:0001251, HP:0001761 (severe intellectual disability, seizure, spasticity, Babinski sign, ataxia, pes cavus)

CaseHPOFreeText: Neonatal onset of seizures, Spasticity in upper and lower limbs, Peripheral neuropathy probably present, sitting delayed, standing delayed, walking delayed, never developed speech

CaseNotHPOs: HP:0001347 (hyperreflexia)

CaseNotHPOFreeText: Bed ridden, recurrent bone fractures

Biochemical analyte testing:

Brain Magnetic Resonance Spectroscopy (MRS): N/A

GAMT activity assay: N/A

Zygosity: Homozygous / compound heterozygous.

Variant 1: c.134G > A (p.Trp45)

ClinVarID: N/A

CAID: N/A

gnomAD: N/A

Variant 2: N/A

ClinVarID: N/A

CAID: N/A

gnomAD: N/A

ParentalGenotypes: Both parents confirmed to be heterozygous for c.134G > A

AlsoPublished: N/A

Case#: V1, Pakistan, male, 25 years old (report),

DiseaseAssertion: GAMT deficiency

FamilyInfo: Patient V1 is a brother of V3. Consanguineous family.

CasePresentingHPOs: HP:0010864, HP:0001250, HP:0001347, HP:0001257, HP:0003487, HP:0001251, HP:0001761 (severe intellectual disability, seizure, hyperreflexia, spasticity, Babinski sign, ataxia, pes cavus)

CaseHPOFreeText: Neonatal onset of seizures, Spasticity in upper and lower limbs, Peripheral neuropathy probably present, sitting delayed, standing delayed, walking delayed, never developed speech, bed ridden since age 17, recurrent bone fractures

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

Biochemical analyte testing: GAA: 13.7 μmol/L, creatine: 2 μmol/L

Brain Magnetic Resonance Spectroscopy (MRS): N/A

GAMT activity assay: N/A

Zygosity: Homozygous

Variant 1: c.134G > A (p.Trp45)

ClinVarID: N/A

CAID: N/A

gnomAD: N/A

Variant 2: N/A

ClinVarID: N/A

CAID: N/A

gnomAD: N/A

ParentalGenotypes: Both parents confirmed to be heterozygous for c.134G > A

AlsoPublished: N/A

Case#: Subject number 2, 37 years

DiseaseAssertion: Late Onset Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0008994 (proximal muscle weakness in lower limbs), HP:0003325 (limb-girdle muscle weakness), HP:0003701 (proximal muscle weakness), HP:0003691 (scapular winging), HP:0002355 (difficulty walking).

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Serum creatin kinase was 7.7 μkat/l

glucosidase activity: Whole uncoagulated blood samples used for leukocyte and DNA isolations.

GAA activity (w/o acarbose) 35 nmol.h.mg–1 (control 37±14).

8 nmol.h.mg–1 (with acarbose) (control 16±6).

Ratio of with/w/o acarbose is 0.24 (control 0.42±0.08).

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.1456G>C

Variant 2 ClinVarID: N/A

Variant 2 CAid: CA401366835

Zygosity: compund heterozygous

ParentalGenotype: N/A

PreviouslyPublished: N/A

Case#: Subject number 1, 18 years

DiseaseAssertion: Late Onset Pompe disease

FamilyInfo: N/A

CasePresentingHPOs: HP:0003325 (limb-girdle muscle weakness), HP:0008994 (proximal muscle weakness in lower limbs), HP:0008968 (muscle hypertrophy of the lower extremities), HP:0007340 (lower limb muscle weakness), HP:0003797 (limb-girdle muscle atrophy), HP:0002515 (waddling gait), HP:0003691 (scapular winging).

CaseHPOFreeText: Positive Trendelenburg sign

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Serum creatin kinase was 19. 9 μkat/l

glucosidase activity: Whole uncoagulated blood samples used for leukocyte and DNA isolations.

GAA activity (w/o acarbose) 29 nmol.h.mg–1 (control 37±14).

3 nmol.h.mg–1 (with acarbose) (control 16±6).

Ratio of with/w/o acarbose is 0.10 (control 0.42±0.08).

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

PMID: 30989758

Gene: SGCA

HGNCID: 10805

Case: 8 year old boy, Chinese.

DiseaseAssertion: LGMD

FamilyInfo: Family members denied relevant family history

CasePresentingHPOs: HP:0006785, HP:0003551, HP:0003391, HP:0003560

MotorAchievement: Noticed around 7 years old that he had trouble climbing stairs and standing up when crouching and had slower activity than other peers.

CreatineKinase: Creatine kinase CK 15550U/L, MB fraction 276 U/L

CasePreviousTesting:430 genes associated with muscular dystrophy were captured with a liquid catch kit.

GenotypingMethod: NGS

PreviouslyPublished: NA

SupplementalData: NA

Variant: NM_000023c.218 C>T

ClinVarID: Unregistered varient

CAID: Unregistered varient

gnomAD: https://gnomad.broadinstitute.org/variant/17-48245003-C-T?dataset=gnomad_r2_1

"0.000 Allele Frequency - East Asian

Case#: p1, male, no ages given DiseaseAssertion: Pompe disease FamilyInfo: None given CasePresentingHPOs: N/A CaseHPOFreeText: bright tongue CaseNotHPOs: HP:0001260, HP:0002015, HP:0012473 CaseNotHPOFreeText: Tongue weak

Case#: p2, male, no ages given DiseaseAssertion: Pompe disease CasePresentingHPOs: HP:0012473 CaseHPOFreeText: Bright tongue CaseNotHPOs: HP:0001260, HP:0002015

Case#: IV-1, male, 11 y.o, Pakistani

DiseaseAssertion: Limb-girdle muscular dystrophy (LGMD2F), sarcoglycanopathy

FamilyInfo: Consanguineous parents, both described as healthy and showing no abnormality. Three unaffected siblings were also reported: IV-2 (male, 10 y.o), IV-4 (male, 7 y.o), and IV-5 (female, 1.5 y.o). A deceased sister is included on the pedigree, but no details about this individual were reported. See Figure 1.

CasePresentingHPOs: HP:0001288, HP:0002650, HP:0003547, HP:0003749, HP:0001655

CaseHPOFreeText: Reduced weight gain noted at 3-4 y.o. Mild cardiac hypertrophy observed on cardiac review (additional echocardiography results reported in "Echocardiography" section). Additional phenotypic information reported in Supplementary Table 1.

CaseNotHPOs: HP:0009077, HP:0000703, HP:0001382, HP:0000365, HP:0001510, HP:0001249, HP:0000478, HP:0030148, HP:0011675

CaseNotHPOFreeText: Extensor muscles of the wrist, toes flexors, and hip abductors noted to be relatively normal. Additional phenotypic information reported in Supplementary Table 1.

MotorAchievement: Sat without assistance at 8 months of age, walked at 15 months of age, ran at 1.5 months of age. Never jumped or hopped. Frequent falls noted, as well as difficulty in walking and climbing stairs since 3 y.o.

CreatineKinase: 18SU (normal: 20SU for children, 10SU for adults) (see Supplementary Table 1). No assertion was made by the authors regarding whether this represents a normal or decreased CK level.

PreviousTesting: Thyroid stimulating hormone: 2.3mU/L (normal: <0.6mU/L); Serum VZV IgG: 286mlU/ml (normal: >150mlU/ml); IGF-1:186 ng/μl (normal: 102-520 ng/μl for males, 14 y.o); PRL: 202 ng/dl (normal: 42.5-414 ng/dl for males); Vitamin D: 47nmol/L (normal: 25-50 nmol/L); Free T4: 17.0 pmol/L (normal:10.8-19.0 pmol/L) (see Supplementary Table 1)

GenotypingMethod: (1) Targeted next generation sequencing of 31 genes associated with LGMD from proband genomic DNA extracted from peripheral blood sample; (2) Sanger sequencing of genomic DNA extracted from peripheral blood samples to confirm SGCD variant of interest in proband and three family members (III-3, III-4, IV-4). Variant was identified in homozygosity in the proband, in heterozygosity in each of the parents, and was not present in the unaffected sibling (IV-4).

Variant: NM_000337.5:c.289C>T (p.Arg97Ter)

CAID: CA3530549

gnomAD: Not reported

CaseAJV: 17 years diagnosis, Australia

DiseaseAssertion: Hypertrophic Cardiomyopathy

FamilyInfo: Father (index case) died awaiting cardiac transplant (carried both variants). Two possibly affected relatives.

CasePresentingHPOs: HP:0001639, HP:0006536

(Hypertrophic cardiomyopathy, Obstructive lung disease)

HPOsFreeText: Maximum left ventricular hypertrophy at 17 mm, Sudden cardiac death event at 17 years, Maximal wall thickness at 22mm,

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CasePreviousTesting: See Table 1

CaseGenotypingMethod: DNA was isolated from peripheral blood. Most participants underwent testing from the Illumina Cardiomyopathy Sequencing Panel, which includes 46 cardiomyopathy related genes. For others, whole exome sequencing or Sanger squencing was used. After the results were returned, variants were filtered for pathogenicity and rarity.

Variant:NM_000257.3:c.1954A>G (p.Arg652Gly)

ClinVarID:177626 https://www.ncbi.nlm.nih.gov/clinvar/variation/177626/

gnomAD: Not in gnomAD

Multiple Gene Variants:

MYBPC3 Variant

Variant: NM_000256.3:c.2980C>T (p.Leu994Phe)

ClinVarID:180992 https://www.ncbi.nlm.nih.gov/clinvar/variation/180992/

gnomAD: European (Non-Finnish) 1.624e-4, Overall 8.461e-5 https://gnomad.broadinstitute.org/variant/11-47355487-G-A

CaseI1-2: Case I1 is the asymptomatic paternal grandfather of proband 2 in family 2. The heterozygous Thr295Ile substitution was found in this individual.

CasePresentingHPOs: HP:0005543, (Reduced protein C activity)

HPOsFreeText: Protein C activity was reduced: Normal range = 70-140% (actual = 39%). Patient also had reduced protein C antigen: Normal range = 70-130% (Actual=36%).

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: This individual was asymptomatic.

CasePMIDs:

CaseI3-2: Case I3 is the asymptomatic grandmother of proband 2 in family 2. The heterozygous Leu-34Pro substitution was found in this individual.

CasePresentingHPOs: HP:0005543, (Reduced protein C activity)

HPOsFreeText: Protein C activity was reduced: Normal range = 70-140% (actual = 48%). Patient also had reduced protein C antigen: Normal range = 70-130% (Actual=36%).

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: This individual was asymptomatic.

CasePMIDs:

CaseII4-2: Case II4 is the asymptomatic mother of proband 2 in family 2. The heterozygous Leu-34Pro substitution was found in this individual.

CasePresentingHPOs: HP:0005543, (Reduced protein C activity)

HPOsFreeText: Protein C activity was reduced: Normal range = 70-140% (actual = 55%). Patient also had reduced protein C antigen: Normal range = 70-130% (Actual=34%).

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: This individual was asymptomatic.

CasePMIDs:

CaseII2-2: Case II2 is the asymptomatic paternal uncle of proband 2 in family 2. The Thr295Ile substitution was found in this individual.

CasePresentingHPOs: HP:0005543, (Reduced protein C activity)

HPOsFreeText: Protein C activity was reduced: Normal range = 70-140% (actual = 44%). Patient also had reduced protein C antigen: Normal range = 70-130% (Actual=33%).

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: This individual was completely asymptomatic.

CasePMIDs:

CaseII3-2: Case II3 is the clinically asymptomatic father of proband 2 in family 2. The Thr295Ile substitution was found in this individual.

CasePresentingHPOs: HP:0005543, (Reduced protein C activity)

HPOsFreeText: Protein C activity was reduced: Normal range = 70-140% (actual = 43%). Patient also had reduced protein C antigen: Normal range = 70-130% (Actual=34%).

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: This individual was completely asymptomatic.

CasePMIDs:

CaseIII1-2: Proband 2 (Case III 1 family 2) was a 19 year old male diagnosed with deep vein thrombosis in both legs since the age of 16. The family of this individual was asymptomatic with respect to thrombolytic disease and was non-consanguineous.

CasePresentingHPOs: HP:0002625, HP:0005543, HP:0004936, (Deep venous thrombosis), (Protein C deficiency), (Venous thrombosis),

HPOsFreeText: Deep vein thrombosis was in both legs since age of 16. This patient also had low protein C antigen.

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: This Case (Case III1-2) was designated as Proband 2.

CasePMIDs:

CaseI1-1: Case I1-1 is a 54 year-old male from Family 1. This individual has a heterozygous Asp255His mutation and is the father of the proband (II1-1). This individual was asymptomatic and lab results were within normal ranges.

CasePresentingHPOs:

HPOsFreeText:

CaseNotHPOs:

NotHPOsFreeText: Patient was completely asymptomatic.

CaseAddInfo:

CasePMIDs:

CaseIII1-1: Proband 1 (Case II1 Family 1) was a 28 year male admitted to the medical facility for deep vein thrombosis (DVT) and mesenteric vein thrombosis. This patient had a history of DVT and pulmonary embolism before admission. The mutation was compound heterozygous.

CasePresentingHPOs: HP:0030780, HP:0002625, HP:0002204, HP:0005543, HP:0004936, (Abnormality of the protein C anticoagulant pathway), (Deep venous thrombosis), (Pulmonary embolism), (Reduced protein C activity), (Venous thrombosis),

HPOsFreeText: Patient had mesenteric vein thrombosis (no HPO# found). The patient also had reduced protein C antigen.

CaseNotHPOs:

NotHPOsFreeText:

CaseAddInfo: This case (II1 family 1) is designated as proband 1. Proband 1 was also given heparin and warfarin (together) in an attempt to control clotting. Doses for this treatment regimen were not included. All other members of the family were asymptomatic with respect to thrombolytic disease and non-consanguineous. CasePMIDs: