1. Last 7 days
    1. c.499 C > T R167W 

      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. 8 patients had germline VHL mutations. Both peripheral blood and tumor tissue samples were sequenced using Big Dye Terminator Ready Reaction mix v.1.1 (Life Technologies, Foster City, CA). Sequencing reactions were loaded on an ABI 3100 capillary sequencer (Life Technologies) and analyzed using the Sequencing Analysis software v.3.7 (PE Applied Biosystems, Grand Island, NY). One Italian patient with a germline missense mutation (c.499C>T; p.Arg167Trp) in the VHL gene was diagnosed at age 43 with brainstem hemangioblastoma. The patient has positive family history for VHL disease.

    2. Polymerase chain reaction (PCR) amplification of DNA from both PB and tumor tissue was performed for the entire VHL coding sequence and the promoter region, including exon-intron boundaries. The set of primers is original (Table 2). Amplifications were performed in a Gene Amp PCR System 9700 (Perkin Elmer, Foster City, CA) in a final reaction volume of 25 µL, containing 100 ng of genomic DNA template, 0.25 nmol/L dNTPs, 20 pmol of each primer, and 1 U HotMaster Taq polymerase (Eppendorf, Milan, Italy) in 10 × PCR Reaction Buffer. Polymerase chain reaction cycling conditions consisted of an initial denaturation step at 94°C for 2 minutes, followed by 35 cycles with denaturation at 94°C for 30 seconds, annealing at the specific temperature for 30 seconds, elongation step at 72°C for 30 seconds, and a final elongation step at 72°C for 10 minutes. Polymerase chain reaction products were purified using GFX PCR DNA and Gel Band Purification Kit (GE Healthcare, Buckinghamshire, UK) and sequenced. Sequencing reactions were performed in 10 µL of final volume using 3.2 pmol of primer, 4 to 6 ng of DNA template, and 1 µL of Big Dye Terminator Ready Reaction mix v.1.1 (Life Technologies, Foster City, CA). Sequencing reactions were loaded on an ABI 3100 capillary sequencer (Life Technologies) and analyzed using the Sequencing Analysis software v.3.7 (PE Applied Biosystems, Grand Island, NY). Once mutations in the DNA from the tumor samples had been detected, we searched for the same mutations in the corresponding PB to identify germline mutations.

      ArticleReferenceSequence: NM_000551.2

      GenotypingMethod: PCR was used to purify products and subsequently sequenced using Big Dye Terminator Ready Reaction mix v.1.1 (Life Technologies, Foster City, CA). Sequencing reactions were loaded on an ABI 3100 capillary sequencer (Life Technologies) and analyzed using the Sequencing Analysis software v.3.7 (PE Applied Biosystems, Grand Island, NY).

      SamplingMethod: tissue resection and peripheral blood

    1. Germline mutations were identified in 300/469 (63%) of the families tested; 137 distinct intragenic germline mutations were detected.

      Germline mutational data on VHL was gathered from various countries to assess variation in germline mutations that produce disease within different populations. Families were grouped according to three possible outcomes of disease: renal cell carcinoma without pheochromocytoma, renal cell carcinoma with pheochromocytoma, or pheochromocytoma alone. SSCP and denaturing gradient gel electrophoresis identified mutations in 300/469 (63%) of families affected with VHL. This germline familial VHL mutation (C77fs (c.228dupC)) was taken from the Cambridge, Department of Pathology database, with an unknown number of members belonging to Family ID 85CA (reported in Table 3, found in VHL families with renal cell carcinoma), and 71CA (reported in Table 4, found in VHL families with pheochromocytoma). Other phenotypes are likely, however not detailed here. It was reported in the paper as c.441insC due to a difference in transcript reference.

    2. Germline mutations were identified in 300/469 (63%) of the families tested; 137 distinct intragenic germline mutations were detected.

      GroupID/ KindredID: 39CA

      DiseaseAssertion: VHL

      GroupSize: N/A

      GroupNumberMales: N/A

      GroupNumberFemales: N/A

      GroupEthnicity: N/A

      GroupAgeRange: N/A

      GroupInfo: This germline familial VHL mutation was taken from the Cambridge, Department of Pathology database, with an unknown number of members belonging to family ID: Family 39CA. Table 5 lists all ID and mutations associated with individuals without detailed clinical information.

      GroupPresentingHPOs: N/A

      GroupHPOFreeText: Described as multiple VHL families without detailed clinical information. Other phenotypes are possible, however not detailed here.

      GroupNotHPOs: N/A

      GroupNotHPOFreeText: N/A

      GroupPreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.S65W (c.194C>G)

      LegacyVariant: p.S65W (c.407C>G)

      CaseProblemVariantFreeText: N/A

      ClinVarID: 43597 https://www.ncbi.nlm.nih.gov/clinvar/variation/43597

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transversion

      CivicName: S65W (c.194C>G)

      MultipleGeneVariants: N/A

    3. Germline mutations were identified in 300/469 (63%) of the families tested; 137 distinct intragenic germline mutations were detected.

      Germline mutational data on VHL was gathered from various countries to assess variation in germline mutations that produce disease within different populations. Families were grouped according to three possible outcomes of disease: renal cell carcinoma without pheochromocytoma, renal cell carcinoma with pheochromocytoma, or pheochromocytoma alone. SSCP and denaturing gradient gel electrophoresis identified mutations in 300/469 (63%) of families affected with VHL. This germline familial VHL mutation (F76del (c.227_229delTCT)) was taken from various families from multiple databases: including: the National Cancer Institute database, the Bristol Myers Squibb database, Department of Uroglogy, Yokohama database, and the Cambridge, Department of Pathology; with an unknown number of members belonging to each. It was reported in the paper as both c.439delTTC and c.440delTCT, due to a difference in transcript reference. As reported in Table 3, this mutation is found in VHL families without pheochromocytoma, and with renal cell carcinoma, including IDs: 2693NCI, 2956NCI, 20BMS, 2YO, 27BMS, 75CA, 48CA, and 144CA. Additionally, table 5 lists all ID and mutations associated with individuals without detailed clinical information, and was found in one family: family ID 134CA. Other phenotypes are possible, however not detailed here. Later publications reference this cohort as being reported in PMIDs: 7728151 and 9829911.

    1. MATERIALS AND METHODS

      ArticleReferenceSequence: Not specified – Assumption: variants assumed to have been documented by the author under reference sequence NM_000551.3 (variant for patient 2 has been documented by the authors under the reference sequence AF010238.1 (Latif et al.) and has been annotated after lift-over under NM_000551.3)

      GenotypingMethod: N/A

      SamplingMethod: N/A

    1. patients with VHL disease (Figs. 1 and 2, and Table 1)

      PatientID: 3

      KindredID: 2

      Case: F, 69Y0M, Arab

      DiseaseAssertion: VHL

      FamilyInfo: No family history of VHL disease was described for this patient. Immediate family members were recommended to genetically test for the relevant variant or monitor for VHL-related symptoms.

      CasePresentingHPOs: HP:0006770; HP:0006880; HP:0009713; HP:0000107; HP:0001737 (clear cell renal cell carcinoma; cerebellar hemangioblastoma; spinal hemangioblastoma; renal cyst; pancreatic cysts)

      CaseHPOFreeText: At 63Y, Patient 3 had a left radical nephrectomy for renal cell carcinoma. She also had multiple pancreatic and right renal cysts. At 67Y, Patient 3 exhibited cerebellar and spinal hemangioblastomas, renal cell carcinoma, and cysts in kidneys and pancreas. She was diagnosed with VHL disease. Two years later, had a right radical nephrectomy for renal cell carcinoma. Her entire pancreas was covered with cysts (see table 1).

      CaseNotHPOs: HP:0002088; HP:0001392; HP:0005264; HP:0001743 (abnormal lung morphology; abnormality of the liver; abnormality of the gallbladder; abnormality of the spleen)

      CaseNotHPOFreeText: No lesions were observed in the lungs, liver, gallbladder, and spleen.

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData:  N/A

      Variant: p.I151T (c.452T>C)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 428803, www.ncbi.nlm.nih.gov/clinvar/variation/428803/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transition

      CivicName: I151T (c.452T>C)

      MultipleGeneVariants: N/A

    1. PatientID: V-39

      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

    1. 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 N131S (c.392A>G) missense mutation was found in 1 VHL type 2 family with both family members having retinal angiomas and pheochromocytomas (family ID 87). 1/2 individuals had hemangioblastomas of the central nervous system and 1/2 had pancreatic cysts or tumor (unspecified).

    1. GroupID: 77

      Case: 23Y0M, 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.491A>G) was found in 1 VHL family with a single patient.

      CasePresentingHPOs: HP:0009711; HP:0002666 (retinal capillary hemangioma; pheochromocytoma)

      CaseHPOFreeText: patient had pheochromocytoma diagnosed at 10Y, a retinal angioma at 23Y.

      CaseNotHPOs: HP:0005584; HP:0006880 (renal cell carcinoma; cerebellar hemangioblastoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: Supplementary Table S1.

      Variant: p.Q164R (c.491A>G)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: 2238 https://www.ncbi.nlm.nih.gov/clinvar/variation/2238/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: Q164R (c.491A>G)

      MultipleGeneVariants: N/A

    1. We used a multi-array and Meso-Scale Discovery (MSD) technology to detect and quantify the levels of phosphorylated and non-phosphorylated intracellular kinase proteins of the PI3K-AKT-mTOR pathway. In all tumor regions, there was evidence of either S6K or 4EPB1 phosphorylation, consistent with pathway activation, relative to normal kidney from each side (Figure 5). In particular, S6K was phosphorylated in the tumor regions harboring the L2427P MTOR mutation. Additionally, immunohistochemical analysis of the mTOR substrates S6K and 4E-BP1 in all tumor regions revealed enhanced staining of either or both substrates relative to normal kidney in a pattern consistent with the proteomic data (Additional file 1: Table S3; Additional file 7). This is in contrast to absent staining of S6K and 4E-BP1 in MTOR wild-type tumor regions in a ccRCC previously reported [11]. We conclude that all tumors displayed functional convergence of mTOR pathway activation, despite distinct evolutionary somatic routes. Tumor four (harboring the FAT domain mutation) demonstrated markedly elevated phosphorylation of AKT, to a similar extent as induced in tumor three (harboring the kinase domain mutation). However, in tumor four there was increased phosphorylation of 4E-BP1 but not of S6K. Absent S6K phosphorylation would appear to be consistent with the lack of an activating mutation in mTOR in this region described earlier. There is evidence indicating that 4E-BP1 is regulated independently of S6K and it remains unclear whether the effect of AKT signaling on 4E-BP1 is wholly integrated by mTOR, or alternative kinases [30,31].
    1. GroupID: 102

      DiseaseAssertion: VHL

      GroupSize: N/A

      GroupNumberMales: N/A

      GroupNumberFemales: N/A

      GroupEthnicity: N/A

      GroupAgeRange: N/A

      GroupInfo: VHL family found to have the c.712C>T (R167W) germline variant of the VHL gene. The number of family members included in this study is not specified.

      GroupPresentingHPOs: HP:0002666 (Pheochromocytoma)

      GroupHPOFreeText: Number of family affected members is not specified.

      GroupNotHPOs: N/A

      GroupNotHPOFreeText: N/A

      GroupPreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

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

      LegacyVariant: c.712C>T

      CaseProblemVariantFreeText: 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?dataset=gnomad_r2_1

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: R167W (c.499C>T)

      MultipleGeneVariants: N/A

    2. 93 families examined at the Clinical Center of the National Institutes of Health (Bethesda, MD) underwent genetic testing for germline mutations of the VHL gene. Whole blood was extracted and genomic DNA was amplified by PCR and products were sequences using a cycle sequencing kit with dye-labeled terminators and automatically sequenced. This mutation was found in VHL type 1 family (lineage 11). The variant was reported as c.488_490del18bp (AF010238.1) and was mapped to G93_Y98del (c.277_294del/c.275_292del) (NM_000551.3).

    1. 41 non-related patients with retinal angiomatosis presenting in the Benjamin Franklin University Eye Clinic between 1988 to 1999 Germany were evaluated for the presence of other VHL lesions. VHL disease was diagnosed clinically in 33 patients based on the presence of other severe VHL lesions (spinal hemangioblastoma 45% prevalence, cerebellar hemangioblastoma 42% prevalence, renal cysts 39% prevalence, pancreatic cyst 39% prevalence, renal carcinoma 18% prevalence, PCC 18% prevalence). Blood samples were taken and analyzed by PCR and single-strand conformational polymorphism (SSCP). VHL germline mutations were identified in 27 out of 29 VHL families screened with molecular genetics. This patient (group 8) with VHL-related retinal angiomatosis was found to have germline missense (c. 233A>G) mutation in the VHL gene. It should be noted that this VHL mutation was stated as c.446A>G in the paper which used the Latif sequence as reference. No other affected family members were described for this patient. Other VHL lesions harbored by the patients were not specified.

    1. VHL promoter variants

      A female 27 year old presented with two right renal masses and several pancreatic cysts at 22Y, as well as a family history of ccRCC. Next generation sequencing and exon level copy number analysis for VHL was performed. VHL gene was found to have 45% mRNA expression levels and western blotting showed 23% protein expression. A heterozygous germline VHL 5' UTR (c.-77_-32del) 45 base pair deletion (including the promoter) was found. The proband was also not found to possess BAP1, CDC73, FH, FLCN, MET, MLH1, MSH2, MSH6, PMS2, PTEN, SDHB, SDHC, SDHD, SMARCB1, TP53,

      TSC1, TSC2, or WT1 mutations. The proband's father, age 45, presented a 2.8cm renal mass and pancreatic cysts. A right nephrectomy was consistent with ccRCC. No evidence of hemangioblastomas was found with brain and spine MRI. The proband’s uncle, age 38, underwent a partial nephrectomy consistent with ccRCC. Segregation analysis returned positive for the variant in both father and uncle.

    1. In our study, group 5 represented the c.262T > C p.Trp88Arg mutation that included 21 patients from 2 families (Figure 4 and Table 3). Variability was observed in the mean age at onset for CHB and RCC, which were 41.1 ± 9.1 (range = 29–62) and 37.4 ± 12.9 (range = 23–65), respectively.

      PatientID: 13

      KindredID: 1 (group ID 5)

      Case: M, 39Y0M, Chinese

      DiseaseAssertion: assumed VHL

      CohortInfo: Clinical characteristics of 258 patients from 80 unrelated Chinese families were reported in this study. Grouped by the 21 mutations found, 2 families with 21 members total were described, and phenotypic information was given for this group.

      FamilyInfo: In family 1, 17 members were described. The first generation describes 5 members with the VHL mutation, each passing on the gene to further generations. Patient 13’s mother and sister had this familial mutation. His son had not been yet tested at the time of the study. See Fig 4 for family pedigree; Table 3 for details.

      CasePresentingHPOs: HP:0010797; HP:0005584 (hemangioblastoma, renal cell carcinoma)

      CaseHPOFreeText: He had hemangioblastoma at 39Y and RCC at 37Y

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

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

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 496053 https://www.ncbi.nlm.nih.gov/clinvar/variation/496053/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: W88R (c.262T>C)

      MultipleGeneVariants: N/A

    2. only three VHL lesions (CHB, RCC, and PCT) presented in the c.194C > G p.Ser65Trp mutational subgroup

      GroupID: 1B

      DiseaseAssertion: assumed VHL

      GroupSize: 7

      GroupNumberMales: N/A

      GroupNumberFemales: N/A

      GroupEthnicity: Chinese

      GroupAgeRange: 17-61Y

      GroupInfo: Clinical characteristics of 258 patients from 80 unrelated Chinese families were reported in this study. Grouped by the 21 mutations found, it is unclear how many distinct families are reported in group 1B. 7 individuals were described. Phenotypic information was given for each mutation.

      GroupPresentingHPOs: HP:0010797; HP:0005584; HP:0001737 (hemangioblastoma, renal cell carcinoma, pancreatic cysts)

      GroupHPOFreeText: 5 of the 7 members presented with CNS hemangioblastoma (mean age of 30.2Y), 4/7 had renal cell carcinoma (mean age of 36.3Y), and pancreatic cysts in 3/7 members (means age of 32.3Y)

      GroupNotHPOs: HP:0009711; HP:0002666; HP:0009715 (retinal capillary hemangioma, pheochromocytoma, papillary cystadenoma of the epididymis)

      GroupNotHPOFreeText: No patients were given with retinal capillary hemangioma, pheochromocytoma, or genital system tumors (epididymis or broad ligament).

      GroupPreviousTesting: N/A

      PreviouslyPublished: 29330336; 28388566

      SupplementalData: N/A

      Variant: p.S65W (c.194C>G)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 43597 https://www.ncbi.nlm.nih.gov/clinvar/variation/43597/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant; transversion

      CivicName: S65W (c.194C>G)

      MultipleGeneVariants: N/A

    1. PatientID: 59

      KindredID: 22

      Case: M, 14Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0002666; HP:0001732; HP:0001737 (Pheochromocytoma, Abnormality of the pancreas, Pancreatic cysts)

      CaseHPOFreeText: The proband presented with multiple pancreatic cysts/tumors at 14 and pheochromocytoma at 11.

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

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

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

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

      Variant: p.V87E (c.260T>A)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351750651; https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.260T%3EA

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: V87E (c.260T>A)

      MultipleGeneVariants: N/A

    2. PatientID: 154

      KindredID: 57

      Case: M, 34Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: N/A

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

      CaseHPOFreeText: The proband presented at age 34 with retinal angioma, multiple pancreatic cysts/tumors, and renal cell carcinoma.

      CaseNotHPOs: HP:0010797; HP:0002666 (Hemangioblastoma, Pheochromocytoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

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

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

      Variant: p.V155Dfs*17 (c.464_468del)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA2499306942; https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA2499306942

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: minus_2_frameshift_variant

      CivicName: V155fs (c.464_468delTGTAT)

      MultipleGeneVariants: N/A

    1. 709 G-->T transversion present in all affected subjects and in four presymptomatic children.

      A Jewish-Kurdish family of 25 individuals has 11 members as likely carriers of this missense mutation (V166F (c.496G>T)). It was reported in the paper under "c.709G>T" due to a difference in the use of an older transcript. All but 2 were diagnosed specifically with the mutation, however two members were said to have died of complications of the disease, and although genotype was not established prior, it is assumed that they carried the same VHL mutation. In the family, seven family members have clinical manifestations of VHL disease. All seven family members had pheochromocytomas. Patient II4 had retinal angiomas and renal cysts and patient II7 developed a cerebellar hemangioblastoma at 25 yr after his initial diagnosis of pheochromocytoma, leading to the clinical diagnosis of VHL in the kindred. Four members were under the age of 5 without any manifestations yet (likely pre-symptomatic). This (member) was published in a future publication: PMID: 33471715. As of this publication, several asymptomatic carriers developed a neuroendocrine tumor, 7 new children were born where 3 of them carry the mutation. In addition, 2 patients died, one of which was due to metastatic PNEN-related liver failure. Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (ACMG code: PP1).

    1. two large deletions

      PatientID: N/A

      KindredID: 13

      Case: F, 32Y0M, Chinese

      DiseaseAssertion: VHL

      FamilyInfo: Patient had family history of VHL disease. The patient's sibling presented with a hemangioblastoma, renal cell carcinoma and multiple pancreatic cysts or tumors at age 23 and then retinal hemangioma at age 24. He/she possessed the same mutation as the patient. The patient's mother presented with hemangioblastoma at age 43; but died prior to diagnosis and genetic testing.

      CohortInfo: 16 Chinese patients clinically diagnosed with VHL disease.

      CasePresentingHPOs: HP:0010797; HP:0005584; HP:0001732 (hemangioblastoma; renal cell carcinoma; abnormality of the pancreas)

      CaseHPOFreeText: The patient presented with a hemangioblastoma, renal cell carcinoma and multiple pancreatic cysts or tumors at age 30.

      CaseNotHPOs: HP:0002666, HP:0030393, HP:0030424; HP:0009711 (pheochromocytoma, endolymphatic sac tumor, epididymal cyst, retinal capillary hemangioma; )

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: Exon 3 Deletion

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: deletion

      CivicName: Exon 3 Deletion

      MultipleGeneVariants: N/A

    1. PMID: 7977367

      PatientID: N/A

      KindredID: 769-P (cell line)

      Case: Sex Unknown, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: Renal cell carcinoma

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0005584 (renal cell carcinoma)

      CaseHPOFreeText: Described as sporadic RCC from cell line 769-P

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.I180N (c.539T>A)

      LegacyVariant: p.I251N (c.752T>A)

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351756277 https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.539T%3EA

      gnomAD: N/A

      VariantEvidence:N/A

      MutationType: missense_variant; transversion

      CivicName: I180N (c.539T>A)

      MultipleGeneVariants: N/A

    1. 36 VHL-related pheochromocytomas (from 21 patients) and 10 VHL-related CNS hemangioblastomas (from 6 patients) were studied using comparative genomic hybridization (CGH) to detect genetic imbalances. The study identified selective loss of chromosome 11 in pheochromocytomas associated with VHL. Patient XIX with VHL-associated pheochromocytoma was found with a germline missense mutation (c.482G>A) in the VHL gene. (stated as c.695G>A in the paper which used the Latif sequence as reference) in the VHL gene. All patients have familial VHL.

    1. Exons 2, 3 deletion

      GroupID/ KindredID: 22 / S 4

      Case: Age unknown, Sex unknown, Polish

      DiseaseAssertion: VHL

      FamilyInfo: This deletion was found in Family No. 22 with 1 member affected. Germline de novo mutations confirmed by analysis of parents’ DNA. Germline mutations (of deletion of exon 2-3) was not detected in DNA extracted from blood leucocytes of the parents.

      CasePresentingHPOs: HP:0009711 (retinal capillary hemangioma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: HP:0005584; HP:0010797 (renal cell carcinoma, hemangioblastoma)

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: Exons 2, 3 deletion

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: N/A

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: exon_loss_variant

      CivicName: EXON 2-3 DELETION

      MultipleGeneVariants: N/A

    1. 9 Yes Yes Yes Yes Yes

      PatientID: 9

      KindredID: 6

      Case: F, 32Y0M, Ethnicity Unknown

      DiseaseAssertion: VHL

      FamilyInfo: Three total family members presented with this germline variant in VHL. No phenotypes were reported for patients 6 and 7 of this family.

      CohortInfo: A retrospective analysis of case notes of 17 patients was performed for this study. Initially, 23 consecutive patients with VHL disease followed by the Department of Endocrinology at St Bartholomew's Hospital since 1988 were reviewed.

      CasePresentingHPOs: HP:0001732; HP:0000077; HP:0002666; HP:0009711; HP:0010797; HP:0002017; HP:0001082 (Abnormality of the pancreas, Abnormality of the kidney, Pheochromocytoma, Retinal capillary hemangioma, Hemangioblastoma, Nausea and vomiting, Cholecystitis)

      CaseHPOFreeText: This patient developed upper abdominal pain, nausea and vomiting, which was attributed to gallstone cholecystitis based on ultrasound findings. Her symptoms settled on conventional treatment for cholecystitis.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.V155E (c.464T>A)

      LegacyVariant: c.677T>A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA351756032, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.464T%3EA

      gnomAD: N/A

      VariantEvidence: Reported as: T677A, assumed to be in Legacy reference sequence (AF010238.1) and mapped to c.464T>A according to NM_000551.3 reference sequence.

      MutationType: missense_variant;transversion

      CivicName: V155E (c.464T>A)

      MultipleGeneVariants: N/A

    1.  c.259_260-insA1 (1)142HBr, HBc, HBsc, RCC, Cr, Cp

      GroupID: None

      Case: Sex Unknown, 42Y0M, Dutch

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CasePresentingHPOs: HP:0009711; HP:0006880; HP:0009713; HP:0005584; HP:0000107; HP:0001737 (Retinal capillary hemangioma, Cerebellar hemangioblastoma, Spinal hemangioblastoma, Renal cell carcinoma, Renal cyst, Pancreatic cysts)

      CaseHPOFreeText: Diagnosed with VHL Type 1.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 31087189

      SupplementalData: N/A

      Variant: p.V87Dfs*45 (c.259_260insA)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA913189242, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_canonicalid?canonicalid=CA913189242

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: insertion; plus_1_frameshift_variant

      CivicName: V87fs (c.259_260insA)

      MultipleGeneVariants: N/A

    1. 5 nonsense mutations

      PatientID: 19

      KindredID: 63

      Case: Sex unknown, Age unknown, French

      DiseaseAssertion: VHL

      FamilyInfo: One other member belonging to family 63 was mentioned (Patient: 11). This patient was found to have a pancreatic endocrine tumour, without pheochromocytoma, or renal cell carcinoma.

      CasePresentingHPOs: HP:0030405; HP:0002666; HP:0005584 (pancreatic endocrine tumour, pheochromocytoma, renal cell carcinoma)

      CaseHPOFreeText: N/A

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.Y175* (c.525C>G)

      CaseProblemVariantFreeText: N/A

      LegacyVariant: N/A

      ClinVarID: 182974 https://www.ncbi.nlm.nih.gov/clinvar/variation/182974/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: stop_gained

      CivicName: Y175* (c.525C>G)

      MultipleGeneVariants: N/A

    1. In a study of 426 unrelated VHL patients, 111 were discovered to have alterations in the VHL gene. 18 novel variants were identified in VHL patients, but none were present in 200 unaffected control individuals. DNA samples from peripheral blood leukocytes underwent polymerase chain reaction (PCR) amplification, denaturing high-performance liquid chromatography (DHPLC), and direct sequence analysis of the entire coding sequence and intron-exon boundaries. The R167L (c.500G>T) germline mutation of the VHL gene, was found in two patients. Patient 24 (57Y) presented with pheochromocytoma, retinal hemangioblastoma and CNS hemangioblastoma. Their father were found to carry the R167L (c.500G>T) germline mutation of the VHL gene. Father, siblings and nephew were analyzed but no phenotype information was provided for these family members. Genotype information for siblings and nephew was not provided. Patient 232 presented with pheochromocytoma, retinal hemangioblastoma and CNS hemangioblastoma. The variant is noted as likely de novo. Mother and sibling were analyzed but no details were provided. Based on likely de novo assertion, it’s assumed that mother was negative for this mutation.

    1. PatientID: 1968

      KindredID: 224

      Case: Sex Unknown, Age Unknown, French

      DiseaseAssertion: VHL

      FamilyInfo: N/A

      CohortInfo: 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.

      CasePresentingHPOs: HP:0005584 (Renal cell carcinoma)

      CaseHPOFreeText: Mild renal disease (simple renal cyst, multicystic kidney[s], small lesion [less than 10 mm in size] of unknown significance, or small solid tumor without indication for surgical removal [less than 30 mm in size]). Individual RCC phenotype is noted as positive.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: 12202531

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

      Variant: p.H115Y (c.343C>T)

      LegacyVariant: N/A

      CaseProblemVariantFreeText: N/A

      ClinVarID: N/A

      CAID: CA16621930, https://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.343C%3ET

      gnomAD: N/A

      VariantEvidence: N/A

      MutationType: missense_variant;transition

      CivicName: H115Y (c.343C>T)

      MultipleGeneVariants: N/A

    1. VHL (c.263G>T; p.W88L)

      A case report revealed a 57Y female caucasian patient presenting with metastatic clear cell renal cell carcinoma, with signs of liver spread, and pelvic and lumbar spinal cord bone metastases. WES (whole-exome sequencing) and Sanger sequencing were performed on peripheral blood, tumor tissue (primary tumor obtained before treatment, in the skull metastasis resected 7 years after temsirolimus treatment initiation). VHL (c.263G>T; p.W88L) and MTOR (c.5920T>C; p.Y1974H) variants were not explicitly stated to be germline in the text but were not present in Supplementary eTable 1 where variants present in tumor/metastasis and absent in blood are listed. The variants affecting genes frequently mutated in ccRCC were detected in all tumor samples analyzed: VHL, BAP1 (c.1359dup; p.E454Rfs*15), and MTOR.

    1. VHL kindreds for germline mutations and calculated the age related tumour risks for different classes of VHL gene mutations.

      In a study of 138 unrelated VHL families, 109 germline mutations were found. Missense mutations were more frequently found in families with pheochromocytoma (PC). Deletions, nonsense, and frameshift mutations were more frequently found in families without PC. Large deletions and mutations predicted to cause truncated protein were associated with lower risk of PC. The mutation R177* (c.499C>T) was referred to in the paper by c.712C>T due to a difference in transcript sequence. This missense mutation was found in one of the VHL families (family ID 153).

    1. PatientID: VI-1

      KindredID: 1

      Case: F, Age Unknown, Ethnicity Unknown

      DiseaseAssertion: Assumed VHL

      FamilyInfo: 13 affected individuals in this family were found. The p.Tyr112Asn (c.334T>A) mutation of the VHL gene cosegregated with the disease in all five tested affected individuals from the family (V-5, VI-1, VI-2, VI-3, and VII-1). 7/13 have had renal cell carcinoma. Other manifestations of the disease in this family include renal cysts, retinal angioma, and CNS hemangioblastoma. There was one case of pheochromocytoma (VII-1). No other pheochromocytomas or related neuroendocrine tumors of the pancreas or adrenal gland have been diagnosed or recognized retrospectively by review of medical records and recall of relatives. The mutation was also found in three asymptomatic relatives (VII-2, VII-3, and VII-4).

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

      CaseHPOFreeText: CNS hemangioblastoma and RCC. Age of onset not provided.

      CaseNotHPOs: N/A

      CaseNotHPOFreeText: N/A

      CasePreviousTesting: N/A

      PreviouslyPublished: N/A

      SupplementalData: N/A

      Variant: p.Y112N (c.334T>A)

      LegacyVariant: T547A

      CaseProblemVariantFreeText: N/A

      ClinVarID: 2228, https://www.ncbi.nlm.nih.gov/clinvar/variation/2228/

      CAID: N/A

      gnomAD: N/A

      VariantEvidence: Variant is inferred in this patient from clinical findings and family history.

      MutationType: missense_variant;transversion

      CivicName: Y112N (c.334T>A)

      MultipleGeneVariants: N/A

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