Case#: CM (II:3), deceased at age 18 years.

CaseHPOs: HP:0002024, HP:0002013, HP:0002570, HP:0001251, HP:0001260, HP:0002495, HP:0001284 (malabsorption, vomiting, steatorrhea, ataxia, dysarthria, impaired vibratory sensation, absent deep tendon reflexes)

CaseHPOsFreeText: Symptoms as early as 4 months of age. Diagnosed with FHBL at 10 month; treatment with medium chain triglycerides (MCT) led to weight gain and a decrease in steatorrhea. Abnormalities in liver function, micronodular cirrhosis at 30 months, thought to be caused by treatment with MCT, progression to portal hypertension and esophageal varices. Neurologic symptoms stabilized on vitamin E therapy. At age 15, hepatitis A and cholelithiasis. He developed seizures, had a cerebrovascular accident, recurrent massive gastrointestinal hemorrhages, and finally cardiac arrest at the age of 18 (further details in PMID: 4135110).

CasePreviousTesting: No detectable plasma apoB by radial immunodiffusion (PMID: 4135110), Total cholesterol 36 mg/dl, triglyceride 12 mg/dl, no detectable LDL-cholesterol, HDL-cholesterol 36 mg/dl at age 15 years. No genetic testing other than APOB sequencing.

CaseGenotypingMethod: See family method

Variant: Compound heterozygous:

Variant 1: NM_000384.2:c.537+1G>T (paternal)

Variant 2: NM_000384.2:c.1315C>T (p.Arg439Ter) (maternal)

ClinVar: N/A

CAID: Variant 1: CA345962364 ; Variant 2: CA052017

gnomAD: Variant 1: Not in gnomAD;<br /> Variant 2: 0.00002640 (Euro non-Finnish)

CasePMIDs: 4135110

Details on readthrough studies from fibroblast extracts from patients carrying the mutations. References a previous publication PMID: 15081804

Case# Baskin YH, Male, 12

CasePreviousTesting patients referred to our high-risk hereditary heart disorders clinic for assessment of possible ARVC, as well as DNA-bearing blood or tissue samples sent for clinical ARVC gene-testing from other physicians, clinics or institutions to our CLIA-approved molecular genetics laboratory at the Hospital for Sick Children (listed on www.genetests.org).

CaseMethod1 PCR

CaseGenotypingMethod direct sequence analysis of all exons and flanking intron sequences of DSP (MIM 125647), PKP2 (MIM 602861), DSC2 (MIM 125645), DSG2 (MIM 125671) and TMEM43.

Variant NM_024334.2(TMEM43):c.1111T>C (p.Tyr371His)

ClinVar 46140

gnomAD 0.01076 link

This variant is mentioned as a reference to a previous publication (PMID: 20157015) which has already been included in the VCI.

Expression of the Ser600Arg variant in OPA1-null mouse embryonic fibroblasts showed complete fragmentation of the mitochondrial network and a slight, non-significant reduction of mtDNA amount indicating that this variant impacts protein function (PMID: 30293569)(PS3_Supporting).

This variant is mentioned in reference to a previously published report (PMID: 27511503)

Lalani, 2016 (AJHG article)

9 cases (5 scored)

NM_152906.6:c.460G>A (p.Gly154Arg)

exons 3-9del

exons 4-6del can be registered (which chr.22 transcript does this paper use? NM_152906.5 does not line up in NC_000022.11 (tested by Courtney))

Case# Subject 1, F, 4yo onset, Hispanic

CasePresentingHPOs HP:0002373, HP:0001260, HP:0006957, HP:0002913, HP:0007359, HP:0002104, HP:0003236, HP:0001987, HP:0001943, HP:0002058, HP:0000252, HP:0006801, HP:0003487, HP:0000577, HP:0002376, HP:0003236, HP:0001249, HP:0003201, HP:0000252

HPOcont: Febrile seizures, Dysarthria, loss of ability to walk, Myoglobinuria, Focal autonomic seizures, Apnea, Hyperammonemia, Hypoglycemia, Myopathic facies, Microcephaly, Brisk DTR, Babinski sign, Exotropia, Developmental regression, Elevated CPK, Hypoglycemia, Intellectual Disability, Rhabdomyolysis, Microcephaly

HPOFreeText: Febrile seizure at 1 year of age, developmental regression in the following 3 years with recurrent seizures, losing the ability to ambulate and speak, as well as right focal seizure, apnea, and unresponsiveness triggered by fever. On hospital admission she was noted to have elevated urine myoglobin, elevated creatine phosphokinase, aspartate aminotransferase, alanine aminotransferase, ammonia and hypoglycemia. MRI showed mild diffuse atrophy of the left cerebral hemisphere. "Ophthalmology evaluation showed intermittent exotropia. Echocardiogram and electrocardiogram (ECG) were unremarkable. Hysical examination was relevant for microcephaly (FOC 47.5 cm; <5th percentile for age), myopathic facies with drooling, increased tone in all extremities, and brisk deep tendon reflexes (DTRs) throughout with positive Babinski sign.

CaseNotHPOs HP:0011675

NotHPOcont: Arrhythmia

CasePreviousTesting "urine myoglobin of 94 ng/ml (normal range 10–65 ng/ml), serum creatine phosphokinase (CPK) of 205,000 U/l (normal range 75–230 U/l), elevated aspartate aminotransferase (AST) of 1,618 U/l (normal range 15–50 U/l), alanine aminotransferase (ALT) of 571 U/l (normal range 10–25 U/l), ammonia of 122 μmol/l (normal range 22–48 μmol/l), and hypoglycemia (blood glucose 30 mg/dl; normal range 70–110 mg/dl)."

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from another individual, subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonconsanguineous, mother tested heterozygous, father unavailable. cSNP data showed no evidence of deletion or uniparental isodisomy of the region.

CasePMIDs n/a

Case# Subject 4, M, 8yo onset, Hispanic

CasePresentingHPOs HP:0001249, HP:0001289, HP:0002066, HP:0009053, HP:0007340, HP:0001987, HP:0002925, HP:0005184, HP:0002058, HP:0002169, HP:0003201, HP:0001250, HP:0003236, HP:0000821, HP:0006801

HPOcont: Intellectual Disability, Confusion, Gait ataxia, Lower limb muscle weakness, Dysarthria, Hyperammonemia, Elevated TSH, Prolonged QTc interval, Myopathic facies, Clonus, Rhabdomyolysis, Seizures, Elevated CPK, Hypothyroidism, Brisk DTR

HPOFreeText: (2 years) uncoordinated gait and intellectual disability. (8 years) disorientation, ataxic gait, weakness in lower extremities, and dysarthria. (12 years) myopathic facies, brisk tendom reflexes, clonus, and impaired gait.

CaseNotHPOs HP:0001943, HP:0002151, HP:0002913

NotHPOcont: Hypoglycemia, Elevated Lactate, Myoglobinuria

CasePreviousTesting "lactate and glucose normal; elevated ammonia(111 μmol/l), elevated CPK (16,674 U/l). Urine was negative for myoglobin. TSH level was increased to 30.8 μIU/ml (range 0.32–5.00 μIU/ml), T3 was 166 ng/dl (range 90–260 ng/dl), and T4 was 5.2 μg/dl (range 6.4–13.3 μg/dl). Urine organic acids were normal."Muscle biopsy showed normal respiratory chain studies. Mitochondrial genome sequencing for common point mutations and deletions were normal."

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES and cSNP results confirmed with Sanger

Variant (1) NM_152906.6:c.460G>A (p.Gly154Arg)

ClinVar (1) 208823

CAID (1) CA358646

gnomAD (1) 0.001549(Other), 0.0001208(Overall)

VariantEvidence (Figure 3) using "EBV-transformed B-lymphoblastoid cell lines (BLCLs) from subject 4 with homozygous c.460G>A (p.Gly154Arg) mutation, and evaluated the Golgi by intracellular staining with WGA, as well as cis Golgi marker, anti-GM130 antibody." WGA stain resolved lower area of golgi bodies in p.Gly154Arg cells than WT. Measured immunoglobulin heavy chain binding protein levels in WT and and patient fibroblasts, BiP levels in patient cells lower than WT after ER induced stress by Brefeldin A.

CaseAddInfo nonsanguineous, confirmed heterozygosity of both parents

CasePMIDs n/a

Supplementary Table 1 (7 cols x 6 rows)

Nucleotide position Type of variation rs ID 1000 Genome MAF % ESP MAF %<br /> Italian Controls (MAF%) SALS (MAF %) c.909A>G p.Val303Val rs141922502 0.18 0.477 37/3960 (0.47) 14/1106 (0.6) c.999C>T p.Ala333Ala rs147351423 0.32 0.19 20/3960 (0.25) 2/1106 (0.1) c.1257C>T p.Ser419Ser rs199590938 0.01 § - - 1/1106 (0.05) c.376-16C>T Intronic rs116486324 0.16 0.21 n.c. 1/1106 (0.05) c.8G>A 3’UTR rs142720001 0.02 0.023 4/3960 (0.05) 1/1106 (0.05) c.48G>A 3’UTR rs11556349 1.7 0.845 46/3960 (0.58) 4/1106 (0.18)

Case#: G5145, 12yo at onset.

CasepresentingHPOs: HP:0000518

CaseHPOfreeText: neural tumors

CaseNotHPOs: HP:0100014, HP:0000365

CasePreviousTesting: SSCP analysis

CaseMethod1: Direct sequencing of both PCR strands

Variant: NM_000268.3:c.586C>T (nonsense)

CAID: CA411142679

Gnomad: not present

Case#: G170692, 4yo at onset.

CasepresentingHPOs:

CaseHPOfreeText: neural tumors

CaseNotHPOs: HP:0100014, HP:0000365, HP:0000518

CasePreviousTesting: SSCP analysis

CaseMethod1: Direct sequencing of both PCR strands

Variant: NM_000268.3:c.551G>A (nonsense)

CAID: CA411142590

Gnomad: not present

This variant is mentioned only in the context of a previous publication

Case1: Female, Austria, 18 yrs report

CasePresentingHPOs: HP:0010628, HP:0001558, HP:0002643, HP:0002015, HP:0040288, HP:0001260, HP:0003690, HP:0009046, HP:0003551, HP:0003798 (Facial weakness, Reduced fetal movement, Neonatal respiratory distress, Swallowing difficulties, Nasogastric tube feeding, Dysarthric speech, Limb weakness, Difficulty running, Difficulty climbing stairs, Nemaline bodies)

HPOsFreeText: 4/5/7 Apgar score

CaseNotHPOs: HP:0002015, HP:0002540, HP:0002650, HP:0002098 (Swallowing difficulties, Non-ambulatory, Scoliosis, Respiratory distress)

NotHPOsFreeText: N/A

CaseAddInfo: N/A

CasePreviousTesting: N/A

CaseGenotypingMethod: Whole exome sequencing of the proband revealed this homozygous LMOD3 mutation.

Variant: NM_198271.4:c.1648C>T (p.Leu550Phe)

ClinVar: 374498 https://www.ncbi.nlm.nih.gov/clinvar/variation/374498/

gnomAD: Not in gnomAD

PMID: 33364235

Gene: RAB39B

Disease: early-onset parkinsonism-intellectual disability syndrome

MonDO: MONDO:0010709

FamilyLabel UM Family 3

FamilyUM3PresentingHPOs HP:0012125 (Prostate Cancer)

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity n/a

Race n/a

FamilyUM3PreviousTesting Screened nonsense and missense variants in 202 candidate genes comprising ~15.5Mb. Established evidence of linkage of 17q21-22.

Affected 5

Unaffected 0

Segregations 4

PublishedLOD n/a

eLOD 1.2

AddSegregationInfo n/a

ProbandLabel UM3 III-1, Male, 45

Variant NM_006361.5(HOXB13):c.251G>A (p.Gly84Glu)

ClinVar 128031

CAID n/a

gnomAD MAF=0.007574(European(Finnish)), 2 homozygotes

FamilyAddInfo ages rounded to nearest 5 year interval

FamilyPMIDs 17120048

FamilyLabel UM Family 1

FamilyUM1PresentingHPOs n/a

FamilyNotHPOs n/a

CountryOrigin n/a

Ethnicity n/a

Race n/a

FamilyUM1PreviousTesting Screened nonsense and missense variants in 202 candidate genes comprising ~15.5Mb. Established evidence of linkage of 17q21-22.

Affected 4

Unaffected 0

Segregations n/a

PublishedLOD n/a

eLOD n/a

AddSegregationInfo One female typed positive(cannot have prostate cancer), one male typed positive(has other cancer)

ProbandLabel UM1 III-9, Male, 50

CasePresentingHPOs HP:0012125 (Prostate Cancer)

Variant NM_006361.5(HOXB13):c.251G>A (p.Gly84Glu)

ClinVar 128031

CAID n/a

gnomAD MAF=0.007574(European(Finnish)), 2 homozygotes

FamilyAddInfo ages rounded to nearest 5 year interval

FamilyPMIDs 17120048

Case#: KMP 7, male, 36 yrs, East Slovakia

DiseaseAssertion: HCM

FamilyInfo: n/a

CasePresentingHPOs: n/a

CaseHPOFreeText: symptomatic; LVOTO yes; LVEF 60%; ECG; echocardiography;

CaseNotHPOs: n/a

CaseNotHPOFreeText: no ICD

CasePreviousTesting: Additional Sanger sequencing of exons 12, 24, 25 of MYBPC3, exon 12 NEBL, exons 12, 20, 21 of SCN5A, exon 7 of TNNI3, and exon 9 of TNNT2 gene

CaseGenotypingMethod: Sanger sequencing;

Variant: NM_000257.4(MYH7):c.2845G>A (p.Glu949Lys)

ClinVar: 14093 https://www.ncbi.nlm.nih.gov/clinvar/variation/14093/

CAID: n/a

gnomAD: absent

Case: Bottillo Patient 17, Female, 50 yrs at diagnosis

CasePresentingHPOs: copy from group

CasePresentingHPOsFreeText: NYHA functional class 2, maximal wall thickness=14mm, left ventricular mass (at CMRI)=91(mg/m2), LVEF=52%, maximal oxygen uptake=78%, diastolic dysfunction grade=3, QT interval corrected for heart rate=0.4ms, thoracic pains, met ECG hypertrophy criteria, left bundle branch block, heart failure, mild intramyocardial CMRI

CaseNOTHPOs:

CaseNOTHPOSFreeText: family history of HCM or SCD

CasePreviousTesting: copy from group

CaseGenotypingMethod: copy from group

Variant: c.4485-6T>C

ClinVarID: or CAID: CA2573331909

gnomAD: This proband has an intronic missense variant that is not present in gnomAD. Pt also has variants in TNNT2 (p.R84S), RBM20 (p.D20G), CAV3 (p.T78M), and MYPN (p.A135A) which are either not present in or have conflicting interpretations of pathogenicity in ClinVar. This proband is scored reduced points.

AddCaseInfo:

PreviouslyPublished: no

VariantEvidence: Predicted branch-point splice site broken.

NonHumanModel: Mus musculus

GeneAlteration: p.Arg386Cys the most frequently reported missense variant linked as a causal pathogenic allele in mucopolysaccharidosis IVA patients

ModelPhenotype: In addition to undetectable GALNS enzyme activity in any assayed tissue, increased keratan sulfate detection in liver tissue and blood serum, the boney deformations missing from previous models were present in this mouse model HP:0004325, MP:0001258, HP:0005736

HumanPhenotype: HP:4000197, HP:0012069, HP:0004322, HP:0005736

ModelEvidence: CRISPR/Cas9 directed site mutagenesis of murine Galns coding sequence at codon homologous to the human p.Arg388Cys mutation cited in human MPSIVA patients. Mouse model showed increased keratan sulfate accumulation in liver and blood serum, undetectable n-acetylgalactosamine-6-sulfatase activity in any body tissue assayed as well as skeletal deformities consistent with human MPSIVA patients

ModelVariant: p.Arg388Cys

WhereInPaper:

Case: Family IV-III:2, 19 year old female

CaseHPOs: HP:0003563 (decreased LDL cholesterol)

CaseNotHPOs: HP:0000819, HP:0001397 (Diabetes, liver steatosis)

CasePreviousTesting: TC 124 mg/dl, LDL-C 49 mg/dl, HDL-C 62 mg/dl, TG 65 mg/dl (see additional values in Table 1)

Variant: NM_000384.2:c.11153C>G (p.Ser3718Ter), heterozygous

CAID: CA345983128

gnomAD: Absent

Variant evidence: APOB- p.Ser3718* mutations lead to the formation of expected truncated ApoB forms (ApoB-81) of 418 kDa (Fig. 1C, right panel) that can be secreted by the liver and lipidated.

CaseAddInfo: Daughter of Family IV-II:1

Case# Katagiri094, Male, Japanese

CasePresentingHPOs HP:0007987, HP:0007675, HP:0000551, HP:0007737

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod PCR of exons 4-11 of CNGA1

Variant NM_000087.3(CNGA1):c.265delC (p.Leu89Phefs)

ClinVar 225315 link

gnomAD 0.001378 link

Case# Katagiri029, female, Japanese

CasePresentingHPOs HP:0007987, HP:0007675, HP:0000551, HP:0007737

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod PCR of exons 4-11 of CNGA1

Variant NM_000087.3(CNGA1):c.265delC (p.Leu89Phefs)

ClinVar 225315 link

gnomAD 0.001378 link

Case#: Li Proband, US

DiseaseAssertion: MPS1 (Hurler)

FamilyInfo: n/a

CasePresentingHPOs: deficient IDUA activity in leukocyte, fibroblasts, or cultured trophoblasts. MPS IH defined as "organomegaly, heart disease, severe mental retardation, and death in childhood" but no individual phenotype information provided.

CaseHPOFreeText:

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: n/a

GenotypingMethod: mutation detection using reverse transcriptional polymerase chain reaction (RT-PCR) and genomic PCR sequencing. Polymorphism analyses were performed on controls by restriction enzyme assays of PCR amplicons flanking nine IDUA intragenic single nucleotide polymorphic alleles.

PreviouslyPublished: n/a

Variant: R628X; Q70X (path classification by LD VCEP). Also has Q33H(187G/T) polymorphism

ClinVar: 550421

CAID: CA2802462

gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).

SupplementalData: n/a

Case1: Female, 45 yrs report

CasePresentingHPOs: HP:0008994, HP:0002015, HP:0003236, HP:0003273, HP:0031237, HP:0003555, HP:0100295, HP:0012548 (Proximal muscle weakness in lower limbs, Dysphagia, Elevated serum creatine phosphokinase, Hip contracture, Internally nucleated skeletal muscle fibers, Fiber splitting, Muscle fiber atrophy, Skeletal muscle fatty infiltration)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband of Family 1, Mother of Case 2, Variant is de novo

CasePreviousTesting: N/A

CaseGenotypingMethod: The TPM2 gene was sequenced and variants identified. No other information is provided.

Variant: NM_003289.3:c.14_16delAGA (p.Lys7del)

ClinVar: 140486 https://www.ncbi.nlm.nih.gov/clinvar/variation/140486/

gnomAD: Not in gnomAD

Case1: Male, Spain, Birth onset

CasePresentingHPOs: HP:0003722, HP:0001324, HP:0000297, HP:0003701, HP:0001252, HP:0001284, HP:0001283, HP:0002540, HP:0002307, HP:0000218, HP:0011471 (Nemaline bodies, Muscle weakness, Facial hypotonia, Proximal muscle weakness, Muscular hypotonia, Areflexia, Bulbar palsy, Inability to walk, Drooling, High palate, PEG-fed in infancy)

HPOsFreeText: Bimodal communication, Wheelchair dependence, Cephalic support, Sedestation

CaseNotHPOs: HP:0002460, HP:0000602, HP:0001249, HP:0001627, HP:0002093, HP:0002650, HP:0006466, HP:0001382, HP:0003798 (Neck flexor weakness, Distal muscle weakness, Ophthalmoplegia, Intellectual disability, cardiac abnormality, Respiratory insufficiency, Scoliosis, Ankle contracture, Joint hypermobility)

NotHPOsFreeText: Mechanic ventilation

CaseAddInfo: Intermediate variant, Paternity/ maternity was confirmed

CasePreviousTesting: N/A

CaseGenotypingMethod: A research panel with 751 genes relating to neurological disorders, including the coding and intronic flanking regions of ACTA1, CFL2, KBTBD13, NEB, TNNT1, TNNT3, TPM2 and TPM3, was used to locate any variants in the proband. These variants were then prioritized and confirmed by Sanger sequencing in the probands and their relatives.

Variant1: NM_001164507.1:c.17779_17780del (p.Tyr5927Hisfs*17)

CAID: CA913203561 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913203561

gnomAD: Not in gnomAD

Variant2: NM_001164507.1:c.11086A>C (p.Thr3696Pro)

CAID: CA348785269 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_001271208.2%3Ac.11086A%3EC

gnomAD: Not in gnomAD

CaseII:II-2: Female, 37 years, Turkey

CasePresentingHPOs: HP:0004912, HP:0004322, HP:0002970, (Hypophosphatemic rickets, Short stature, Genu varum)

HPOsFreeText: -3.95 standard deviation score

CaseNotHPOs: HP:0000083, HP:0002024, HP:0001947 (Renal failure, Malabsorption, Renal tubular acidosis)

NotHPOsFreeText: Other tubulopathies that cause secondary hypophosphatemia, Vitamin D-dependent rickets type 1 and 2

CaseAddInfo: Variant is asserted novel, Mother of II:II-3

CasePreviousTesting: Calcium levels (9.8 mg/dL), Decreased serum phosphate levels (2.1 mg/dL; reference 2.7-4.5), Normal serum ALP (111 IU/L; reference 41-120), 25OHD3 levels (10.5 ng/ml), 1,25(OH)2D3 levels (N/A pg/mL), PTH levels (73 ng/L), TPR levels (87), Decreased TmP/GFR levels (1.70; reference 2.2-3.6)

CaseGenotypingMethod: Genomic DNA was isolated from peripheral blood leukocytes, amplified, and directly sequenced in all the coding exons and intron-exon boundaries of PHEX. If no mutations were found, FGF23 followed by consecutive analysis of DMP1, ENPP1, CLCN5, SLC34A3 and SLC34A1 was performed. Significance of found mutations was predicted by computational programs and sorted.

Variant: NM_000444.5:c.979_983dup (p.His329Thrfs*4)

CAID: CA913187410 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA913187410

gnomAD: Not in gnomAD

This family's affected individuals have some phenotypes consistent with COQ10 deficiency (hypotonia, seizures, uniform developmental delay or intellectual disability), but the COQ5 variant was heterozygous which is inconsistent with the MOI for COQ5-AR COQ10 deficiency. Additionally, variants in other genes were found that could explain the phenotype.

NonPatientCell myocardium, UBERON:0002349

GeneAlteration isolated adult rat ventricular myocytes infected with adenoviruses for expression of either the wild-type (WT) or mutant forms of CASQ2. Cytosolic and intra-SR [Ca2+]

FunctionalEvidence Causes leakage of Ca2+ transients from SR (fig. 5)

FAVariants NM_001232.3(CASQ2):c.97C>T (p.Arg33Ter), 41043 link

Case# F3-II1, female, 23yo report, Greek

CasePresentingHPOs HP:0008947, HP:0003155, HP:0010837, HP:0003124, HP:0003141, HP:0012347, HP:0012358, HP:0001263 (Infantile Hypotonia, Elevated alkaline phosphatase, Low ceruloplasmin, Elevated cholesterol, Elevated LDL-C, Abnormla N-glycosylation, Abnormal O-glycosylation, Psychomotor delay)

HPOsFreeText Elevated amino transferases

CaseNotHPOs n/a

CasePreviousTesting Serum ALT 36–172 U/l [normal range, 0–50 U/l], AST 31–119 U/l [normal range, 0–50 U/l], ALP 132–1,528 U/l [normal range, < 360 U/l], ceruloplasmin 17–24 mg/dl [normal range, 15–60 mg/dl], cholesterol 231–257 mg/dl [normal range, 120–200 mg/dl], LDL-C 161–171 mg/dl [normal range, 50–130 mg/dl], type 2 CDG

CaseMethod1 Sanger

CaseMethod2 n/a

CaseGenotypingMethod Sanger on patient and parents found variant in heterozygous state in both parents

Variant NM_152464.2(TMEM199):c.92G>C (p.Arg31Pro), homozygous

ClinVar 218964

gnomAD 0.00008933(Latino), 0.00004108(Overall), 10 heterozygotes

VariantEvidence n/a

CaseAddInfo nonconsanguineous

CasePMIDs n/a

Case# F2-II2, male, 41yo report

CasePresentingHPOs HP:0003155, HP:0010837, HP:0003124, HP:0001397, HP:0025321, HP:0003141, HP:0012347, HP:0006579, HP:0000023, HP:0003236 (Elevated alkaline phosphatase, Low ceruloplasmin, Elevated cholesterol, Steatosis, Copper accumulation in liver, Elevated LDL-C, Abnormal N-glycosylation, Neonatal jaundice, Inguinal hernia, Elevated CPK)

HPOsFreeText Inguinal hernia and increased CPK (11yo) minimal fibrosis (30yo), elevated amino transferases (11yo)

CaseNotHPOs HP:0200032 ( Kayser-Fleischer rings)

CasePreviousTesting serum ALT 190 U/l [normal range, 0–50 U/l], AST 153 U/l [normal range, 0–50 U/l], and ALP 718 U/l [normal range, < 360 U/l] (11yo), hepatic dry copper weight of 90 μg/g [normal range, <40 μg/g], ceruloplasmin 8.8 mg/dl [normal range, 15–60 mg/dl], cholesterol 204–337 mg/dl [normal range, 120–200 mg/dl], LDL-C 182–226 mg/dl [normal range, 50–130 mg/dl], type 2 CDG.

19067230: Laboratory tests excluded celiac disease, alpha1-antitrypsin deficiency, cystic fibrosis, galactosaemia and hypobetalipoproteinaemia. Liver iron concentration was normal, normal saturation of transferrin and ferriten, negative for hepatotrophic viruses. Serum anithrombin III (57%, normal range 80–120%) and clotting factor XI (42% , normal range 60–140%) were low.

CaseMethod1 WES

CaseMethod2 n/a

CaseGenotypingMethod WES in patient, sequenced father and mother found to be heterozygous for either variant

Variant NM_152464.2(TMEM199):c.[376-1G>A];[40G>C]

ClinVar 427819

gnomAD n/a for both

VariantEvidence Fig 2C, Western blot: reduced TMEM199 expression in patient fibroblasts

CaseAddInfo nonconsanguineous, father had history of hypercholesterolemia and ischemic heart disease.

CasePMIDs 19067230

Family#PresentingHPOs HP:0003155, HP:0010837, HP:0003124, HP:0001397, HP:0010836, HP:0003141, HP:0012347, HP:0012358, HP:0001976 (Elevated alkaline phosphatase, Low ceruloplasmin, Elevated cholesterol, Steatosis, Abnormality of copper homeostasis, Elevated LDL-C, Abnormal N-glycosylation, Abnormal O-glycosylation, Reduced antithrombin III activity)

HPOsFreeText Elevated amino transferases, minimal fibrosis, slightly decreased coagulation factors XI, XIII, and antithrombin-III

FamilyNotHPOs HP:0200032 (Kayser-Fleischer rings)

CountryOrigin n/a

Ethnicity Greek

Race n/a

Family#PreviousTesting Metabolic work up and anyalysis of coagulation factors, the latter of which showed decreased antithrombin-II, factor XI, factor XIII, and protein S, type 2 CDG. No mutations found in ATP7B, Wilson's disease excluded.

Family#Method1 WES

Family#Method2 Sanger

Family#GenotypingMethod WES on siblings, confirmed heterozygous in parents with Sanger

Affected 2

Unaffected 2

Segregations n/a

PublishedLOD n/a

eLOD n/a

AddSegregationInfo consanguineous

ProbandLabel F1-II2, male, 14yo report

Case1PreviousTesting Serum ALT 54 U/l [normal range, 0–50 U/l], AST 73 U/l [normal range, 0–50 U/l], ALP 745 U/l [normal range, < 360 U/l], ceruloplasmin 11.5 mg/dl [normal range, 15–60 mg/dl], urine copper/creatine ratio 86.9 μg/g [normal range, < 60 μg/g], cholesterol 253 mg/dl [normal range, 120–200 mg/dl], LDL cholesterol 188 mg/dl [normal range, 50–130 mg/dl]

Case2 F1-II3, male, 6yo report

Case2PreviousTesting ALT 210 U/l [normal range, 0–50 U/l], AST 246 U/l [normal range, 0–50 U/l], ALP 1162 U/l [normal range, < 360 U/l], ceruloplasmin 15.6 mg/dl [normal range, 15–60 mg/dl], urine copper/creatine ratio 72.8 μg/g [normal range, < 60 μg/g], cholesterol 336 mg/dl [normal range, 120–200 mg/dl], LDL cholesterol 277 mg/dl [normal range, 50–130 mg/dl]

Variant NM_152464.2(TMEM199):c.20C>A (p.Ala7Glu), homozygous

ClinVar 218965

gnomAD 23 total heterozygotes (sampled from ~242458) for missense changes at this locus, no entry for this particular variant

Variant Evidence Fig 2C, Western blot: reduced TMEM199 expression in patient fibroblasts

FamilyAddInfo n/a

FamilyPMIDs n/a

PMID: 33390680

Gene: GALNS

Disease: Mucopolysaccharidosis IVA

MonDO: MONDO:0009659

InheritancePattern: AR

Notes: Case report

No genetic or enzymatic confirmation of MPSIVA

Family#PresentingHPOs HP:0031317, HP:0011663

FamilyNotHPOs HP:0001635

CountryOrigin Newfoundland

Ethnicity NonHispanic/Latino

Race White

Family#PreviousTesting No

Family#GenotypingMethod Bidirectional resequencing

ClinVar NM_024334.2(TMEM43):c.1073C>T (p.Ser358Leu), ClinVarID: 734

FamilyPMIDs 3386698

***Note, this patient shows overlap of several homozygous regions and alterations with PAtient 1. Althgouh they state they are unrelated, it seems evident that they may be distantly related, the Parents of Patient 2 are consanguineous and the Turkish population. Patietn 1 is Turkish, and the parents are not marked as being consanguineous.

Case: Patient 2, female, Turkish

CasePresentingHPOs: 

CaseNOTHPOs:

CasePreviousTesting: Negative for mutations in SLC35D1 (Schneckenbecken dysplasia MIM 269250), and INPPL1 (opsismodysplasia; MIM 258480).

CaseGenotypingMethod: WES

Variant: NM_001440.3: c.953C>T(p.P318L)

CA ID: CA370858101

Homozygous

gnomAD: no homozygotes, only 2 hets in Euro-ND populatin CA370858101

AddCaseInfo:

VariantEvidence: WEstern blot analysis of EXTL3 from patinet 1 cells shows expression of hte P318L variant (Figure 1B), indicating the protein is still produced. However, a glycosyltransferase assay using the wildtype EXTL3 and th eP318L variant showed reduced enzyme activity in the P318L variant compared to wildtype, and simiar levels of activity as untransfected/ mock controls. This indicates the P318L mutation acts as a loss of protein function of the enzyme activity.

Family#PresentingHPOs: P1: HP:0000943, HP:0008922, HP:0002650, HP:0001537, HP:0020152, HP:0002515, HP:0002808, HP:0007957, HP:0008480, HP:0005180, HP:0002857,HP:0012069, HP:0002870 P2:HP:0001537, HP:0002857, HP:0007957, HP:0005180, HP:6000342, HP:0001385, HP:0000768, HP:0100559, HP:0012069 occipitocervical stenosis, myelomalacia

FamilyNotHPOs:

CountryOrigin:

Ethnicity:

Race:

Family#PreviousTesting:

Family#Method1:

Family#Method2:

Family#GenotypingMethod: unspecified NGS technique followed by GALNS specific Sanger seq of exons and targeted intronic regions

Affected: 2

Unaffected: 2

Segregations:

PublishedLOD:

eLOD:

AddSegregationInfo:

ProbandLabel: DeLong_P1, DeLong_P2

Variant: NM_000512.5(GALNS):c.899-397_1003-1862del

ClinVar: 1048483

CAID: CA2499223751

gnomAD: n/a

FamilyAddInfo:

FamilyPMIDs:

Case: Family 12 Proband, 5yo at onset, 38yo at report

CasePresentingHPOs:

CasePresentingHPOsFreeText: Muscle weakness (hyposthenia), followed by vision problems in the dark (14), BCVA=6/18, 6/7.5, retinitis pigmentosa, nystagmus, infantile appearance, hypertelorism, undeveloped fertile function, constricted visual field

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting: negative IRD gene panel analysis

CaseGenotypingMethod: "genome-wide analysis" -exome or genome sequencing

Variant: c.367 C > T p.(Arg123Trp); c.682-7 T > G p.(Gln230); p.(Leu193Phefs27)

ClinVarID: or CAID: CA6828832; CA6828747

gnomAD: This non-canonical splice site variant, c.682-7T>G, is present in gnomAD v4.1.0 with a MAF=0.001031 (66/64040 alleles) in the European Finnish population with 0 homozygotes.

This missense variant, p.Arg123Trp, is present in gnomAD v4.1.0 with a MAF=0.00002665 (2/75052 alleles) in the African/African American population and 0 homozygotes.

AddCaseInfo: only family member noted to be affected, others do not have genotype information available

PreviouslyPublished: n/a

VariantEvidence:

Family Name: Family 6

FamilyPresentingHPOs: HP:0000705

FamilyNotHPOs:

CountryOrigin: Turkey

Ethnicity: Turkish

Race: n/a

FamilyPreviousTesting: candidate gene sequencing, array comparative genomic hybridization, or exome sequencing

FamilyGenotypingMethod: WES

Affected: 2

Unaffected: 3

Segregations: 1

PublishedLOD: n/a

eLOD: 1.0

AddSegregationInfo: non-consanguineous family

ProbandLabel: Family 6: III:1, female, 11 yo

Variant 1: NM_033068.2(ACP4):c.382G>C (p.Ala128Pro)

ClinVar or CAID: 374865, https://www.ncbi.nlm.nih.gov/clinvar/variation/374865/

genomAD: 2.449e-5, http://gnomad.broadinstitute.org/variant/19-51294991-G-C

Variant 2: NM_033068.2(ACP4):c.397G>A (p.Glu133Lys)

ClinVar: 374866, https://www.ncbi.nlm.nih.gov/clinvar/variation/374866/

genomAD: 8.196e-6, http://gnomad.broadinstitute.org/variant/19-51295006-G-A

FamilyAddInfo: parents unaffected

CasePresentingHPOs: HP:0006297, HP:0011077, HP:0000698

CasePresentingHPOTerm: hypoplastic enamel, destructed first molars, mandibular anterior teeth had incisal edges,

CaseNotHPOs: HP:0011073

AddCaseInfo: compound heterozygous mutations

VariantEvidence:

This variant was only mentioned in reference to a previous publication (PMID: 30689204).

PMID 9516413

Notes discusses transactivation function of PST rich domain made up of exons 10-13

This variant is mentioned as one that causes an intermediate phenotype of MPS1 with a reference to a paper (PMID: 9391892) where it was previously reported. No new cases or experiments.

CaseB:III-2: Male, 2 years onset, China

CasePresentingHPOs: HP:0004912, HP:0003109, HP:0003155, HP:0006505, HP:0002753, HP:0002982, HP:0004349, HP:0000944, HP:0011849, HP:0002970, HP:0003170 (Hypophosphatemic rickets, Hyperphosphaturia, Elevated alkaline phosphatase, Abnormality of limb epiphysis morphology, Thin cortices, Tibial bowing, Reduced bone mineral density, Abnormality of the metaphysis, Abnormal bone ossification, Genu varum, Abnormality of the acetabulum)

HPOsFreeText: Fuzzy structures

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Proband is hemizygous for this mutation, Has a mother and grandmother with the same mutation/disease at 141.3 cm and 142.8 cm respectively

CasePreviousTesting: For all probands: Decreased serum phosphorus levels (0.64–0.9 mM; normal range, 1.29–1.94 mM), Increased 24-h urinary phosphorus levels (49.8–68.4 mmol/day; normal range, 12.9–42.0 mmol/day), Elevated blood alkaline phosphatase levels (350–668.7 U/L; normal range, 42–390 U/L), Lower limit of normal serum 1,25-dihydroxyvitamin D3 levels, Normal blood PTH, serum calcium levels and urine calcium/creatinine ratio, Elevated serum FGF23 (>1500 pg/mL; lower than 28 pg/mL in healthy family members)

CaseGenotypingMethod: Peripheral blood from the probands and affected family members was collected and genomic DNA extracted and quantified. Next-generation sequencing was performed on the probands following PCR amplification and the results were examined with the TruSight One Sequencing Panel, with such genes as PHEX, FGF23, SLC34A3, DMP1 and ENPP1. The mutations were then compared to a reference sequence and filtered for pathogenicity. Sanger sequencing was performed on the probands and family members to confirm the detected mutations.

Variant: NM_000444.5:c.433G>T (p.Glu145Ter)

CAID: CA412571205 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvs=NM_000444.5%3Ac.433G%3ET

gnomAD: Not in gnomAD

Case19 Male, Finland

CasePresentingHPOs HP:0000347, HP:0002101, HP:0000238, HP:0001341, HP:0007370, HP:0010664, HP:0002126, HP:0007260

(Micrognathia, Defective lung lobation, Hydrocephalus, Olfactory lobe agenesis, Callosal agenesis, Fused thalami, Polymicrogyria, Type II lissencephaly)

HPOsFreeText Crown-heel body length 49cm, body weight 3864g, brain weight 286g, abnormal larynx/trachea, hydrocephalus/open-book, occipitotemporal hypoplasia, infratentorial hypoplasia, occipitoschisis/keyhole, leptomeningeal heterotopia, neuroepithelial rosettes, absent developed and identifiable mamillary bodies, absent anterior commissure, difficult to identify nucleus dentatus, (Fig6:) markedly narrowed basis pontis with minute corticospinal tract and a larger tg above, dysplastic dentate nucleus with irregular neuronal strands and intermingled matrix-like small cells is seen in the cerebellar hilus

CaseNotHPOs HP:0001161, HP:0001829, HP:0001627, HP:0000157, HP:0007165

(Hand polydactyly, Foot polydactyly, Congenital heart defect, Tongue abnormality, Periventricular neuronal heterotopia)

NotHPOsFreeText Uterus duplex, hydranencephaly/anencephaly, true alobar or semilobar holoprosencephaly

CasePreviousTesting n/a

Variant NM_145014.2(HYLS1):c.632A>G (p.Asp211Gly), homozygous

ClinVar 1143

gnomAD MAF= 0.009594(European(Finnish)), no homozygotes

CaseAddInfo died 1 minute after birth, 40+6wk gestational age

CasePMIDs n/a

Family#PresentingHPOs HP:0003124, HP:0003236, HP:0003155, HP:0010837, HP:0001397, HP:0011967, HP:0001405 (High cholesterol, Elevated CK, Elevated alkaline phosphatase, Decreased serum ceruloplasmin, Steatosis, Copper deficiency, Periportal fibrosis)

HPOsFreeText hypertransaminasemia and slight hepatomegaly(2yo), focal steatosis

FamilyNotHPOs n/a

CountryOrigin Italy

Ethnicity n/a

Race n/a

Family#PreviousTesting serum metabolic testing: elevated AST, ALT, ALP, cholesterol(LDL and HDL), and CK, reduced ceruloplasmin and copper, normal haptoglobin. High liver copper, type 2 CDG

Family#Method1 WES

Family#Method2 n/a

Family#GenotypingMethod n/a

Affected 2

Unaffected n/a

Segregations n/a

PublishedLOD n/a

eLOD n/a

AddSegregationInfo n/a

ProbandLabel Patient 1, Female, 2yo onset

Case1PreviousTesting serum metabolic testing: AST 349[nv < 41 U/L], ALT 329[nv < 45 U/L], ALP 1995[nv < 475 U/L], total cholesterol 340[nv < 200 mg/dL], HDL chol 49[nv > 45 mg/dL], LDL chol 256[nv < 160 mg/dL] CK 799 [nv 0-170 U/L], Ceruloplasmin 6 [nv 20-46 mg/dL], Haptoglobin 20[nv 30-250 mg/dL], Copper <40[nv 69-122 μg/dL] recorded at 2yo, retested with similar outcome at 27yo save for restored AST 53U/L and ALT 23U/L

Case2 Patient 2, male, 2yo onset

Case2Previoustesting serum metabolic testing: AST 299[nv < 41 U/L], ALT 221[nv < 45 U/L], ALP 3990[nv < 475 U/L], total cholesterol 240[nv < 200 mg/dL], HDL chol 45[nv > 45 mg/dL], LDL chol 176[nv < 160 mg/dL] CK 442 [nv 0-170 U/L], Ceruloplasmin 4 [nv 20-46 mg/dL], Haptoglobin 40[nv 30-250 mg/dL], Copper <40[nv 69-122 μg/dL] recorded at 2yo. Remained elevated at next check at age 24 save for ALT 50 U/L.

Variant (1) NM_152464.2:c.13_14del (p.Leu5AlafsTer30) (2) NM_152464.2(TMEM199):c.92G>C (p.Arg31Pro)

ClinVar (2) 218964

CAID (1) CA8456913

gnomAD (1) 0.00004607(European (Non-Finnish)), 0.00002063(total)-5 heterozygotes (2) 0.00008933(Latino), 0.00004108(Total)-10 heterozygotes

Variant Evidence No detectable TMEM199 in patient fibroblasts on western blot.

FamilyAddInfo n/a

FamilyPMIDs 26833330

Case 3: Female, diagnosed at 30 yrs, 18mm septal wall thickness, no mutations in HCM associated genes, no family history

HP:0002094, HP:0006689, (dyspnea, bacterial endocarditis)

Variant: NM_020433.4(JPH2):c.494C>T (p.Ser165Phe),

ClinVar ID: 30457

https://www.ncbi.nlm.nih.gov/clinvar/variation/30457/

not in ExAC

Case44: Female, 7 yrs onset

CasePresentingHPOs: HP:0006785, HP:0003236, HP:0040083, HP:0003307, HP:0002527, HP:0003701, HP:0003323, HP:0009042, HP:0003458, HP:0100305, HP:0031542 (Limb-girdle muscular dystrophy, Elevated serum creatine kinase, Toe walking, Hyperlordosis, Falls, Proximal muscle weakness, Progressive muscle weakness, Marked muscular hypertrophy, EMG: myopathic abnormalities, Ring fibers, Myelin-like whorls in vacuolated fibers)

HPOsFreeText: Wheelchair at 14 yrs

CaseNotHPOs: HP:0003115, HP:0100543 (Abnormal EKG, Cognitive impairment)

NotHPOsFreeText: N/A

CaseAddInfo: Proband is homozygous for this duplication, Parents are confirmed heterozygous

CasePreviousTesting: Peak CPK at 20,000 IU/l, Partially absent α- and β-sarcoglycan staining, Normal dystrophin content, Totally absent γ-sarcoglycan staining

CaseGenotypingMethod: Total mRNA was isolated from muscle biopsies and cDNA was synthesized from it via reverse transcriptase. PCR and SSCP analysis was performed and excised, amplified, and sequenced. After finding the mutations, DNA from peripheral blood leukocytes or muscle biposies was isolated, PCR amplified, and sequenced to confirm the results.

Variant: NM_000231.2(SGCG):c.87dup (p.Gly30fs)

ClinVar: 2008 https://www.ncbi.nlm.nih.gov/clinvar/variation/2008/

gnomAD: 0.000008805, https://gnomad.broadinstitute.org/variant/13-23777919-A-AT

Hollander CF

Family#PresentingHPOs HP:0007663

FamilyNotHPOs

CountryOrigin Italy

Ethnicity NonHispanic

Race White

Family#GenotypingMethod GeneChip Mapping 250K Nsp Array; Affymetrix, Santa Clara, CA) at the Microarray Core of the Dana-Farber Cancer Institute. The genotyping data were analyzed for homozygous regions using dCHIP

Affected 4

Unaffected 3

Segregations 4

eLOD 2.18

AddSegregationInfo consanguineous

ProbandLabel Hollander II:1

CasePresentingHPOs HP:0011505

Variant NM_002900.2:c.3238G>A

CAID CA344701

gnomAD 0.00006537

Patient: H02

Variant: c.685 + 2_685 + 13del

CAID: CA2580612034

Functional effect: Normal exon inclusion (band A) *, exon 4 skipping (band B), exon 4 + 6 skipping. Observed in blood.

MonDO: MONDO:0032706

Case: 58-year-old male of Greek origin presenting with a progressive cerebellar syndrome starting at the age of 33 years with mild gait imbalance, ataxia and dysarthria. Apart from dyslipidaemia, type 2 diabetes, and chronic diarrhoea presenting at 37 years of age and attributed to irritable bowel syndrome, the rest of the patient’s medical history is unremarkable. Proband has NM_017686.4; c.134delC with mother as carrier.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo: His relatives have reported personality changes with emotional lability, aggressive behaviour and depressive episodes. Family history is negative for neurological disorders. Both parents originated from the same small village but there was no known consanguinity in the family

CasePresentingHPOs: HP:0002141, HP:0002070, HP:0002066, HP:0001260, HP:0003119, HP:0005978, HP:0002028, HP:0000726 (Gait imbalance, Limb Ataxia, Gait Ataxia, Dysarthria, Abnormal circulating lipid concentration, Type II diabetes mellitus, Chronic diarrhea, Dementia)

CasePreviousTesting: Neurological examination at the age of 50, when the proband was first seen, showed severe gait ataxia with mild pyramidal features consisting of brisk reflexes, dysmetria, dysdiadochokinesia, cerebellar dysarthria, jerky pursuit and nystagmus, mild behavioural changes, and disturbances of short-term memory. Follow-up neurological examination at the age of 58, revealed severe gait disturbance, dysmetria, dysdiadochokinesia and brisk deep tendon reflexes with flexor plantar responses, as well as gaze-evoked nystagmus, jerky pursuit, hypermetric saccades, cerebellar dysarthria, and mild sensory loss in the lower limbs (Supplementary Video 1). Scale for the assessment and rating of ataxia (SARA) score at that time was 31/40 and Mini-Mental State Examination (MMSE) score was 24/30. A detailed neuropsychological assessment was performed, revealing widespread deficits in encoding, learning, and consolidating new verbal information. Overall, the patient exhibited prominent deficits in episodic memory, verbal working memory, and executive functions. A brain MRI scan, including susceptibility-weighted imaging (SWI), was performed and revealed marked cerebellar atrophy affecting the hemispheres and more significantly the vermis, as well as mild cortical atrophy, midbrain and pons atrophy. Nerve conduction studies (NCS), electromyography (EMG) and ophthalmological evaluation were all normal. Laboratory testing of alpha-fetoprotein levels, vitamin E, copper, and folic acid were also normal. To exclude the possibility of an underlying autoimmune disease, the patient’s serum was tested for binding to various markers, including a panel of paraneoplastic markers of autoimmunity, GAD, NMDA, AMPA, GABAB, DPPX and VGKC, as well as monkey cerebellum frozen tissue. No binding to any of these markers was detected.

GenotypingMethod: Blood samples from the proband and his mother were collected for whole exome sequencing ans Sanger confirmation. Initial screening for Friedreich’s ataxia, as well as spinocerebellar ataxia (SCA) types 1, 2, 3, 6 and 7 in the proband was negative.

Variant: GDAP2:c.134del, p.(Pro45Leufs*22)

CAID: CA2574039871

gnomAD: Total AF 0.000001866, gnomAD v4.1 (https://gnomad.broadinstitute.org/variant/1-117920223-AG-A?dataset=gnomad_r4)

Family1: N/A

FamilyPresentingHPOs: HP:0009027, HP:0031374, HP:0008963, HP:0001761, HP:0012515, HP:0008944, HP:0008948, HP:0003484, HP:0001265, HP:0003458 (Foot dorsiflexor weakness, Ankle weakness, Tibialis muscle weakness, Pes cavus, Hip flexor weakness, Distal lower limb amyotrophy, Proximal upper limb amyotrophy, Upper limb muscle weakness, Hyporeflexia, EMG: myopathic abnormalities)

HPOsFreeText: N/A

FamilyNotHPOs: HP:0009130, HP:0003474, HP:0003445 (Hand muscle atrophy, Sensory impairment, EMG: neuropathic changes)

NotHPOsFreeText: N/A

FamilyPreviousTesting: Genomic DNA was extracted and RFLP was performed on all family members. Fragments were separated, hybridized, and subject to linkage analysis.

FamilyGenotypingMethod: A refined linkage analysis was performed with the deaths of some family members and additions of others, allowing for the narrowing of the genomic region. Afterwards, RNA was extracted from a frozen sample of the proband and cDNA was sequenced. PCR amplification and direct sequencing was used to confirm the mutation in the proband. SSCP was used to screen the family members and other NM probands for the mutation.

FamilyAddInfo: Pedigree in Figure 1

FamilyPMIDs: 1347195 (Family Characterization)

Affected: 9 Alive, 2 Now deceased

Unaffected: 11

Segregations: 10

PublishedLOD: 4.52 at zero recombination with candidate gene sequencing

AddSegregationInfo: Annotate with other pertinent information as needed.

ProbandLabel: IV-3

Variant: NM_152263.4(TPM3):c.26T>G (p.Met9Arg)

ClinVar: 12446 https://www.ncbi.nlm.nih.gov/clinvar/variation/12446/

gnomAD: European (Non-Finnish) 8.828e-6, Overall 4.009e-6 https://gnomad.broadinstitute.org/variant/1-154164469-AT-A

Case: Zampieri SD2, Male

DiseaseAssertion: Sandhoff Disease

FamilyInfo: patient's genotype was confirmed in parents

CasePresentingHPOs: HP:0000007, HP:0033978

CaseHPOFreeText: neurological symptoms (unspecified)

CaseNOTHPOs:

CaseNOTHPOFreeText:

CasePreviousTesting: Patients presented with neurological symptoms and diagnosis was confirmed by the demonstration of reduced Hex A and Hex B activity in peripheral white blood cells or cultured fibroblasts.

GenotypingMethod: PCR

PreviouslyPublished: n/a

SupplementalData: n/a

Variant: c.850C>T (p.R284X) on allele 1

CAID: CA116495

gnomAD: MAF: 0.0002286 South Asian, gnomAD variant ID: 5-74009409-C-T

VariantEvidence: PMID:8162015 previously reported this variant to be associated with the infantile form of SD. A fibroblast line from this patient with the infantile form of the disease was investigated for mutations by single strand conformation polymorphism analysis and direct sequencing of PCR products. A nonsense mutation was found which generated a stop codon at codon 284. The study investigated the steady-state level of mRNA produced by cells containing stop codons using a competitive polymerase chain reaction technique and found that at codon 284, the mRNA levels were 0.8%, as percent of normal per single gene dose.

MultipleGeneVariants: AR, different variant in second allele

GeneName: HEXB

Variant: c.1613+2T>G (p.E538ins4X5) on allele 2

CAID: CA3306214

gnomAD: MAF: 0.000008808, European (non-Finnish), gnomAD ID: 5-74016574-T-G

VariantEvidence: PMID: 8535449 previously reported this variant to be associated with the infantile form of SD. This study found the total Hex activity to be 8% of the normal level, with only 0.5% being hex B which was reported to be insignificant. This intronic mutation affects the 5' donor site of intron 13 and results in insertion of 48 nucleotides which shifts the reading frame and results in the generation of a PTC.

Case# Monnier 3:12, died age 30, male, French

CasePresentingHPOs HP:0001649, HP:0006682, HP:0012416, HP:0001695, HP:0001945

CasePreviousTesting N/A

CaseMethod1 PCR

CaseGenotypingMethod PCR and sequencing gel for CACNL1A3.PCR1 amplimer

Variant NM_000069.2(CACNA1S):c.3257G>A (p.Arg1086His)

ClinVar 17626

gnomAD 0.00002978 link

VariantEvidence N/A

Case#: 1

Variant: homozygous NM_014495.3:c.286_288del (ANGPTL3) p.Glu96del ← listed in Allele Registry, but paper lists it as p.Glu95del

ClinVar: not in ClinVar

gnomAD: total allele count: 42, allele frequency for African population with an allele count of 16: 0.0006458

Case#: 2

Variant: homozygous NM_014495.3(ANGPTL3):c.439_442del (p.Asn147Terfs)

CAId: CA145485

ClinVar: 91865

gnomAD: 37 allele count, 0.0001966 allele frequency for European with allele count of 23

Case#: 3 (previously report in PMID 20942659)

Variant: compound heterozygous NM_014495.3(ANGPTL3):c.385G>T (p.Glu129Ter) and NM_014495.3(ANGPTL3):c.50_51delCCinsGA (p.Ser17Ter)

ClinVar: 18439 (p.Ser17Ter), 18440 (p.Glu129Ter), for both variants - 1 assertion for pathogenic based on OMIM but no assertion criteria provided

gnomAD: not in gnomAD

Case#: 4

Variant: compound heterozygous NM_014495.3(ANGPTL3):c.439_442del (p.Asn147Terfs) and NM_014495.3(ANGPTL3):c.883T>C (p.Phe295Leu)

ClinVar: 91865 and 91867

gnomAD: not in gnomAD

Case#: 5

Variant: heterozygous c.355_360delAACT

ClinVar: not in ClinVar

CAId: none

gnomAD: not in gnomAD

Case#: 6

Variant: heterozygous c.62 insCTCAT

ClinVar: not in ClinVar

CAId: none

gnomAD: not in gnomAD

Case#: 7

Variant: heterozygous NM_014495.3:c.167G>T (ANGPTL3)

ClinVar: not in ClinVar

CAId: CA340600195

gnomAD: not in gnomAD

Case#: 8

Variant: heterozygous NM_014495.3:c.995G>A

CAID: CA886769

ClinVar: not in ClinVar

gnomAD: 0.0001476 total allele freq, 37 allele count, 0.0008191 is largest allele freq for Other population with allele count of 5

Case#: Consequence 11 Table 1 in Data Supplement (4 cases)

DiseaseAssertion: HCM

FamilyInfo: N/A

CasePresentingHPOs: N/A

CaseHPOFreeText: Cardiac magnetic resonance imaging, BSA, NYHA functional class, obstructive HCM, atrial fibrillation, coronary artery disease, NSVT, Syncope, SCD family hitory, wall thickness

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: Additional oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing for MYBPC3, TMP1, TNNC1, TNNI2, TNNI3, TNNT2, ACTC1, MYL3

CaseGenotypingMethod: oligonucleotide hybridization–based DNA sequencing and dideoxy-based DNA sequencing

Variant: NM_000257.4(MYH7):c.2779G>A (p.Glu927Lys)

ClinVar: 42932 https://www.ncbi.nlm.nih.gov/clinvar/variation/42932/

CAID: n/a

gnomAD: absent

Case#: Greenwood Genetic Center Molecular Diagnostic Laboratory Patient 6

DiseaseAssertion: MPS 1

FamilyInfo:

CasePresentingHPOs:

CaseHPOFreeText: N/A

CaseNotHPOs:

CaseNotHPOFreeText:

PreviouslyPublished: no

Variant: NM_000203.3 c.1728-1G>C (IVS12)/ c.1403-1G>T (IVS9) ‡

ClinVar:

CAID: CA355965306

SupplementalData: ESM 4 contains proband info

PMID 28813500

Variant c.3268G>A

Phenotypes HP:0001402, HP:0001394

Phenotypes free-text hepatocellular carcinoma, cirrhosis

Variant NM_144668.5:c.3007_3337del

ClinVar 586974

Case: Family 2 Kismet Proband, Turkish, male

CasePresentingHPOs: HP:0000407, HP:0002240, HP:0004322, HP:0025289, HP:0033176, HP:0100727

CasePresentingHPOsFreeText: Rapidly growing orbital mass with SHML histopathology. Retropharyngeal lymphadenopathy. Filling of lymph node sinuses with histiocytes, plasma cells and lymphocytes. Histiocytes had a benign appearance, were CD-1a negative but positive for CD68 and S-100.

CaseNOTHPOs:

CaseNOTHPOSFreeText:

CasePreviousTesting: direct sequencing of PRF1 and UNC5B

CaseGenotypingMethod: genotyping (genome-wide linkage scan was performed using Affymetrix 250k SNP arrays), direct sequencing, PCR

Variant: p.Gly437Arg; p.Phe103X

ClinVarID: or CAID: 565; 30947

gnomAD: The missense variant G437R is present in gnomAD v4.0.0 with a MAF=0.00006666 (4/60002 alleles) in the Admixed American population and 0 homozygotes.

The nonsense variant, p.Phe103Ter found in exon 2/6, is present in gnomAD v4.0.0 with a MAF=0.0005201 (3/5768 alleles) in the Middle Eastern population and 0 homozygotes.

AddCaseInfo: 2 affected brothers

PreviouslyPublished: 16118898

VariantEvidence: Functional characterization of G437R in Xenopus oocytes showed that transport activity was approximately half of WT SLC29A3. Studies in NIH 3T3 fibroblasts demonstrated accelerated turnover of the G437R mutant compared to WT, suggesting decreased stability (Kang et al. 2010; PMID: 20595384)

MonDO: MONDO:0032706

Case: Patient AW, Belgian female developed mild gait imbalance at age 38 years with progressive decline with clear dementia at age 53 years. She died at age 62 years due to infectious complications. Homozygous for GCAP2:c.1198_1199insG; p.(His400fs*15). The variant and its segregation were confirmed in the proband and her daughter using standard Sanger sequencing methodology.

DiseaseAssertion: Cerebellar ataxia

FamilyInfo: No consanguineous family. Her brother died from brain tumor, her father had epilepsy and died at 84 years old, her mother was alive without ataxia or gait disorder at age 85 years. Daughter is healthy.

CasePresentingHPOs: HP:0002141, HP:0007240, HP:0001348, HP:0033687, HP:0000708, HP:0002061, HP:0002540, HP:0001268, HP:0000741, HP:0000718, HP:0000716, HP:0002546, HP:0002015, HP:0002300, HP:0000726 (Gait imbalance, Progressive gait ataxia, Brisk reflexes, Short term memory impairment, Atypical behavior, Lower limb spasticity, Inability to walk, Mental deterioration, Apathy, Aggressive behavior, Depression, Incomprehensible speech, Dysphagia, Mutism, Dementia

CaseHPOFreeText: Speech problems, jerky eye movements, dysexecutive syndrome, bed ridden

CaseNOTHPOs: HP:0000639 (Nystagmus)

CasePreviousTesting: Brain MRI at age 53 years revealed severe atrophy of the cerebellum, both vermian and hemispheric, mainly of the superior aspect, and also global cerebral atrophy (cortical and central). Levels of alpha-fetoprotein, vitamin E, copper, and folic acid were normal. Screening for trinucleotide repeat expansions was negative for SCAs 1, 2, 3, 6, 7, 8, 10, 12, and 17, and for Friedreich’s ataxia. Post-mortem brain examination revealed cerebellar atrophy in combination with a mild atrophy of the pes pontis. Normal nerve conduction studies. Normal opthalmological evaluation.

GenotypingMethod: Exome sequencing. Sanger sequencing was performed for confirmation of the variants and for segregation analyses using standard techniques. 90 560 single-nucleotide variations and 8961 indels were called. No obvious variants in known ataxia genes were observed. Variants were filtered for variant type, rarirty (MAF <0.5%) and conservation (>0.75, phyloP). Trio-sequencing analysis to detect putativede novo variants was not possible because of the unavailability of paternal DNA for Patient NIJ and parental DNA for Patient AW.

Variant: c.1198_1199insG; p.(His400fs*15) Homozygous

ClinVarID: 624620

CAID: CA30125084

gnomAD: Total AF 0.000004342, gnomAD v4.1. https://gnomad.broadinstitute.org/variant/1-117883536-T-TC?dataset=gnomad_r4

Functional evidence: Drosophila fly GDAP2 model supports a role of GDAP2 in motor behaviour and suggests that cellular stress might be driving the neurodegenerative cascade. Ubiquitous Gdap2 RNAi-1 knockdown results in droopy wings. Gdap2 knockdown does not result in increased levels of apoptotic cell death in central brain upon 18 hours paraquat exposure.

CaseA032-IV-1 male, unknown age, Han Chinese

CasePresentingHPOs HP:0003251, HP:0012868, HP:0012207

(male infertility, sperm tail anomaly, reduced sperm motility)

HPOsFreeText Table S1: Sperm volume: 1.1mL, sperm concentration: 15.5million/mL, progressive motility: 1.5%, motility: 9.5%, normal spermatozoa: 7.0%, absent flagella: 12.0%, short flagella: 55.0%, coiled flagella: 23.0%, angulation: 1.0%, irregular caliber: 2.0%. Semen volume and sperm concentration were normal to the standards.

CaseNotHPOs n/a

CasePreviousTesting Ejaculation disorder, erectile dysfunction, and orchiatrophy not detected. Chromosomal karyotypes were normal (46; XY) and no deletion detected in the human Y chromosome. In addition, primary ciliary dyskinesia-related symptoms of sinusitis, bronchitis, pneumonia, and otitis media were also excluded.

Variant 1. NM_144668.5:c.415C>T(p.Gln139Ter), 2. NM_144668.5:c.1722del(p.Phe574LeufsTer3)

ClinVar 1. n/a, 2. n/a

CAID 1. CA387002758, 2. CA891834513

gnomAD 1. Maximum population minor allele frequency in gnomAD = 0.00005574 (East Asian); no homozygotes, 2. not in gnomAD

CaseAddInfo phase confirmed in parents, in trans in patient

CasePMIDs n/a

Family L has this variant segregating through

Family A autosomal recessive variant found in CHST9 (MIM: 610191; c.1133A>G [p.Asn378Ser] [GenBank: NM_031422])

ExperimentName: Ojala 2016 hiPSC-derived CMs

PatientCell: CL_0002620 (skin fibroblasts)

GeneFunction: GO:0008016 (regulation of heart contraction)

GeneAlteration: hiPSC-derived cardiomyocytes (CMs) generated from skin fibroblasts collected from patients carrying a TPM1-Asp175Asn mutation

FunctionalEvidence: Figure 2 shows enlarged cardiomyocytes (CMs) (a-b), an increase in multinucleated CMs (c), and calcium handling abnormalities (d) for the HCM-TPM1 variant CMs compared to WT CMs.

FAVariants: NM_001018005.2(TPM1):c.523G>A (p.Asp175Asn), CA018106

Case2: Female, Birth onset

CasePresentingHPOs: HP:0002093, HP:0002938, HP:0002015, HP:0003798, HP:0003200, HP:0003548 (Respiratory insufficiency, Lumbar hyperlordosis, Dysphagia, Nemaline bodies, Ragged-red fibers, Subsarcolemmal accumulations of abnormally shaped mitochondria)

HPOsFreeText: N/A

CaseNotHPOs: N/A

NotHPOsFreeText: N/A

CaseAddInfo: Mother of proband

CasePreviousTesting: N/A

CaseGenotypingMethod: See Family

Variant: NM_003289.3:c.397C>T (p.Arg133Trp)

ClinVar: 12463 https://www.ncbi.nlm.nih.gov/clinvar/variation/12463/

gnomAD: Not in gnomAD

Case1: Female, Birth onset

CasePresentingHPOs: HP:0008947, HP:0008872, HP:0002033, HP:0030043, HP:0001349, HP:0001488, HP:0010804, HP:0002650 (Infantile hypotonia, Feeding difficulties in infancy, Poor suck, Hip subluxation, Facial diplegia, Bilateral ptosis, Tented mouth, Scoliosis)

HPOsFreeText:Disorganized myofibrils and thickened Z bands

CaseNotHPOs: HP:0003798 (Nemaline bodies)

NotHPOsFreeText: N/A

CaseAddInfo: Proband of Family 1

CasePreviousTesting: N/A

CaseGenotypingMethod: See Family

Variant: NM_003289.3:c.397C>T (p.Arg133Trp)

ClinVar: 12463 https://www.ncbi.nlm.nih.gov/clinvar/variation/12463/

gnomAD: Not in gnomAD

PMID: 27825773

Gene: GALNS

Disease: Mucopolysaccharidosis IVA/Morquio A

MonDO: MONDO:0009659

InheritancePattern: AR

Notes:

Important citations to study how TERC relates to genetic anticipation (inheriting not only TBD genes but short telomeres to begin with, leading to earlier onset)

Case#: Family 1, Individual III-1, Female, 27 yo, dx at 3 months old

CasePresentingHPOs: HP:0000639, HP:0001332, HP:0001270, HP:0002497, HP:0001272, HP:0002062, HP:0000571, HP:0002540, HP:0000511, HP:0012547, HP:0001260, HP:0030187, HP:0001332, HP:0000473

CaseNotHPOs: HP:0003474, HP:0007108

CasePreviousTesting: MRI showing brain hypomyelination

CaseGenotypingMethod: combination of homozygosity mapping and WES, haplotype analysis

Variant: NM_177400.2(NKX6-2):c.121A>T (p.Lys41Ter)

ClinVar: 430622, https://www.ncbi.nlm.nih.gov/clinvar/variation/430622/

gnomAD: n/a

VariantEvidence:

CaseAddInfo: Wheelchair bound at 27 yo

CasePMIDs:

Case#: Vazna Patient #15, female, Czech Republic or Slovakia, onset in infancy, 10mo at dx, 12yo at report

DiseaseAssertion: MPS1, H/S

FamilyInfo:

CasePresentingHPOs: HP:0008301, HP:0002159, HP:0000280, HP:0000943, HP:0007957, HP:0004322, HP:0000256, HP:0001387, HP:0001263, HP:0001433, HP:0031664, HP:0000023, HP:0000158

CaseHPOFreeText: Deficiency of IDUA activity in leukocytes showed either no or very low residual enzyme activity (no exact amount specified), systolic murmur 3–4/6. After ERT: decreased illness (obstructive bronchitis), decreased excretion of GAGs in the urine, decreased organomegaly, increased mobility

CaseNotHPOs:

CaseNotHPOFreeText:

CasePreviousTesting: n/a

GenotypingMethod: Direct sequencing of PCR products

PreviouslyPublished: n/a

Variant: p.Q70X (pathogenic); p.R628X. Compound heterozygosity was confirmed by analysis of parental samples. Also has p.A8, p.A20, p.Q33H, p.L118

ClinVar: 550421

CAID: CA2802462

gnomAD: The highest population minor allele frequency in gnomAD v4.1.0. is 0.00005038 (2/39700 alleles) in the East Asian population, which is lower than the ClinGen Lysosomal Diseases VCEP’s threshold for PM2_Supporting (<0.00025), meeting this criterion (PM2_Supporting).

SupplementalData: n/a

NonHumanModel: Zhang_Mouse

GeneAlteration: Exon 2 of RAB39B was targeted using two gRNAs and Cas9 mRNA in the C57BL/6N background. Mice harboring 397-bp deletions in exon 2 were obtained.

ModelPhenotype: HP:0000256 Social and memory deficits

HumanPhenotype: HP:0001249, HP:0000256

ModelEvidence: Similar to PMID: 33364235, authors show through ASD-related tests that KO mice exhibit social and memory deficits. They also show that RAB39B variation results in over-proliferation and differentiation deficits of neural progenitor cells, which results in larger that normal number of neurons. Mice therefore have macrocephaly.

ModelVariant:

WhereInPaper:

The model is scored reduced points as the mice recapitulate the ASD phenotype seen in some human patients with RAB39B variants, but does not provide evidence for the Parkinson disease phenotype. (0.5)

PMID 22079513

Disease Idiopathic pulmonary fibrosis

Case# Subject 2, male, 8mo report, Hispanic

CasePresentingHPOs HP:0001276, HP:0000341, HP:0000294, HP:0000316, HP:0000286, HP:0000494, HP:0000664, HP:0008589, HP:0005989, HP:0001257 (Hypertonia, Narrow forehead, Low anterior hairline, Hypertelorism, Downslanted palpebral fissures, Epicanthus, Synophrys, Hypoplastic helices, Redundant neck skin, Spasticity)

HPOFreeText: Hypertonic(postnatal), bifrontal narrowing, low anterior hairline, mild hypertelorism, bilateral epicanthal folds, downslanted palpebral fissures, synophrys, mild hypoplastic helices, redundant nuchal skin, and spasticity of all four extremities with upper limbs being more affected than lower limbs (8 months old)

CaseNotHPOs HP:0002194, HP:0001252, HP:0012443, HP:0012372, HP:0000453, HP:0001627, HP:0000077, HP:0002650 (Gross motor delay, Hypotonia, Abnormality of the brain, Abnormal eye morphology, Choanal atresia, Congenital heart defects, Renal anomaly, Scoliosis)

CasePreviousTesting Screen for BRAF, CBL, HRAS, KRAS, MAP2K1, NRAS, PTPN11, RAF1, SCHOC2, and SOS1 was normal.

CaseMethod1 WES

CaseMethod2 Sanger

CaseGenotypingMethod WES confirmed with sanger in patient and parents

Variant NM_012102.3:c.248dup (p.Ser84ValfsTer4), de novo

ClinVar n/a

CAID CA658820860

gnomAD n/a

VariantEvidence n/a

CaseAddInfo n/a

CasePMIDs n/a

Family#PresentingHPOs HP:0001263, HP:0010864, HP:0002370, HP:0000664, HP:0000675, HP:0000545, HP:0001763, HP:0008763, HP:0000430, HP:0012471, HP:0000331, HP:0000303, HP:0000662, HP:0000529, HP:0011228

Absent or single-word speech, box-shaped face

FamilyNotHPOs

CountryOrigin Pakistani

Ethnicity

Race

Family#PreviousTesting None

Family#Method1

Family#Method2

Family#GenotypingMethod DNA samples from three affected (V-2, VI-2, VI-3) and two unaffected individuals (V-3, V-4), were genotyped using the Affymetrix Genome-Wide Human SNP 6.0 microarray.

homozygosity-by-descent (HBD) or autozygosity mapping and copy number variation (CNV) analysis was performed using dChip software.

direct Sanger sequencing of VPS13B was performed, based on homozygosity mapping results, for all 62 exons and splice junctions of VPS13B.

Potential candidate variants were further validated in Pakistani population controls through Sanger sequencing.

Affected 2

Unaffected 0

Segregations 1

PublishedLOD No

eLOD 0.6

AddSegregationInfo Pedigree in Figure 1. 5 affected and 3 unaffected individuals clinically determined.

ProbandLabel RQMR10_V-2

Variant NM_017890.4:c.6879delT(p.Phe2293Leufs*24)

ClinVar

CAID CA4824093

gnomAD 0.00003250 (South Asian)

FamilyAddInfo Complete biochemical testing in affected and unaffected. neurological, psychological, ophthalmological, skeletal, behavioral, dental examinations in affecteds. RQMR10_VI-2 underwent fundoscopic examination.

Case# Tun66275, Female, 20, Tunisia

CasePresentingHPOs HP:0002066, HP:0001260, HP:0001257

CaseNotHPOs HP:0001272

CaseMethod1 Exome

CaseMethod2 Sanger

Variant NM_005186.3:c.1534C>T(p.R512C)

CAID CA6093457

gnomAD 0.000008977

VariantEvidence none

CaseAddInfo in supplement

PatientID: IV-13

KindredID: 2

Case: F, Age Unknown, German

DiseaseAssertion: VHL (Asymptomatic)

FamilyInfo: Family 2 is comprised of 131 individuals over six generations including 65 members (50% of those at risk) with VHL type 2A (72% clinically affected, 12% obligate carriers, and 15% positive genetic analysis alone) and nearly equal gender distribution for affected status (54% male). An additional six members (II-3, II-4, II -5, III-1, III-2, and III-3) are suspected to have VHL without confirmation. Of note, the nuclear family (branch IV-13) contains 13 siblings, of whom 12 have been diagnosed with pheo. The presenting tumor types in Family 2 were pheo (70%), HB (17%), and RA (13%). No Family 2 member had RCC as the initial manifestation. Distribution of HB and RA are not described except for patient IV-8.

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: HP:0005584; HP:0002666 (Renal cell carcinoma, Pheochromocytoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 7759077

SupplementalData: N/A

Variant: p.Y98H (c.292T>C)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 2223, https://www.ncbi.nlm.nih.gov/clinvar/variation/2223/

CAID: N/A

gnomAD: 0.00001343, https://gnomad.broadinstitute.org/variant/3-10183823-T-C

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: Y98H (c.292T>C)

MultipleGeneVariants: N/A

PatientID: V-12

KindredID: 2

Case: M, Age Unknown, German

DiseaseAssertion: VHL (Asymptomatic)

FamilyInfo: Family 2 is comprised of 131 individuals over six generations including 65 members (50% of those at risk) with VHL type 2A (72% clinically affected, 12% obligate carriers, and 15% positive genetic analysis alone) and nearly equal gender distribution for affected status (54% male). An additional six members (II-3, II-4, II -5, III-1, III-2, and III-3) are suspected to have VHL without confirmation. Of note, the nuclear family (branch IV-13) contains 13 siblings, of whom 12 have been diagnosed with pheo. The presenting tumor types in Family 2 were pheo (70%), HB (17%), and RA (13%). No Family 2 member had RCC as the initial manifestation. Distribution of HB and RA are not described except for patient IV-8.

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: HP:0005584; HP:0002666 (Renal cell carcinoma, Pheochromocytoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 7759077

SupplementalData: N/A

Variant: p.Y98H (c.292T>C)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 2223, https://www.ncbi.nlm.nih.gov/clinvar/variation/2223/

CAID: N/A

gnomAD: 0.00001343, https://gnomad.broadinstitute.org/variant/3-10183823-T-C

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: Y98H (c.292T>C)

MultipleGeneVariants: N/A

PatientID: 25

KindredID: 6012

Case: F, 50Y0M, Ethnicity Unknown

DiseaseAssertion: VHL

FamilyInfo: Another member of her family, (patient 26) presented with one radiologic pancreatic neuroendocrine tumor and had the same VHL gene mutation.

CasePresentingHPOs: HP:0030405 (pancreatic endocrine tumour)

CaseHPOFreeText: She presented with two radiologic pancreatic endocrine tumour.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.A149S (c.445G>T)

LegacyVariant: p.A149S (c.658G>T)

CaseProblemVariantFreeText: N/A

ClinVar:127829 https://www.ncbi.nlm.nih.gov/clinvar/variation/127829/

CAID: CA020355 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.445G%3ET

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: A149S (c.445G>T)

MultipleGeneVariants: N/A

PMID: 33397040

Gene: VHL

StandardizedReferenceSequence: NM_000551.3

PatientID: HGB-19

KindredID: 4

Case: Sex Unknown, 44Y0M, Italian

DiseaseAssertion: VHL

FamilyInfo: None.

CohortInfo: The patient cohort consisted of 57 patients (26 male and 31 female) from Southern Italy, most of whom (55 of 57) presented with solitary HGB of the CNS: 6 were syndromic and 51 were apparently sporadic.

CasePresentingHPOs: HP:0006880, HP:0009713 (cerebellar hemangioblastoma, spinal hemangioblastoma)

CaseHPOFreeText: The patient had a single cerebellar hemangioblastoma that was diagnosed at age 32. The patient had a spinal cord hemangioblastoma at age 40.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.G114V(c.341G>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA351753604 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.341G%3ET

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: G114V (c.341G>T)

MultipleGeneVariants: N/A

PatientID: None

KindredID: 7

Case: F, 13Y0M, Ethnicity unknown

DiseaseAssertion: pheochromocytoma

FamilyInfo: No familial/syndromic (FS) association

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: Benign bilateral pheochromocytoma at age 13 Y

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: SDHB,SDHC, SDHD, and exons 10, 11, 13, 14, 15 and 16 of RET proto-oncogene

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.R167Q (c.500G>A)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVar: 2216 https://www.ncbi.nlm.nih.gov/clinvar/variation/2216/

CAID: N/A

gnomAD: 0.000003977 https://gnomad.broadinstitute.org/variant/3-10191507-G-A

VariantEvidence:N/A

MutationType: missense_variant;transition

CivicName: R167Q (c.500G>A)

MultipleGeneVariants: N/A

PatientID: None

KindredID: 6

Case: F, 18Y0M, Ethnicity unknown

DiseaseAssertion: assumed VHL

FamilyInfo: Familial/syndromic (FS) association

CasePresentingHPOs: HP:0002666; HP:0002668; HP:0010797; HP:0030405 (Pheochromocytoma; paraganglioma; hemangioblastoma; pancreatic endocrine tumor)

CaseHPOFreeText: Benign bilateral pheochromocytoma and sympathetic PGL, CNS hemangioblastoma and PNET at age 18

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: SDHB,SDHC, SDHD, and exons 10, 11, 13, 14, 15 and 16 of RET proto-oncogene

PreviouslyPublished: N/A

SupplementalData: N/A

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

CaseProblemVariantFreeText: N/A

LegacyVariant: N/A

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

CAID: N/A

gnomAD: 0.000007954 https://gnomad.broadinstitute.org/variant/3-10191506-C-T

VariantEvidence: N/A

MutationType: missense_variant; transition

CivicName: R167W (c.499C>T)

MultipleGeneVariants: N/A