Case:Female, 35.

DiseaseAssertion:Hypertrophic cardiomyopathy (HCM) with left ventricular noncompaction (LVNC) and conduction abnormalities.

Familyinfo:The patient's father had hypertrophic cardiomyopathy and carried a heterozygous MYBPC3 p.(Pro1066Arg) variant. The patient's mother was also heterozygous for the MYBPC3 variant. The patient had one sister who did not have reported cardiac abnormalities and was heterozygous for the MYBPC3 variant. The family was initially considered non-consanguineous. Genetic analysis identified a 26 Mb region of homozygosity, suggesting distant parental relatedness.

ParentalTesting:Both parents were tested. The father and mother were heterozygous for MYBPC3 c.3197C>G (p.Pro1066Arg). The affected daughter inherited the variant from both parents and was homozygous.

CasePresentingHPOs:HP:0031992, HP:0001685, HP:0005157, HP:0031295, HP:0001667, HP:0001670, HP:0001712, HP:0005144, HP: 0031195, HP:0030682, HP:0005135, HP: 0006682, HP: 0004763

CaseHPOFreeText:The patient developed severe cardiac manifestations associated with homozygous MYBPC3 p.(Pro1066Arg). Cardiac MRI showed ventricular hypertrophy, myocardial fibrosis, and features of left ventricular noncompaction. At follow-up, imaging showed asymmetric ventricular wall thickness, with a maximum diastolic thickness of 20 mm in the mid-lateral segment. She also had apical hypokinesia and left atrial enlargement. Electrocardiography and Holter monitoring showed premature ventricular complexes and a 20-beat episode of nonsustained ventricular tachycardia.

CaseNotHPOs:No specific negative HPO findings were established for the affected daughter in the reported HPO table.

CaseNOTHPOFreeText:not reported

CasePreviousTesting:Cardiac MRI, echocardiography, electrocardiography, and 24-hour Holter monitoring were performed. Genetic evaluation was also conducted to identify the MYBPC3 and MYH7 variants.

GenotypingMethod:Whole-exome sequencing (WES) trio analysis was performed using DNA from the affected daughter and both parents. Family segregation analysis was performed by Sanger sequencing using an Applied Biosystems 3130 sequencer.

FunctionalAnalysis:No direct functional analysis of the MYBPC3 variant was reported.

Variant:NM_000256.3 (MYBPC3): c.3197C>G; p.(Pro1066Arg).

ClinVar: 1171602

CAID:not reported

gnomAD:not reported

AdditionalInfo:The patient was homozygous for the MYBPC3 p.(Pro1066Arg) variant. Both parents carried the variant in the heterozygous state. A 26 Mb region of homozygosity was identified on chromosome 11, supporting the possibility of distant parental relatedness. The variant was initially classified as a variant of uncertain significance and was subsequently reclassified as likely pathogenic following family segregation analysis.

Case#: a 2‐year‐old white girl who was found to have RCM following an evaluation precipitated by the sudden death of her older brother.

DiseaseAssertion: Restrictive cardiomyopathy

FamilyInfo: 4‐year‐old brother presented with a sudden cardiac arrest while running on a soccer field and could not be resuscitated. Her father had restrictive physiology and arrhythmias. The TNNT2 variant was found in the father and two children

ParentalTesting: Father carried the variant. For both paternal grandparents tested negative and the proband inherited the variant from her father.

CasePresentingHPOs: HP:0001723, HP:0001639, HP:0031295, HP:0030718, HP:0001695

CaseHPOFreeText: "Her ECG demonstrated criteria for right and left atrial enlargement with marked repolarization abnormality. Echocardiogram revealed mild right atrial and severe left atrial enlargement (left atrial volume, 61.5 cc/m2; normal, 16–28), with mildly increased left ventricular mass and otherwise normal ventricular dimensions. Right and left ventricular systolic function was preserved. "

CaseNotHPOs: not reported

CaseNotHPOFreeText: Ventricular dimensions and biventricular systolic function were reported as normal.

CasePreviousTesting: Cardiomyopathy‐based panel testing (Familion; Transgenomic, Inc., New Haven, CT) was conducted on the proband, demonstrating a single, heterozygous, variant TNNT2‐R94C (c.280C>T).

Genotyping Method: Clinical genetic testing was performed on family members using the same HCM panel test.

FunctionalAnalysis: Biophysical experiments using recombinant human TNNT2‐R94C demonstrated impaired cardiac regulation at the molecular level attributed to reduced calcium‐dependent blocking of myosin's interaction with the thin filament.

Variant: c.835C>T, p.Gln279Ter

ClinVar: 165549

CAID: CA004288

gnomAD: not reported

AdditionalInfo: not reported

PMID: 32098556

Gene: TNNT2

HGNC ID: 11949

Case1: 11 year old female

DiseaseAssertion: hypertrophic cardiomyopathy, restrictive cardiomyopathy

FamilyInfo: twin sister carrier identical mutation, both sisters expired, no family history of cardiomyopathy

ParentalTesting: sanger sequencing

CasePresentingHPOs:HP:0001629, HP:0001640, HP:0034314,HP:0002098, HP:0001723

CaseHPOFreeText:bilateral atrial dilation with mid ventricular hypertrophy, accelerated cardiac sound, liver palpable 2cm below costal margin, cold extremities, cardiac condition was New York Heart Association class (NYHA) III.

CaseNotHPOs: NR

CaseNotHPOFreeText: no gallop rhythm, no murmur, no blood test abnormalities, no metabolic disorders

CasePreviousTesting: cardiac catheterization, cardiac magnetic resonance, echocardiography, Chest Xray, electrocardiography,

Genotyping Method: sanger sequencing

FunctionalAnalysis: NR

Variant: TNNI3 c.574 C>T p.Arg192Cys

ClinVar: 165510

CAID: CA021951

gnomAD:NR

Case 2: 15 year old female

DiseaseAssertion: restrictive cardiomyopathy, hypertrophic cardiomyopathy

FamilyInfo: twin sister carrier identical mutation, both sisters expired, no family history of cardiomyopathy

ParentalTesting: Sanger Sequencing

CasePresentingHPOs:HP:0002875, HP:0001723

CaseHPOFreeText: Abnormal ECG, LV hypertrophy, enlargement of both atria, high LVEF levels, accelerated cardiac sound, liver was palpable 3 cm, extremities were warm, and cardiac condition was NYHA II.

CaseNotHPOs:NR

CaseNotHPOFreeText: no gallop rhythm, no murmur, no blood test abnormalities, no metabolic disorders

CasePreviousTesting: cardiac catheterization, cardiac auscultation, myocardial disarray with myocyte hypertrophy

Genotyping Method: Sanger sequencing

FunctionalAnalysis: NR

Variant: TNNI3 c.574 C>T p.Arg192Cys

ClinVar: 165510

CAID: CA021951

gnomAD:NR

PMID: 37108997

Gene: TNNT2

HGNC ID: 11949

Case#: Male half-brother with mild left ventricular dilation from early childhood and mild left ventricular impairment; latest reported ejection fraction was 51%.

DiseaseAssertion: DCM

FamilyInfo: several of the siblings DCM, two died at age of 12, father had DCM, and heart transplant for an individual who later died

ParentalTesting: father was an obligate carrier

CasePresentingHPOs: HP:0001644

CaseHPOFreeText: Mild left ventricular dilation and mildly increased LV volumes

CaseNotHPOs: not reported

CaseNotHPOFreeText: not reported

CasePreviousTesting: panel-based genetic test was conducted in the index patient.

Genotyping Method: panel-based genetic test was conducted in the index patient. sanger confirmation

FunctionalAnalysis: not reported

Variant: c.659_661del p.(Lys220del)

ClinVar: 43659

CAID: CA006429

gnomAD: not reported

AdditionalInfo: not reported

Case#: A 2-year-old girl with dilated cardiomyopathy (DCM) and left ventricular noncompaction, who received a heart transplant at 26 months.

DiseaseAssertion: DCM with left ventricular noncompaction

FamilyInfo: Family history revealed that three of the father’s (A.II.2) sisters (A.II.4-A.II.6) died in infancy due to cardiac failure.

ParentalTesting: The father and paternal grandmother tested positive for the same TNNT2 variant

CasePresentingHPOs: HP:0001644, HP:0030682, HP:0001635

CaseHPOFreeText: The heart failure signs began at 2 months and got worse. Then got a heart transplant at 26 months.

CaseNotHPOs: not reported

CaseNotHPOFreeText: nothing found

CasePreviousTesting: a genetic panel test, including the genes LDB3, LMNA, MYH7, MYBPC3, and TNNT2, was performed.

Genotyping Method: Variants were confirmed in first-degree family members by Sanger sequencing.

FunctionalAnalysis: not reported

Variant: c.316G>A (p.Glu106Lys)

ClinVar: 224775

CAID: CA088557

gnomAD: not reported

AdditionalInfo: not reported

PMID: 39759977 Gene: ACTC1 HGNC ID: 143

PMID: 34066613

GENE: TNNT2

HGNC ID: 11949

Case#: 19-year-old boy with coarctation of the aorta who complained of mild exertional dyspnea.

DiseaseAssertion: dilated cardiomyopathy (DCMP). LV systolic dysfunction.

FamilyInfo: The family history was positive to sudden death (his cousin died, aged 3 months) and to DCMP and heart transplant (HT): a maternal aunt and her son who then died at 42 and 24 years old. Cascade family screening revealed a TNNT2 variant in the mother (II.1) and his cousin (IV.3).

ParentalTesting: The 19 year old brother's was tested and carried the TNNT2 variant. She was also affected by DCM. The father’s testing status was not reported.

CasePresentingHPOs: HP:0001680, HP:0002875, HP:0025169, HP:4000141

CaseHPOFreeText: surgically repaired coarctation of the aorta who complained of mild exertional dyspnea repaired at birth (NYHA class II–III). Cardiac MRI showed a moderately dilated, hypokinetic LV with an ejection fraction of 45%; echocardiography showed an ejection fraction around 42%.

CaseNotHPOs: not reported

CaseNotHPOFreeText: Nothing was found that was correlated.

CasePreviousTesting: genetic investigations through next generation sequencing (NGS) with a panel of 325 genes, known to be associated with cardiomyopathies

Genotyping Method: targeted next generation sequencing

FunctionalAnalysis: not reported

Variant: c.518G>A (p. Arg173Gln)

ClinVar: 43649

CAID: CA004727

gnomAD: not reported

AdditionalInfo: not reported

PMID: 21483645

Gene: TNNT2

HGNC ID: 11949

Case#: Female, 6, non-Hispanic white

DiseaseAssertion: Dilated Cardiomyopathy

FamilyInfo: Father and Paternal uncle diagnosed with DCM at age 34.

ParentalTesting: Her father underwent cardiac screening based on family history several years later at age 34

CasePresentingHPOs: HP:0001640

CaseHPOFreeText: NA

CaseNotHPOs: NA

CaseNotHPOFreeText: Acute viral illness and gastroenteritis

CasePreviousTesting: NR

Genotyping Method: Sanger Sequencing

FunctionalAnalysis: NR

Variant: NM_001276345.2:c.149A>G

ClinVar: 2005620

CAID: CA344207232

gnomAD: 1:201337304 T / C

AdditionalInfo: NA

PMID: 19293840

Gene: TNNT2

HGNC ID: 11949

Case#: Male, 65

DiseaseAssertion: Idiopathic dilated cardiomyopathy

FamilyInfo:None of his five siblings were affected

ParentalTesting: NR

CasePresentingHPOs: HP:0005110

CaseHPOFreeText: Slow progression to severe heart failure

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

CasePreviousTesting: NR

Genotyping Method: Bidirectional dna sequencing

FunctionalAnalysis: NR

Variant: NM_001276345.2:c.869A>G

ClinVar: 4881578

CAID: CA344201883

gnomAD: NA

AdditionalInfo: HTX. The index patient carried a known TNNT2 K247R mutation as well as two novel intronic variants in MYH7 (IVS39+7C>A) and MYBPC3 (IVS25+13T>A).

Case:Female, born at 34 weeks of gestation, 5 years old at the first detailed examination, 8 years old during a later clinical description.

DiseaseAssertion:Arthrogryposis multiplex congenita (AMC). Cardiomyopathy not reported.

Familyinfo:The patient was the first child of unrelated parents. Her mother and one maternal aunt were born with bilateral clubfeet and later developed scoliosis. The mother also had a history of cleft palate. Neither the mother nor the patient had a reported history of cardiac problems.

ParentalTesting:The patient's mother carried the same heterozygous ACTC1 c.325G>A (p.Glu109Lys) variant. The variant was therefore inherited from the mother.

CasePresentingHPOs:Bilateral clubfeet, scoliosis, cleft palate, neck webbing, camptodactyly, joint contractures.

CaseHPOFreeText:The patient was born by cesarean section at 34 weeks of gestation. Bilateral clubfeet, cleft palate, neck webbing, and spinal deformity were noted. At age 5, she had severe scoliosis measuring 120 degrees and severe short stature. At age 8, mild camptodactyly of both hands and mild contractures of the neck, left hip, both knees, and feet were observed. She had no significant mobility or cognitive difficulties and was independent in self-care activities.

CaseNotHPOs:No reported cardiac problems, no significant cognitive difficulties, no significant mobility difficulties.

CaseNOTHPOFreeText:The patient had no reported cardiac phenotype despite carrying an ACTC1 variant. Her mother also had no history of cardiac problems.

CasePreviousTesting:Genome sequencing was performed to identify genetic variants associated with the patient's clinical presentation.

GenotypingMethod:Genome sequencing. Plasmid sequencing was also verified by Sanger sequencing for the experimental functional studies.

FunctionalAnalysis:In vitro functional studies were performed using MC3T3-E1 preosteoblastic cells. The p.Glu109Lys variant caused decreased ACTC1 protein levels and impaired actin filament assembly. Immunofluorescence and Western blotting were used to evaluate protein expression and actin filament organization.

Variant:NM_005159.5 (ACTC1): c.325G>A; p.Glu109Lys.

ClinVar:not reported

CAID:not reported

gnomAD:not found

AdditionalInfo:The variant was inherited from the patient's mother, who also had bilateral clubfeet, scoliosis, and a history of cleft palate. The authors classified the variant as likely pathogenic using ACMG criteria (PM1, PM2, PP1, PP2, PP3). The functional studies demonstrated reduced ACTC1 protein levels and impaired actin filament assembly.

PMID: 20458009

Gene: TNNT2

HGNC ID: 11949

Case#: Female, 20, non-Hispanic white

DiseaseAssertion: Peripartum cardiomyopathy

FamilyInfo: NR

ParentalTesting: NR

CasePresentingHPOs: HP:0034807, HP:0001640

CaseHPOFreeText: NA

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: NR

Genotyping Method: Sanger sequencing

FunctionalAnalysis: demonstrated decreased calcium sensitivity, which indicated that this mutation was likely to be disease causing

Variant: NM_001276345.2:c.505C>G

ClinVar: 2953222

CAID: CA344204620

gnomAD: NR

AdditionalInfo: PPCM was diagnosed one week postpartum.

Case#: Male, 47

DiseaseAssertion: hypertrophic cardiomyopathy

FamilyInfo:

ParentalTesting:

CasePresentingHPOs: HP:0025169, HP:0034307, HP:0001712,

CaseHPOFreeText: Severe alterations in inter ventricular septum thickness and left ventricular posterior wall thickness

CaseNotHPOs: NR

CaseNotHPOFreeText: NR

CasePreviousTesting: NR

Genotyping Method: Sanger sequencing

FunctionalAnalysis: NA

Variant: NM_001276345.2:c.423G>A

ClinVar: NR

CAID: CA422532259

gnomAD: NR

AdditionalInfo: IVST, average of 19.2 mm and LVPWT; average of 11.5 mm

PMID: 40421724 Gene: ACTC1 HGNC ID: 143

Case#:7-year-old boy

DiseaseAssertion: restrictive cardiomyopathy

FamilyInfo: his parents were in generally good health and other family members denied a history of syncope, sudden death or cardiomyopathy

ParentalTesting: sanger sequencing

CasePresentingHPOs:HP:0007185, HP:0001695, HP:0005943, HP:0002516, HP:0001663

CaseHPOFreeText:electrocardiogram (ECG) revealed Ptf-V 1 < –0.04 mm⋅s and biphasic P waves, indicating left atrial enlargement and the chest X-ray revealed an enlarged heart shadow. The echocardiogram showed biatrial enlargement, especially in the left atrium (LA: 32 mm, RA: 30 mm), decreased diastolic function (E/A = 2.6; E Peak deceleration time 130 ms; Constant volume diastolic time 49 ms), moderate mitral valve regurgitation and left ventricular ejection fraction of 51.8%.

CaseNotHPOs:HP:0000969

CaseNotHPOFreeText:Except for bilateral enlargement, cardiac magnetic resonance (CMR) indicated no abnormalities

CasePreviousTesting: brain MRI, video electrocephalogram, electrocardiogram

Genotyping Method: sanger sequencing

FunctionalAnalysis:

Variant: TNNI3 c.611(exon8)G>A,p.R204H

ClinVar:177679

CAID:CA022060

gnomAD:chr19-55151856-C-T

PMID: 37626566

Gene: TNNT2

HGNC ID: 11949

Case#: a 20-year-old, female, adopted Indian patient with over 662 Mb regions of homozy-gosity who presented with intellectual disability, ataxia, schizophrenia, retinal dystrophy, moder-ate-to-severe progressive sensorineural hearing loss (SNHL), congenital hypothyroidism, cleft mi-tral valve with mild mitral valve regurgitation, and dysmorphic features.

DiseaseAssertion: a cleft mitral valve with mild regurgitation

FamilyInfo: adopted

ParentalTesting: not reported

CasePresentingHPOs: HP:0001249, HP:0001251, HP:0100753, HP:0000556, HP:0000407, HP:0000851, HP:0001633, HP:0001653

CaseHPOFreeText: cleft mitral valve and dysmorphic features

CaseNotHPOs: HP:0001638

CaseNotHPOFreeText: echocardiograms at 18 were normal

CasePreviousTesting: genetic testing, including targeted panel analysis, exome sequencing on a clinical basis, and a research-based review of her raw clinical exome data, led to identifying at least three causal gene disorders to explain distinct aspects of her complex phenotype.

Genotyping Method: Genome-wide single-nucleotide polymorphism (SNP) microarray analysis was clinically performed, with no pathogenic deletions or duplications detected.

FunctionalAnalysis: not reported

Variant: NM_001001430.2:c.68-1592

ClinVar: not reported

CAID: CA032911

gnomAD: total allele frequency: 0.00004522

AdditionalInfo: n/r

Case#: A 50-year-old man diagnosed with HCM at age 41, with asymmetric septal hypertrophy and exertional chest discomfort and pain

DiseaseAssertion: Hypertrophic cardiomyopathy

FamilyInfo: His third elder sister, niece and daughter were also clinically affected by HCM. The proband's mother and eldest sister had suffered from sudden cardiac death. The proband's father, second elder sister (HCM1 in Fig. 1A), nephew (HCM5 in Fig. 1A) and son (HCM7 in Fig. 1A) were 87, 65, 35, and 14 years old, respectively, and had normal echocardiographic measurements.

ParentalTesting: The mother had died suddenly; the 87-year-old father had normal echocardiographic measurements. There was no testing reported.

CasePresentingHPOs: HP:0001639, HP:0005144, HP:0100749, HP:0011712

CaseHPOFreeText: chest distress and chest pain during exercise for 9 years. He presented with an asymmetric hypertrophic interventricular septum and a maximum interventricular septum thickness of 18.04 mm

CaseNotHPOs: not reported

CaseNotHPOFreeText: no findings found in the proband

CasePreviousTesting: nothing reported in the article

Genotyping Method: hole exome sequencing (WES) Exons were captured using Sure Select Human All Exon V5 kit. Sequenced by Illumina HiSeq 4000 sequencer.

FunctionalAnalysis: not reported

Variant: rs796925245 (g.1:201359630G>A, c.835C>T, p.Gln279Ter) (c.835C>T, p.Gln279Ter)

ClinVar: 1175037

CAID: CA088451

gnomAD: not reported

AdditionalInfo: n/r

PMID: 32846832

Gene: TNNT2

HGNC ID: 11949

PMID: 35728000

Gene: TNNT2

HGNC ID: 11949

Case#: 15

DiseaseAssertion: Dilated cardiomyopathy

FamilyInfo: NR

ParentalTesting: NR

CasePresentingHPOs: NA

CaseHPOFreeText: decreased cardiac contractility

CaseNotHPOs: NA

CaseNotHPOFreeText: NA

CasePreviousTesting: NR

Genotyping Method: Sanger sequencing

FunctionalAnalysis: NR

Variant: NM_001276345.2:c.577C>T

ClinVar: 834548

CAID: CA088264

gnomAD: NR

AdditionalInfo: NA

Case1: 2-year-old female

DiseaseAssertion: restrictive cardiomyopathy, dilated cardiomyopathy

FamilyInfo:The maternal family history was negative for any form of cardiomyopathy or sudden death. Paternal family history was unknown, the mother (1-II:2) and maternal half-brother (1-III:2) were both heterozygous for the TNNI3 p.Arg136∗ variant, mother (1-II:2, age 20) and half-brother (1-III:2, age 21 months) demonstrated normal heart function on echocardiography. ParentalTesting: Clinical exome sequencing done on mother of proband

CasePresentingHPOs: HP:0032025, HP:0002140, HP:0005180, HP:0001653, HP:0005117

CaseHPOFreeText: left-sided facial and extremity weakness, enlarged cardiac silhouette with interstitial opacities, dilated left and right atria, unusual morphology of the chordae tendineae of both atrioventricular valves was noted, leading to a tethering phenomenon

CaseNotHPOs: HP:0001712,

CaseNotHPOFreeText: normal systolic function

CasePreviousTesting: Chest Xray, Echocardiogram, Head CT

Genotyping Method: clinical exome sequencing

FunctionalAnalysis: Immunostaining on heart tissue from patient, Quantitative analysis of heart tissue, Transmission electron microscopy with immersion fixed heart samples

Variant:homozygous TNNI3 nonsense variant, c.406C>T (p.Arg136∗)

ClinVar:488853

CAID:CA407440677

gnomAD:chr19-55154173-G-A v4

PMID: 35717150 Gene: MYBPC3 HGNC ID: 7551

PMID: 21135372

Gene: TNNT2

HGNC ID: 11949

Case:Female, 21.

DiseaseAssertion:Left ventricular noncompaction cardiomyopathy (LVNC).

Familyinfo:The patient's father had hypertrophic cardiomyopathy. Her paternal grandfather and paternal uncle also reportedly had cardiac disease, although detailed clinical information was unavailable. The patient's mother had microscopic hematuria and was diagnosed with thin basement membrane nephropathy. The maternal grandmother also had a history of kidney disease.

ParentalTesting:The mother was tested and did not carry the ACTC1 c.922T>C variant. The father could not be tested because the patient had no contact with him. The authors presumed paternal inheritance of the ACTC1 variant based on the family history, but paternal inheritance was not genetically confirmed.

CasePresentingHPOs:Left ventricular noncompaction cardiomyopathy, Abnormal cardiac morphology, Cardiac hypertrophy, Hematuria

CaseHPOFreeText:The patient had microscopic hematuria beginning at age 6. At the same age, routine school screening identified cardiac dysfunction, and echocardiography revealed a myocardial densification defect. At age 21, echocardiography showed a noncompacted-to-compacted myocardial ratio greater than 2:1, consistent with LVNC. Electrocardiography showed sinus rhythm with ST-T wave flattening in leads V4–V6, indicative of cardiac hypertrophy. The patient remained without cardiac symptoms and had a normal ejection fraction. Her BNP level increased to 204 pg/mL. She had normal renal function, with a serum creatinine level of 0.58 mg/dL, and no proteinuria.

CaseNotHPOs:Hearing impairment: not reported, Ophthalmological abnormalities: not reported, Cardiac symptoms: not reported

CaseNOTHPOFreeText:The patient remained asymptomatic despite the cardiac findings. No hearing impairment or ophthalmological abnormalities were identified.

CasePreviousTesting:Echocardiography identified LVNC during childhood. Further cardiac evaluation included electrocardiography and follow-up BNP measurements. Renal evaluation included serum creatinine testing, urinalysis, abdominal ultrasonography, and genetic evaluation for hereditary kidney disease.

GenotypingMethod:Whole exome sequencing was performed using DNA extracted from the patient's blood sample. Sanger sequencing was used to confirm both identified variants. The mother's DNA was also analyzed to determine inheritance.

FunctionalAnalysis:No direct functional studies were performed on the ACTC1 variant. The authors used AlphaFold3 protein structure prediction to examine the effect of the amino acid substitution. The variant was located near the ATP-binding site, suggesting a possible effect on ACTC1 function and ATP binding.

Variant:NM_005159.5 (ACTC1): c.922T>C; p.(Tyr308His).

ClinVar:accession: VCV000948806.7.

CAID:not reported

gnomAD:not reported

AdditionalInfo:The patient carried two separate heterozygous variants associated with different conditions. The COL4A4 c.2510G>C (p.Gly837Ala) variant was associated with autosomal dominant Alport syndrome, while the ACTC1 c.922T>C (p.Tyr308His) variant was identified as a candidate associated with LVNC. The ACTC1 variant was classified as a variant of uncertain significance (VUS) by the authors using ACMG criteria (PM2, PP3, PP4). The authors noted that there were no functional studies confirming its effect on ACTC1 protein function.

PatientID: IV-1

KindredID: 1

Case: M, Age Unknown, Ethnicity Unknown

DiseaseAssertion: Assumed VHL

FamilyInfo: 38 family members had been affected at the date of 1986, and 10 had passed away. Pheochromocytoma, cerebellar, spinal and retinal hemangioblastomas, and various cysts were clinical manifestations of VHL seen throughout the family. This patient (IV-1) appears to have inherited this disease from his father, along with many of his siblings. See Fig. 1 for family pedigree.

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: This member had pheochromocytoma which was not further described.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

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

LegacyVariant: N/A

CaseProblemVariantFreeText: Although never given at the time of this publication, the germline mutation is confirmed in this family in later publications (PMID 7987306; 29437867) for this specific family. It is only here assumed this member had the VHL mutation.

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?dataset=gnomad_r2_1

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: R167W (c.499C>T)

MultipleGeneVariants: N/A

PatientID: IV-27

KindredID: 1

Case: F, Age Unknown, Ethnicity Unknown

DiseaseAssertion: Assumed VHL

FamilyInfo: 38 family members had been affected at the date of 1986, and 10 had passed away. Pheochromocytoma, cerebellar, spinal and retinal hemangioblastomas, and various cysts were clinical manifestations of VHL seen throughout the family. This patient (IV-27) appears to have inherited this disease from her father. See Fig. 1 for family pedigree.

CasePresentingHPOs: HP:0006880 (cerebellar hemangioblastoma)

CaseHPOFreeText: This member was examined in St. Johns at the Memorial University of Newfoundland. She had cerebellar hemangioblastoma which were not further described. She also presented with Vitamin-D-Resistant rickets, likely inherited from her father, and non-VHL affected grandmother.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

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

LegacyVariant: N/A

CaseProblemVariantFreeText: Although never given at the time of this publication, the germline mutation is confirmed in this family in later publications (PMID 7987306; 29437867) for this specific family. It is only here assumed this member had the VHL mutation.

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?dataset=gnomad_r2_1

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: R167W (c.499C>T)

MultipleGeneVariants: N/A

A previous study of 26 Japanese, VHL families was extended to 41 additional families. Germline mutations were detected in 55 of 77 Japanese families using SSCP, direct sequencing, and Southern Blot analysis of peripheral blood samples. The Q73Rfs*86 (c.217del) germline mutation was found in a VHL type 1 patient with hemangioblastomas of the central nervous system and retinal angiomas (family ID 98). The variant was reported as c.428del and mapped to c.215del which is equivalent to c.217del.

PatientID: N/A (younger son of index case)

KindredID: 1

Case: M, 13Y0M, Ethnicity Unknown

DiseaseAssertion: VHL

FamilyInfo: The patient's mother was the index case in this VHL family, as she was diagnosed with bilateral pheochromocytoma at age 23 and underwent bilateral adrenalectomy. Genetic screening of the mother revealed the VHL variant, which prompted screening of family members. DNA sequencing from blood of consenting family members confirmed the presence of the VHL variant in seven family members (three generations from the maternal side) (see figure 1 for familial pedigree). This included the mother (index case), the patient, his brother, maternal grandmother, uncle and two cousins. The brother, who was 3 years older, was asymptomatic until age 7, where an abdominal ultrasound revealed a left adrenal mass. A total adrenalectomy was performed and at age 1 another mouse was found in the right adrenal gland, which was also removed. 6 years later he was asymptomatic. The uncle developed hemangioblastoma, multiple bilateral renal cell carcinomas, bilateral pheochromocytomas, and succumbed to his disease at age 45. The uncle's two daughters both had the mutation. One of which was found to have pheochromocytoma at age 15 due to routine screening. The other 8 year old daughter has not had any manifestations. No phenotype was noted for the grandmother.

CasePresentingHPOs: HP:0006748 (adrenal pheochromocytoma)

CaseHPOFreeText: Patient presented with an adrenal mass at 11Y0M, which required total adrenalectomy and remains well 2.5 years later.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.V170G (c.509T>G)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA351756196, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.509T%3EG

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant; tranversion

CivicName: V170G (c.509T>G)

MultipleGeneVariants: N/A

GroupID: 237

DiseaseAssertion: VHL

GroupSize: 2

GroupNumberMales: N/A

GroupNumberFemales: N/A

GroupEthnicity: French

GroupAgeRange: N/A

GroupInfo: 2 members of this family were found to harbor a germline large rearrangement of the VHL gene. Member 7398 had no renal involvement. Member 645 presented with severe renal disease (RCC). Families were recruited from the French VHL Registry. Enrolment in the study required identification of the germline VHL mutation (currently 85% of the families included in the French VHL Registry) and available data regarding renal phenotype. A total of 126 families fulfilled these criteria.

GroupPresentingHPOs: HP:0005584 (Renal cell carcinoma)

GroupHPOFreeText: Severe renal disease (any solid lesion before 25 years of age, five or more solid lesions within one or two kidneys, or metastasis of renal cell carcinoma).

GroupNotHPOs: N/A

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: Paper states that this family is previously reported in PMID 12202531, where 12 individuals with this mutation are reported. It is unclear which of the previously reported individuals correspond to which of the currently reported families/individuals (i.e. families 40, 90, 174, 237, 264, 284, 307 or 394).

SupplementalData: Phenotype and genotype information can be found in Supplementary Table S1.

Variant: Rearrangement

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: rearrangement_region

CivicName: Rearrangement

MultipleGeneVariants: N/A

GroupID: 51

DiseaseAssertion: VHL

GroupSize: 4

GroupNumberMales: N/A

GroupNumberFemales: N/A

GroupEthnicity: French

GroupAgeRange: N/A

GroupInfo: 4 members of this family were found to harbor the c.571delC germline variant of the VHL gene. Members 2127, 1184 and 1182 had unknown renal involvement. Member 1183 presented with severe renal disease (RCC). Families were recruited from the French VHL Registry. Enrolment in the study required identification of the germline VHL mutation (currently 85% of the families included in the French VHL Registry) and available data regarding renal phenotype. A total of 126 families fulfilled these criteria.

GroupPresentingHPOs: HP:0005584 (Renal cell carcinoma)

GroupHPOFreeText: Severe renal disease (any solid lesion before 25 years of age, five or more solid lesions within one or two kidneys, or metastasis of renal cell carcinoma).

GroupNotHPOs: N/A

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: Paper states that this family is previously reported in PMID 12202531 and/or 9829912, where 1 and 1 individuals respectively with this mutation are reported. It is unclear if one or both of these previously reported groups are the same as the current family.

SupplementalData: Phenotype and genotype information can be found in Supplementary Table S1.

Variant: p.H191Tfs*11 (c.571del)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA658795182, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.571del

gnomAD: N/A

VariantEvidence: N/A

MutationType: deletion; minus_1_frameshift_variant

CivicName: H191Tfs*11 (c.571del)

MultipleGeneVariants: N/A

Molecular and clinical analysis of 126 French VHL families tested for renal involvement revealed 92 different mutations. 90 of these families had renal involvement. The p.L188P (c.563T>C) germline variant of the VHL gene was detected in 2 individuals (ID 5730/Family 269 and ID 8828/Family 1005) who both presented with renal cell carcinoma. The paper states that these families are previously reported in PMID 12202531 and/or 9829912.

Molecular and clinical analysis of 126 French VHL families tested for renal involvement revealed 92 different mutations. 90 of these families had renal involvement. The p.R161Q (c.482G>A) germline variant of the VHL gene was detected in a family (ID 60). Member 1603 presented with mild renal disease. Member 1601 presented with severe renal disease (RCC). An individual from another family (ID 6270, Family 279) was also found with this variant and presented with renal cell carcinoma. The paper states that these families are previously reported in PMID 12202531 and/or 9829912.

PatientID: II:9

KindredID: 1

Case: M, Age Unknown, Jewish

DiseaseAssertion: VHL

FamilyInfo: This kindred of Jewish-Kurdish origin consisted of 3 generations of 25 members. 7 were clinically affected subjects with pheochromocytoma (5 of which had the confirmed mutation - I:1, II:2, II:4, II:7 and II:9, as the other 2, II:5 and II:10 were said to have passed due to complications of the disease - prior to any genetic testing), and 4 others were carriers, or pre-symptomatic (III:1, III:3, III:7 and III:12). Subject 11:7 developed a cerebellar hemangioblastoma 25 yr after his initial diagnosis of pheochromocytoma, leading to the clinical diagnosis of VHL in the kindred.

CasePresentingHPOs: HP:0002666; HP:0002668 (pheochromocytoma, paraganglioma)

CaseHPOFreeText: patient had bilateral pheochromocytoma, and extra-adrenal chromafin tumors (abdominal paraganglioma). He also had malignant disease with local recurrence

CaseNotHPOs: HP:0005584 (renal cell carcinoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 33471715

SupplementalData: N/A

Variant: p.V166F (c.496G>T)

LegacyVariant: p.V166F (c.709G>T)

CaseProblemVariantFreeText: N/A

ClinVarID: 2224, https://www.ncbi.nlm.nih.gov/clinvar/variation/2224/

CAID: N/A

VariantEvidence: N/A

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: V166F (c.496G>T)

MultipleGeneVariants: N/A

PatientID: I:1

KindredID: 1

Case: F, Age Unknown, Jewish

DiseaseAssertion: VHL

FamilyInfo: This kindred of Jewish-Kurdish origin consisted of 3 generations of 25 members. 7 were clinically affected subjects with pheochromocytoma (5 of which had the confirmed mutation - I:1, II:2, II:4, II:7 and II:9, as the other 2, II:5 and II:10 were said to have passed due to complications of the disease - prior to any genetic testing), and 4 others were carriers, or pre-symptomatic (III:1, III:3, III:7 and III:12). Subject 11:7 developed a cerebellar hemangioblastoma 25 yr after his initial diagnosis of pheochromocytoma, leading to the clinical diagnosis of VHL in the kindred.

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: patient had bilateral pheochromocytoma

CaseNotHPOs: HP:0005584 (renal cell carcinoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 33471715

SupplementalData: N/A

Variant: p.V166F (c.496G>T)

LegacyVariant: p.V166F (c.709G>T)

CaseProblemVariantFreeText: N/A

ClinVarID: 2224, https://www.ncbi.nlm.nih.gov/clinvar/variation/2224/

CAID: N/A

VariantEvidence: N/A

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: V166F (c.496G>T)

MultipleGeneVariants: N/A

PatientID: 25

KindredID: 7

Case: M, 58Y0M, Chinese

DiseaseAssertion: VHL

FamilyInfo: The proband, patient 23, had a brother (patient 24) and father (patient 25) who were both genetically confirmed with the mutation. The brother presented with a CNS hemangioblastoma, renal cell carcinoma, and pancreatic cysts/tumors at age 32. The father presented with renal cell carcinoma and pancreatic cysts/tumors at age 58.

CasePresentingHPOs: HP:0001737; HP:0001732; HP:0005584 (Pancreatic cysts, Abnormality of the pancreas, Renal cell carcinoma)

CaseHPOFreeText: The proband's father, patient 25, presented with renal cell carcinoma and multiple pancreatic cysts/tumors.

CaseNotHPOs: HP:0002666; HP:0009711; HP:0010797 (Pheochromocytoma, Retinal capillary hemangioma, Hemangioblastoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: This cohort 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.R69Afs*63 (c.204_205insG)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA913189244; https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.204_205insG

gnomAD: N/A

VariantEvidence: N/A

MutationType: plus_1_frameshift_variant

CivicName: R69AFS*63 (c.204_205insG)

MultipleGeneVariants: N/A

PatientID: 251

KindredID: 96

Case: F, 44Y0M, Chinese

DiseaseAssertion: VHL

FamilyInfo: The proband (patient 250) presented with a CNS hemangioblastoma at 23, retinal angioma at 17, and multiple pancreatic cysts/tumors at 19. His mother (patient 251) presented with a CNS hemangioblastoma at age 43, retinal angioma at 35, renal cell carcinoma/multiple pancreatic cysts/tumors at 44.

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

CaseHPOFreeText: The patient's mother presented with a CNS hemangioblastoma at age 43, retinal angioma at 35, renal cell carcinoma/multiple pancreatic cysts/tumors at 44.

CaseNotHPOs: HP:0002666 (Pheochromocytoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: This cohort 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: 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

A retrospective cohort study included all the VHL patients diagnosed at Peking University First Hospital (Beijing, China) prior to June 1 2016. A total of 291 patients from 115 different families were included for analysis. This mutation was found in family #23 with 4 members genetically confirmed for the mutation and 7 affected members. The male proband (patient 60) was diagnosed with CNS hemangioblastoma at 25Y, retinal angioma at 25Y, renal cell carcinoma at 30Y, multiple pancreatic cysts or tumours at 30Y (mutation confirmed); son of unknown age (patient 61) with no manifestations (mutation confirmed); daughter of unknown age (patient 62) with no manifestations (mutation confirmed); father (patient 63) diagnosed with CNS hemangioblastoma at 35Y and retinal angioma at 35Y (passed away before diagnosis/ before mutation confirmed); Sister (patient 64) diagnosed with CNS hemangioblastoma at 24Y, and multiple pancreatic cysts or tumours at 31Y (passed away before diagnosis/ before mutation confirmed); aunt 1 (patient 65) diagnosed with CNS hemangioblastoma at 35Y; aunt 2 (patient 66) diagnosed with CNS hemangioblastoma at 20Y (passed away before diagnosis/ before mutation confirmed); aunt 3 diagnosed with CNS hemangioblastoma at 44Y (passed away before diagnosis/ before mutation confirmed); son of aunt 3 (patient 67) diagnosed with CNS hemangioblastoma at 26Y (mutation confirmed).This cohort was also published in a paper by Wang et al., 2018 (PMID: 29330336).

PatientID: 53

KindredID: 18

Case: F, 11Y0M, Chinese

DiseaseAssertion: VHL

FamilyInfo: The proband (patient 51) has a father (patient 52) who passed away before he could be diagnosed/ genetically confirmed with this mutation. The father had renal cell carcinoma at 52. The proband's daughter (patient 53) was confirmed with the mutation and had retinal angioma at 11.

CasePresentingHPOs: HP:0009711 (Retinal capillary hemangioma)

CaseHPOFreeText: The proband presented with a CNS hemangioblastoma at 31, and renal cell carcinoma and multiple pancreatic cysts/tumors at 32.

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

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.P86S (c.256C>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 178692; https://www.ncbi.nlm.nih.gov/clinvar/variation/178692/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: P86S (c.256C>T)

MultipleGeneVariants: N/A

A retrospective cohort study included all the VHL patients diagnosed at Peking University First Hospital (Beijing, China) prior to June 1 2016. A total of 291 patients from 115 different families were included for analysis. A male patient (family #16, patient #45) was confirmed with this missense mutation (p.R82P(c.245G>C)) in the VHL gene. He was diagnosed with CNS hemangioblastoma at 40Y and multiple pancreatic cysts or tumours at 26Y. This patient was also published in a paper by Wang et al., 2018 (PMID: 29330336).

216 patients with clinically expected VHL disease due to family history or presence of VHL typical tumours were routinely examined in an eye centre in Germany between January 2019 and January 2020, majority of which were of European descent (~95%). Since data on the genotype–phenotype correlation of the onset of Retinal Hemangioblastoma (RH) is scarce in relation to VHL disease, this study wanted to inversitage the relationship between VHL gene variants (truncating vs single amino acid substitutions) and the ocular phenotype of the disease. 42 different rare VHL gene variants in 148 patients were detected - some of whom had RH and some who did not. Although date of onset of RH, as well as data on central nervous system haemangioblastomas (CNSH), pheochromocytoma/paraganglioma (PPGL), clear cell renal cell carcinoma (ccRCC) and pancreatic neuroendocrine neoplasm (PNEN) were collected, it was not reported on a per patient basis and therefore could not be discussed per variant. Out of the 72 patients with a p.Y98H (c.292T>C) mutation, 57% (41/72) of individuals had RH while the other 43% (31/72) did not. No family information was provided.

GroupID: 10

Case: Sex Unknown, Age Unknown, Ethnicity Unknown

DiseaseAssertion: VHL

CohortInfo: a retrospective cohort study from an eye centre in Germany involved 148 VHL patients and their genetic data involved in retinal capillary hemangiomas.

CasePresentingHPOs: N/A

CaseHPOFreeText: This individual patient did NOT have retinal capillary hemangiomas. Other VHL manifestations were discussed but not per- variant.

CaseNotHPOs: HP:0009711 (retinal capillary hemangioma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: Yes - Supplementary Table S1

Variant: p.F136Lfs*23 (c.408delT)

LegacyVariant: N/A

GroupProblemVariantFreeText: N/A

ClinVarID: 43601 https://www.ncbi.nlm.nih.gov/clinvar/variation/43601/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: minus_1_frameshift_variant

CivicName: F136LFS*23 (c.408del)

MultipleGeneVariants: N/A

PatientID: 5

KindredID: 5

Case: M, 43Y0M, Korean

DiseaseAssertion: VHL

FamilyInfo: No family history of VHL.

CohortInfo: 26 Korean patients with more than one HAB in the CNS or eye, a single HAB in the CNS or retina plus a visceral manifestation (multiple renal, pancreatic or hepatic cysts, pheochromocytoma and RCC) and positive family history plus any one of the above manifestations.

CasePresentingHPOs: HP:0010797; HP:0005562 (Hemangioblastoma, Multiple renal cysts)

CaseHPOFreeText: Multiple or bilateral CNS hemangioblastoma and renal cysts. Diagnosed with VHL Type 1. Phenotypes revised from previous reports (see “PreviouslyPublished” section below for PMID).

CaseNotHPOs: HP:0002666; HP:0009711; HP:0005584 (Pheochromocytoma, Retinal capillary hemangioma, Renal cell carcinoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 19270817 and/or 19949673

SupplementalData: N/A

Variant: p.E70K (c.208G>A)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 43598, https://www.ncbi.nlm.nih.gov/clinvar/variation/43598/

CAID: N/A

gnomAD: 0.000004365, https://gnomad.broadinstitute.org/variant/3-10183739-G-A

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: E70K (c.208G>A)

MultipleGeneVariants: N/A

PatientID: 31

KindredID: 31

Case: F, 42Y0M, Korean

DiseaseAssertion: VHL

FamilyInfo: No family history of VHL.

CohortInfo: 26 Korean patients with more than one HAB in the CNS or eye, a single HAB in the CNS or retina plus a visceral manifestation (multiple renal, pancreatic or hepatic cysts, pheochromocytoma and RCC) and positive family history plus any one of the above manifestations.

CasePresentingHPOs: HP:0010797; HP:0005584 (Hemangioblastoma, Renal cell carcinoma)

CaseHPOFreeText: CNS hemangioblastoma. Other phenotypes presented but not specified (one or more of: pancreatic cyst or tumor, renal or hepatic cyst). Diagnosed with VHL Type 1.

CaseNotHPOs: HP:0002666; HP:0009711 (Pheochromocytoma, Retinal capillary hemangioma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.L128P (c.383T>C)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 1208816, https://www.ncbi.nlm.nih.gov/clinvar/variation/1208816/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant;transition

CivicName: L128P (c.383T>C)

MultipleGeneVariants: N/A

Between 1994 and 2001, the Dutch VHL working group conducted DNA analysis on 146 probands with VHL-associated manifestations. DNA of probands was extracted from peripheral blood samples. Exons 1, 2 and 3 of the VHL gene and their flanking untranslated and intronic coding sequences were amplified by PCR and subjected to semi-automated sequence analysis. Screening for structural rearrangements, including deletions, involving the VHL gene was performed by Southern blot analysis and the multiplex ligation-dependent probe amplification (MLPA) assay. Deletions encompassing the entire VHL gene were confirmed by FISH analysis on lymphocytes from affected individuals. VHL mutations were identified in 43 families. This mutation (c.509T>A) was detected in 14 VHL patients (family no. 18). Six had retinal hemangioblastoma, 9 had CNS hemangioblastoma, 7 had renal cell carcinoma, 8 had renal cysts, 4 had pheochromocytoma, 5 had pancreatic cysts, 2 had endolymphatic sac tumors, 1 with adnexal papillary tumor of probably mesonephric origin, and 5 had hepatic cysts.

PatientID: V-6

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

ArticleReferenceSequence: Not specified – Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3

GenotypingMethod: Exons 1, 2, and 3 of the VHL gene and their immediately flanking sequences were amplified by use of polymerase chain reaction (PCR). Amplicons were denatured at 94°C and renatured at 25°C for heteroduplex analysis. Denaturing acetonitrile gradient profiles and melting temperatures were established by the Wavemaker 3.0 software prediction. Equal amounts (50 ng) of PCR product were mixed with reference human wild-type genomic DNA and after denaturation-renaturation, were screened for heteroduplexes by dHPLC

SamplingMethod: peripheral blood

Peripheral blood from unrelated patients with pheochromocytoma was tested for mutations of proto-oncogene RET, tumor suppressor gene VHL, succinate dehydrogenase subunit D (SDHD) gene, and the succinate dehydrogenase subunit B (SDHB) gene. Of 271 patients with nonsydromic pheochromocytoma and no family history of the disease, 30 mutations were found in VHL. Multiple pheochromocytomas were statistically more frequent among patients with mutations than among patients without mutations (21 of 66 vs. 5 of 205, P<0.001). The mutation F136C (c.407T>G) was detected in the patient, referred to in the paper by c.620T>G due to a difference in transcript sequence. This missense mutation was found in the VHL gene and one patient with pheochromocytoma.

Peripheral blood from unrelated patients with pheochromocytoma was tested for mutations of proto-oncogene RET, tumor suppressor gene VHL, succinate dehydrogenase subunit D (SDHD) gene, and the succinate dehydrogenase subunit B (SDHB) gene. Of 271 patients with nonsydromic pheochromocytoma and no family history of the disease, 30 mutations were found in VHL. Multiple pheochromocytomas were statistically more frequent among patients with mutations than among patients without mutations (21 of 66 vs. 5 of 205, P<0.001). The Q195* (c.583C>T) mutation was detected in the patient, referred to in the paper by c.796C>T due to a difference in transcript sequence. This nonsense mutation was found in the VHL gene and one patient with pheochromocytoma. This study contains very strong evidence of pathogenicity in the form of a nonsense variant in a gene where loss-of-function is a known mechanism of disease (ACMG code: PVS1).

PatientID: N/A

KindredID: 10

Case: Sex, Age, Ethnicity Unknown

DiseaseAssertion: pheochromocytoma

FamilyInfo: N/A

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: Nonsyndromic pheochromocytoma.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: RET, SDHB, SDHD

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.F119L (c.357C>G)

CaseProblemVariantFreeText: N/A

LegacyVariant: p.F119L (c.570C>G)

ClinVarID: 625240 https://www.ncbi.nlm.nih.gov/clinvar/variation/625240/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant; transversion

CivicName: F119L (c.357C>G)

MultipleGeneVariants: N/A

PatientID: 23

KindredID: KS

Case: M, 27Y0M, Indian

DiseaseAssertion: VHL

FamilyInfo: N/A

CasePresentingHPOs: HP:0010797; HP:0001737 (Hemangioblastoma, Pancreatic cysts)

CaseHPOFreeText: CNS hemangioblastoma and multi-cystic pancreatic lesions.

CaseNotHPOs: HP:0030393; HP:0009711; HP:0002666; HP:0005584 (Endolymphatic sac tumor, Retinal capillary hemangioma, Pheochromocytoma, Renal cell carcinoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: Complete Deletion

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: N/A

gnomAD: N/A

VariantEvidence: This variant is noted as a full-length deletion involving genes BRK1 and FANCD2.

MutationType: deletion

CivicName: Deletion

MultipleGeneVariants: N/A

PatientID: 17

KindredID: S4

Case: F, 20Y0M, Indian

DiseaseAssertion: VHL

FamilyInfo: N/A

CasePresentingHPOs: HP:0009711; HP:0002666 (Retinal capillary hemangioma, Pheochromocytoma)

CaseHPOFreeText: Retinal angioma and pheochromocytoma.

CaseNotHPOs: HP:0030393; HP:0010797; HP:0001737; HP:0005584 (Endolymphatic sac tumor, Hemangioblastoma, Pancreatic cysts, Renal cell carcinoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.V155G (c.464T>G)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA16621938, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.464T%3EG

gnomAD: N/A

VariantEvidence: N/A

MutationType: splice_site_variant; missense_variant;transversion

CivicName: V155G (c.464T>G) and c.463+43A>G

MultipleGeneVariants: Germline, VHL, c.463+43A>G

PatientID: N/A (sibling 1)

KindredID: 1

Case: Sex Unknown, 23Y0M, Ethnicity Unknown

DiseaseAssertion: pheochromocytoma

FamilyInfo: Her father had bilateral pheochromocytoma at the age of 13 and her grandfather had died of an unknown renal disease at the age of 50. They were both however not tested for any variants. There were no reports of hereditary cutaneous or uterine leiomyomas, renal cell cancer, neuroendocrine tumors or hemangioblastomas of the CNS/retina. Family evaluation revealed clinical and biochemical evidence of (bilateral) pheochromocytoma in two siblings 17 and age 19. These members also had the VHL mutation, while 2 unaffected family members were negative.

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: clinical and biochemical evidence showed bilateral pheochromocytoma

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: FH/RET/MAX/NF1/SDHB/SDHC/SDHD/TMEM127

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.G114G (c.342T>C)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA432421783 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.342T%3EC

gnomAD: N/A

VariantEvidence: The FH variant is reported in 9/116704 alleles in the ExAC database. The VHL variant was no reported, however, an T>A transition at the same nucleotide position has been reported once in 1/121408 alleles (ExAC). Researchers suspect synonymous mutation has effects on transcript splicing (2 nucleotides into exon 2).

MutationType: synonymous_variant

CivicName: G114G (c.342T>C)

MultipleGeneVariants: N/A

PMID: 31308404

Gene: VHL

StandardizedReferenceSequence: NM_000551.3

GroupID: 4578

DiseaseAssertion: VHL

GroupSize: 8

GroupNumberMales: N/A

GroupNumberFemales: N/A

GroupEthnicity: N/A

GroupAgeRange: N/A

GroupInfo: This group is a family of eight people with the same mutation.

GroupPresentingHPOs: HP:0002666; HP:0005584; HP:0010797; HP:0009711 (Pheochromocytoma, Renal cell carcinoma, Hemangioblastoma, Retinal capillary hemangioma)

GroupHPOFreeText: 4/8 family members had a pheochromocytoma, 7/8 had renal cell carcinoma, 5/8 had hemangioblastoma of the CNS, and 3/8 had retinal angioma. 2/8 family members were described to have cysts but the type or location was not specified.

GroupNotHPOs: HP:0030405 (pancreatic endocrine tumour)

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.N78S (c.233A>G)

CaseProblemVariantFreeText: N/A

LegacyVariant: c.446A>G

ClinVarID: 93326, https://www.ncbi.nlm.nih.gov/clinvar/variation/93326/

CAID: N/A

gnomAD: N/A

VariantEvidence: Variant reported as 446, A to G (Asp to Ser), assumed to be reported in legacy nomenclature (AF010238.1) and mapped to c.233A>G, p.Asn78Ser (NM_000551.3). Error on author's part regarding protein change.

MutationType: missense_variant; transition

CivicName: N78S (c.233A>G)

MultipleGeneVariants: N/A

GroupID: 4577

DiseaseAssertion: VHL

GroupSize: 3

GroupNumberMales: N/A

GroupNumberFemales: N/A

GroupEthnicity: N/A

GroupAgeRange: N/A

GroupInfo: Each group represents a family.

GroupPresentingHPOs: HP:0009711; HP:0010797; HP:0002666; HP:0005584 (Retinal capillary hemangioma, Hemangioblastoma, Pheochromocytoma, Renal cell carcinoma)

GroupHPOFreeText: 2/3 members with pheochromocytoma, 1/3 members with CNS hemangioblastoma, 1/3 members with retinal angioma and 1/3 members with RCC. Diagnosed as a VHL Type 2B family.

GroupNotHPOs: N/A

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.F119L (c.357C>G)

LegacyVariant: c.570C>G

CaseProblemVariantFreeText: N/A

ClinVarID: 625240, https://www.ncbi.nlm.nih.gov/clinvar/variation/625240/

CAID: N/A

gnomAD: N/A

VariantEvidence: Variant reported as 570, C to G (Phe to Leu), assumed to be reported in legacy nomenclature (AF010238.1) and mapped to c.357C>G, p.Phe119Leu (NM_000551.3).

MutationType: missense_variant;transversion

CivicName: F119L (c.357C>G)

MultipleGeneVariants: N/A

In a study of 114 unrelated VHL families, 85 germline mutations were found. VHL mutations were detected in affected family members, but not in unaffected family members or 96 normal individuals. This nonsense mutation was found in a VHL type 1 patient and familiy of 4 individuals (family IDs 3760 and 3759), using PCR and SSCP sequencing. The mutation of c.336C>A was referred to in the paper by c.549C>A due to a difference in transcript sequence. In family 3759, 3 of 4 individuals were identified with retinal angiomas, 1 with CNS hemangioblastoma, and one with renal cell carcinoma. For individual 3760, they had retinal and CNS hemangiomas. ACMG codes as follows: Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PP1). Patient's phenotype is highly specific for a disease with a single genetic etiology (PP4).

GroupID: 4414

DiseaseAssertion: assumed VHL

GroupSize: 7

GroupNumberMales: N/A

GroupNumberFemales: N/A

GroupEthnicity: N/A

GroupAgeRange: N/A

GroupInfo: Familial VHL stated; 7 family members recorded with this mutation.

GroupPresentingHPOs: HP:0010797; HP:0009711; HP:0005584; HP:0002666 (hemangioblastoma, retinal capillary hemangioma, renal cell carcinoma, pheochromocytoma)

GroupHPOFreeText: 2/7 members had retinal angiomas (hemangiomas), 3 had CNS hemangioblastomas, 1 had RCC and 1 had pheochromocytoma

GroupNotHPOs: N/A

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: 7728151 (type 2 4414NCI)

SupplementalData: N/A

Variant: p.F119L (c.357C>G)

CaseProblemVariantFreeText: N/A

LegacyVariant: p.F190L (c.570C>G)

ClinVarID: 625240 https://www.ncbi.nlm.nih.gov/clinvar/variation/625240/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant; transversion

CivicName: F119L (c.357C>G)

MultipleGeneVariants: N/A

GroupID: 3315

DiseaseAssertion: assumed VHL

GroupSize: 4

GroupNumberMales: N/A

GroupNumberFemales: N/A

GroupEthnicity: N/A

GroupAgeRange: N/A

GroupInfo: Familial VHL stated; 4 family members recorded with this mutation.

GroupPresentingHPOs: HP:0010797; HP:0009711; HP:0005584 (hemangioblastoma, retinal capillary hemangioma, renal cell carcinoma)

GroupHPOFreeText: 1/4 members had a retinal angioma (hemangioma), 2 had CNS hemangioblastoma, and 2 had RCC

GroupNotHPOs: HP:0002666 (pheochromocytoma)

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: Possibly previously published in PMID 9829911

SupplementalData: N/A

Variant: p.S111N (c.332G>A)

CaseProblemVariantFreeText: N/A

LegacyVariant: p.S182N (c.545G>A)

ClinVarID: 223186 https://www.ncbi.nlm.nih.gov/clinvar/variation/223186/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant; transition

CivicName: S111N (c.332G>A)

MultipleGeneVariants: N/A

540 patients from 187 unrelated Chinese VHL families at the Peking University First Hospital were all screened for VHL clinical features and germline mutations. Of these, clinical characteristics were observed in 258 patients from 80 unrelated Chinese families. These were reported in this study, grouped by the 21 mutations found. PCR and MLPA on peripheral blood detected the VHL mutations. Possessing the p.R113* (c.337C>T) mutation, 6 members total from 2 families were described, and phenotypic information was given for this group. With ages ranging from 17-66Y, hemangioblastomas were observed in 3/6 members, retinal capillary hemangioma in 3, renal cell carcinoma in 3, pancreatic cysts in 2, and in a papillary cystadenoma of the epididymis genital system tumor (epididymis or broad ligament) 1 member. See more information as this cohort has been previously published in PMID 29330336

540 patients from 187 unrelated Chinese VHL families at the Peking University First Hospital were all screened for VHL clinical features and germline mutations. Of these, clinical characteristics were observed in 258 patients from 80 unrelated Chinese families. These were reported in this study, grouped by the 21 mutations found. PCR and MLPA on peripheral blood detected the VHL mutations. Possessing the p.S65L (c.194C>T) mutation, 24 members total from an unknown number of families were described, and phenotypic information was given for this group. With ages ranging from 15-65Y, hemangioblastomas were observed in 15/24 members, retinal capillary hemangioma in 2, renal cell carcinoma in 9, pancreatic cysts in 11, pheochromocytoma in 1, and a genital system tumor (epididymis or broad ligament) in 4 members. This cohort has been previously published in PMID 29330336; 28388566.

540 patients from 187 unrelated Chinese VHL families at the Peking University First Hospital were all screened for VHL clinical features and germline mutations. Of these, clinical characteristics were observed in 258 patients from 80 unrelated Chinese families. These were reported in this study, grouped by the 21 mutations found. PCR and MLPA on peripheral blood detected the VHL mutations. Possessing the p.P86L (c.257C>T) mutation, 3 families with 4 members total were described, and phenotypic information was given for this group. With ages ranging from 30.3Y +/- 8.0Y, hemangioblastoma was observed in 3/4 members, retinal capillary hemangioma in 2, renal cell carcinoma in 3, pancreatic cysts in 3, and  a genital system tumor (epididymis or broad ligament) in 1 member. Ssee more information as this cohort has been previously published in PMID 29330336 (as 2 families of 3 people total), and 28388566 (as family #20, 21).

540 patients from 187 unrelated Chinese VHL families at the Peking University First Hospital were all screened for VHL clinical features and germline mutations. Of these, clinical characteristics were observed in 258 patients from 80 unrelated Chinese families. These were reported in this study, grouped by the 21 mutations found. PCR and MLPA on peripheral blood detected the VHL mutations. Possessing the p.P86S (c.256C>T) mutation, 3 families with 9 members total were described, and phenotypic information was given for this group. With ages ranging from 35.0Y +/- 15.8Y, hemangioblastoma in 3/9 members, retinal capillary hemangioma in 2, renal cell carcinoma in 5, pancreatic cysts in 3, and pheochromocytoma in 1 member was found. See more information as this cohort has been previously published in PMID 29330336 (3 families with 7 members total), and 28388566 (family #18 and #19).

PatientID: IV-8

KindredID: 1

Case: F, Age Unknown, Ethnicity Unknown

DiseaseAssertion: VHL

FamilyInfo: The proband (V-5), his mother (IV-8), maternal grandmother (III-6), maternal aunts (IV-10, IV-12), cousin (V-9) and brother (V-6) were found to harbour the VHL mutation p.P86A (c.256 C>G). All were symptomatic of VHL except for his cousin.

CasePresentingHPOs: HP:0010797; HP:0000107; HP:0030405; HP:0009711 (Hemangioblastoma, Renal cyst, Pancreatic endocrine tumor, Retinal capillary hemangioma)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 7728151(family 4416); 20375333

SupplementalData: Information obtained from Figure 1.

Variant: p.P86A (c.256 C>G)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 93327, https://www.ncbi.nlm.nih.gov/clinvar/variation/93327/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant; transversion

CivicName: P86A (c.256C>G)

MultipleGeneVariants: N/A

PatientID: CII2

KindredID: C

Case: M, 63Y0M, Serbian

DiseaseAssertion: VHL

FamilyInfo: Families were selected based on their clinical data and family history. Patient’s son (CIII1) retinal capillary hemangioma, CNS hemangioblastoma and renal cell carcinoma, but was not genetically tested. The patient’s brother also had retinal capillary hemangioma, CNS hemangioblastoma and renal cell carcinoma, but was not genetically tested. Patient’s grandson (CIV2) was diagnosed with retinal hemangioblastoma at 12Y0M. Then, multiple pancreatic and kidney cysts were detected at 29Y0M and left kidney cancer was found at age 35Y0M. He possessed the same mutation as the patient. The grandson’s children aged 12Y0M (CV2) and 15Y0M (CV1) are carriers of the same genetic mutation, but are both currently asymptomatic. See pedigree in figure 1.

CasePresentingHPOs: HP:0009711; HP:0010797; HP:0005584 (retinal capillary hemangioma; hemangioblastoma; renal cell carcinoma)

CaseHPOFreeText: The patient had the first symptoms of retinal hemangioblastoma at 60Y0M and deceased due to renal cell carcinoma in both kidneys at 63Y0M.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.W88R (c.262T>A)

LegacyVariant: p.W88R (c.475T>A)

CaseProblemVariantFreeText: N/A

ClinVarID: 456577, https://www.ncbi.nlm.nih.gov/clinvar/variation/456577/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense variant; transversion

CivicName: W88R (c.262T>A)

MultipleGeneVariants: N/A

PatientID: CV1

KindredID: C

Case: M, 15Y0M, Serbian

DiseaseAssertion: Asymptomatic

FamilyInfo: Families were selected based on their clinical data and family history. Patient and his brother (CV2) are both currently asymptomatic, but possess the same variant as their father (CIV2), who was diagnosed with retinal hemangioblastoma at 12Y0M. Then, multiple pancreatic and kidney cysts were detected at 29Y0M and left kidney cancer was found at age 35Y0M. Patient’s grandfather, great grandfather and great uncle (CIII1; CII1, CII2) had retinal capillary hemangioma, CNS hemangioblastoma and renal cell carcinoma. Out of the three of them, only the great grandfather had genetic testing performed and was found to have the same mutation as the patient. See pedigree in figure 1.

CasePresentingHPOs: N/A

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.W88R (c.262T>A)

LegacyVariant: p.W88R (c.475T>A)

CaseProblemVariantFreeText: N/A

ClinVarID: 456577, https://www.ncbi.nlm.nih.gov/clinvar/variation/456577/

CAID: N/A

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense variant; transversion

CivicName: W88R (c.262T>A)

MultipleGeneVariants: N/A

The VHL gene was analyzed in 3 families from a Serbain population. Genomic DNA was screened by SSCP analysis and patients with variant bands were subjected to sequencing and confirmatory re-sequencing. 3 male members (BI1; BII2; BIII3) from Family B had pheochromocytoma. Two of them (BII2; BIII3) were genetically tested and confirmed to possess the missense V84M (c.250G>A) VHL mutation, reported in the paper as V84M (c.463G>A) due to a difference in transcript sequence. Patient BII2 and BIII3 were diagnosed at 40Y and 1Y with pheochromocytoma, respectively.

ArticleReferenceSequence: Not specified – Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3

GenotypingMethod: N/A

SamplingMethod: N/A

PatientID: 8

KindredID: 8

Case: Sex Unknown, 31Y0M, Italian

DiseaseAssertion: pheochromocytoma

FamilyInfo: Present - potential pathogenic relevance due to a family history, although no further information present

CasePresentingHPOs: HP:0006748 (Adrenal pheochromocytoma)

CaseHPOFreeText: adrenal bilateral pheochromocytoma with an age of diagnosis of 31Y

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.G93C (c.277G>T)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 223175 https://www.ncbi.nlm.nih.gov/clinvar/variation/223175/

CAID: N/A

gnomAD: 0.000004476 https://gnomad.broadinstitute.org/variant/3-10183808-G-T

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: G93C (c.277G>T)

MultipleGeneVariants: N/A

One hundred and sixteen unrelated VHL disease patients have been investigated by molecular genetic analysis. Twenty-two of these were previously shown to have germline deletions on Southern analysis, and in the present study the remaining 94 patients were screened for intragenic mutations via SSCP and heteroduplex analysis of 855 bp of the VHL coding sequence and 800 bp of the 3' UTR. An intragenic mutation was identified in 55 (59%) out of 94 patients without germline deletions on Southern analysis. In all patients with multiple affected family members the missense mutation segregated with the disease. Large deletions or intragenic mutations predicted to cause a truncated protein were found in 36 of 53 families without pheochromocytoma (VHL type 1) and 2 of 12 families with pheochromocytoma (VHL type 2). This study also investigated the frequency of different mutation classes between kindreds with and without pheochromocytoma. The p.N78H(c.232A>C) missense mutation (noted as p.N149H (c.445A>C) in the paper due to a difference in reference transcript used) was found in at least one patient in kindred 34. Pheochromocytoma was not observed in any members of this kindred (implying the affected patient(s) had VHL disease type 1). No other familial phenotypic information could be inferred from the paper.

One hundred and sixteen unrelated VHL disease patients have been investigated by molecular genetic analysis. Twenty-two of these were previously shown to have germline deletions on Southern analysis, and in the present study the remaining 94 patients were screened for intragenic mutations via SSCP and heteroduplex analysis of 855 bp of the VHL coding sequence and 800 bp of the 3' UTR. An intragenic mutation was identified in 55 (59%) out of 94 patients without germline deletions on Southern analysis. In all patients with multiple affected family members the missense mutation segregated with the disease. Large deletions or intragenic mutations predicted to cause a truncated protein were found in 36 of 53 families without pheochromocytoma (VHL type 1) and 2 of 12 families with pheochromocytoma (VHL type 2). This study also investigated the frequency of different mutation classes between kindreds with and without pheochromocytoma. The p.E94 (c.280G>T) missense mutation (noted as p.E165 (c.493G>T) in the paper due to a difference in reference transcript used) was found in at least one patient in kindred 51. Pheochromocytoma was not observed in any members of this kindred (implying the affected patient(s) had VHL disease type 1). No other familial phenotypic information could be inferred from the paper.

PatientID: 1

KindredID: 1

Case: F, 66Y0M, Taiwanese (East-Asian)

DiseaseAssertion: renal cell carcinoma

FamilyInfo: N/A

CohortInfo: 8 of 19 patients presenting with clear cell renal cell carcinoma were found to be heterozygous for the germline variant rs1642742 in VHL (c.*294G>A). All but one of these patients (7/8) also presented with the germline variant rs779805 (c.-195G>A) in VHL.

CasePresentingHPOs: HP:0006770 (clear cell renal cell carcinoma)

CaseHPOFreeText: She had stage III clear cell renal cell carcinoma

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 21982469

SupplementalData: Yes - Additional file 1: Figure S1

Variant: c.*294G>A

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 342407 https://www.ncbi.nlm.nih.gov/clinvar/variation/342407/

CAID: N/A

gnomAD: 0.5911 https://gnomad.broadinstitute.org/variant/3-10191943-G-A

VariantEvidence: Heterozygous for both, she also presented with the germline variant c.-195G>A in VHL. LOH (G) of both mutations was found in the tumor tissue as well

MutationType: 3_prime_UTR_variant

CivicName: c.-195G>A AND c.*294G>A

MultipleGeneVariants: Germline, VHL, c.-195G>A

GroupID: 64

Case: 49Y0M, Sex Unknown, Ethnicity Unknown

DiseaseAssertion: assumed VHL

FamilyInfo: 1 of the 573 patients discussed in this paper were found to have this variant. This mutation (c.340G>T) was found in 1 VHL family with a single patient.

CasePresentingHPOs: HP:0006880 (cerebellar hemangioblastoma)

CaseHPOFreeText: patient had cerebellar hemangioblastoma diagnosed at 49Y

CaseNotHPOs: HP:0005584; HP:0009711; HP:0002666 (renal cell carcinoma; retinal capillary hemangioma; pheochromocytoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: Supplementary Table S1.

Variant: p.G114C (c.340G>T)

CaseProblemVariantFreeText: N/A

LegacyVariant: N/A

ClinVarID: N/A

CAID: CA351751376 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.340G%3ET

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: G114C (c.340G>T)

MultipleGeneVariants: N/A

Genotype-phenotype correlations of 573 VHL patients were analyzed and confirmed that higher risk of pheochromocytoma is associated with missense mutations that result in substitution of a surface amino acid or that disrupt the structural integrity of the VHL gene product (pVHL). Age-related risks of retinal hemangoblastomas and renal cell carcinoma were higher in patients with nonsense or frameshift mutations. This nonsense mutation (c.264G>A) was found in a VHL family with 3 affected members, 1 had retinal hemangioblastomas, 1 had cerebellar hemangioblastomas, 2 had renal cell carcinoma, and 1 had pheochromocytoma. There is very strong evidence for pathogenicity in the form of a nonsense variant in a gene where loss-of-function is known mechanism of disease (ACMG code: PVS1).

Genotype-phenotype correlations of 573 VHL patients from 200 kindreds were analyzed. Higher risk of pheochromocytoma was associated with missense mutations that result in substitution of a surface amino acid (p<=0.004) than for patients with missense mutations that disrupt the structural integrity of the VHL gene product (pVHL) or other loss of function mutations (either germline deletions or truncating mutations). This missense mutation (c.533T>C), affecting residue on the surface of pVHL, was found in a VHL family of 3. All family members had retinal hemangioblastomas and cerebellar hemangioblastomas. Two had renal cell carcinoma. Another family in this study was observed with a L178R (c.533T>G) mutation. ACMG codes as follows: Supporting evidence of pathogenicity because Missense variant in a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease (PP2).

Genotype-phenotype correlations of 573 VHL patients from 200 kindreds were analyzed. Higher risk of pheochromocytoma was associated with missense mutations that result in substitution of a surface amino acid (p<=0.004) than for patients with missense mutations that disrupt the structural integrity of the VHL gene product (pVHL) or other loss of function mutations (either germline deletions or truncating mutations). This missense mutation (c.332G>A), affecting surface residue of pVHL, was found in 3 VHL type 1 families with 10 affected individuals altogether. Four of 10 individuals had retinal angioma, 6 had cerebellar hemangioblastoma, and 2 had renal cell carcinoma.

In a robotic adrenalectomy case report, a 13-year-old male pediatric case was noted with intermittent tachycardic and hypertensiveity during hospitalization for a pneumonia episode. He found to have a 6cm right adrenal mass. It was resected and he remains disease-free at 19 months of post-operative follow-up. Patient’s father has VHL, and had undergone bilateral adrenalectomy for pheochromocytoma and bilateral nephrectomy for renal cell carcinoma. A VHL mutation (c.583C>T, p.Q195*) was found in the patient and his father. No information was mentioned regarding genotyping method or sampling method.

GroupID: 14

DiseaseAssertion: VHL

GroupSize: 2

GroupNumberMales: N/A

GroupNumberFemales: N/A GroupEthnicity: Japanese GroupAgeRange: N/A

GroupInfo: The 2 patients are grouped based on both having the same mutation. They are unrelated to one another.

GroupPresentingHPOs: HP:0005584 (Renal cell carcinoma)

GroupHPOFreeText: 2/2 patients in this group presented with RCC.

GroupNotHPOs: HP:0009711; HP:0010797; HP:0002666 (Retinal capillary hemangioma, Hemangioblastoma, Pheochromocytoma)

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: 10761708

SupplementalData: N/A

Variant: p.R120Nfs*40 (c.358_359insAC)

LegacyVariant: codon 191 (c.571insAC)

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA2573106245, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA2573106245

gnomAD: N/A

VariantEvidence: Nucleotide deletion (i.e. 571insAC) coincides with legacy variant nomenclature (i.e. AF010238.1) and was mapped to c.358_359insAC (NM_000551.3).

MutationType: insertion; plus_2_frameshift_variant

CivicName: R120fs (c.358_359insAC)

MultipleGeneVariants: N/A

PatientID: 12

KindredID: 12

Case: 32Y0M, Sex Unknown, Argentinian

DiseaseAssertion: VHL

FamilyInfo: Family history unremarkable; Patient was confirmed to have a de novo mutation.

CasePresentingHPOs: HP:0010797; HP:0009711; HP:0000107; HP:0030424 (hemangioblastoma; retinal capillary hemangioma; renal cyst; epididymal cyst)

CaseHPOFreeText: Aged 32Y at diagnosis (genetic testing); fulfils type 1 VHL clinical diagnosis. Retinal hemangioblastomas and CNS hemangioblastomas diagnosed at 32Y, renal cysts were also diagnosed at 32Y, while epididymal cysts were diagnosed first at 23Y (See Table 1 & 2).

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.V74Sfs*53 (c.219_232delGGTCATCTTCTGCA)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: N/A

CAID: CA2497423672 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2497423672

gnomAD: N/A

VariantEvidence: N/A

MutationType: minus_2_frameshift_variant

CivicName: V74Sfs*53 (c.219_232delGGTCATCTTCTGCA)

MultipleGeneVariants: N/A

A 6Y old boy presented at the Children's Hospital with left adrenal pheochromocytoma, and relapsed with right adrenal pheochromocytoma a year later. His outcome was uneventful in a five year follow-up. His father had left adrenal pheochromocytoma and left extra-adrenal paraganglioma when the father was 11Y, and had an uneventful outcome. A germline VHL missense transversion mutation NM_000551.3:c.488T>G(L163R) was confirmed in both the son and father, and was found by sequencing with polymerase chain reaction (PCR) and analysis with single-strand conformation polymorphism (SSCP). The patient's mother and 3 other siblings had no symptoms and no mutation. Note that the paper describes this variant as c.701T>G since it uses an older reference sequence (Latif et al.).

Fourty-four of 389 patients with VHL (between 1988-1999) screened positive for PNETs either by pathologic analysis of tissue specimens or by characteristic radiographic appearance on CT and MRI. VHL gene germline mutations were determined by quantitative Southern blotting to detect deletions of the gene and gene rearrangements as well as complete gene sequencing. Patient 16, a 24-year-old female, was found to harbour the c.555C>G mutation in the VHL gene (stated as 768 C to G in the paper which used the Latif sequence as reference) leading to a premature stop codon at protein position 185 in exon 3. She presented with a single pathologic pancreatic neuroendocrine tumor. ACMG evidence codes: 'PP4' since the patient presents phenotypes highly specific for a disease with a single genetic etiology.

PatientID: 23

KindredID: 6011

Case: M, 34Y0M, Ethnicity Unknown

DiseaseAssertion: VHL

FamilyInfo: N/A

CasePresentingHPOs: HP:0030405 (pancreatic endocrine tumour)

CaseHPOFreeText: He presented with one pathologic pancreatic endocrine tumour.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.G114R (c.340G>C)

LegacyVariant: p.G114R (c.553G>C)

CaseProblemVariantFreeText: N/A

ClinVar: 223193 https://www.ncbi.nlm.nih.gov/clinvar/variation/223193/

CAID: CA357101 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.340G%3EC

gnomAD: N/A

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: G114R (c.340G>C)

MultipleGeneVariants: N/A

PatientID: III-6

KindredID: Family A

Case: M, 31Y0M, Ethnicity unknown

DiseaseAssertion: VHL

FamilyInfo: Patient’s grandfather (I-1), now deceased, and aunt (II-1) had CNS/spinal hemangioblastoma and the confirmed VHL gene mutation. His aunts II-2 and II-3 both had confirmed VHL and CNS hemangioblastoma. His dad (II-3) has confirmed VHL gene and pancreatic and renal cysts. His cousins (2 boys 1 girl: III-3; III-5; III-3) were all found with the confirmed VHL gene mutation; III-3 and III-5 with retinal hemangioblastoma and CNS/spinal hemangioblastomas and III-4 with pancreatic and ovarian cysts. Patient’s son and nephew IV-1 and IV-3, were confirmed with the VHL gene mutation although no other manifestations.

CasePresentingHPOs: HP:0005584; HP:001079 (renal cell carcinoma, hemangioblastoma)

CaseHPOFreeText: N/A

CaseNotHPOs: HP:0009711; HP:0002666 (retinal capillary hemangioblastoma, pheochromocytoma)

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: Deletion of exon 3 (c.464-?_642+?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 3 deletion

MultipleGeneVariants: N/A

PatientID: None

KindredID: 32165

Case: Age unknown, Sex unknown, Turkish

DiseaseAssertion: VHL

FamilyInfo: familial Turkish germline mutation

CasePresentingHPOs: HP:0010797; HP:0002666 (hemangioblastoma, pheochromocytoma)

CaseHPOFreeText: Bilateral pheochromocytoma and CNS hemangioblastoma

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: Yes

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

LegacyVariant: N/A

CaseProblemVariantFreeText: N/A

ClinVarID: 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