PatientID: 21 (tumour 36)

KindredID: 4

Case: Sex Unknown, Age Unknown, Ethnicity Unknown

DiseaseAssertion: VHL

FamilyInfo: Two other members of this patient's family (patient 19 and patient 20) were found to harbour the same VHL gene mutation.

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: Patient had one benign pheochromocytoma.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: RET

PreviouslyPublished: 7759077, 9681856

SupplementalData: N/A

Variant: p.L188V (c.562C>G)

LegacyVariant: p.L188V (c.775C>G)

CaseProblemVariantFreeText: N/A

ClinVar: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: CA020488 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.562C%3EG

gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

VariantEvidence: Refer to Table 1 for LOH information.

MutationType: missense_variant;transversion

CivicName: L188V (c.562C>G)

MultipleGeneVariants: N/A

GroupID/KindredID: 5959

DiseaseAssertion:VHL

GroupSize: 2

GroupNumberMales: N/A

GroupNumberFemales: N/A

GroupEthnicity: N/A

GroupAgeRange: N/A

GroupInfo: These two patients were from the same family (5959) and both had the same VHL gene mutations.

GroupPresentingHPOs: HP:0002666; HP:0009711; HP:0030405 (Pheochromocytoma, Retinal capillary hemangioma, Pancreatic endocrine tumor)

GroupHPOFreeText: One patient in this family had a pheochromocytoma and cysts (type of cyst was not specified). Both patients had retinal angioma. It is unclear how many of the patients had pancreatic endocrine tumors.

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

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.L188V (c.562C>G)

CaseProblemVariantFreeText: N/A

LegacyVariant: c.775C>G

ClinVarID: 2225, https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: N/A

gnomAD: 0.00002121, https://gnomad.broadinstitute.org/variant/3-10191569-C-G?dataset=gnomad_r2_1

VariantEvidence: Variant reported as 775, C to G (Leu to Val), assumed to be reported in legacy nomenclature (AF010238.1) and mapped to c.562C>G, p.Leu188Val (NM_000551.3).

MutationType: missense_variant;transversion

CivicName: L188V (c.562C>G)

MultipleGeneVariants: Germline, VHL, c.241C>T (p.Pro81Ser)

3-year-old white male child presented with hematuria of two days and a CT scan showed a right renal mass determined to be renal cell carcinoma. A nephrectomy was done and the tumour tissue was sent for karyotyping. Peripheral blood samples were also taken and sent for sequence analysis of the VHL gene. Genetic testing confirmed 2 mutations: a translocation between chromosome X and 1 t(X;1)(p11.2; p34.3) and a germline missense mutation, c.562C>G (p.Leu188Val) in the VHL gene. Family history was remarkable for a renal tumour in the paternal grandmother at age 65, treated by nephrectomy in 1998. Furthermore, a maternal uncle had a history of thyroid cancer, and a maternal cousin had a history of breast cancer. The patient’s parents and a 13-year-old half-brother were healthy.

PatientID: N/A

KindredID: 1

Case: M, 3Y0M, Caucasian

DiseaseAssertion: VHL

FamilyInfo: Family history was remarkable for a renal tumor in the paternal grandmother at age 65, treated by nephrectomy in 1998. Furthermore, a maternal uncle had a history of thyroid cancer, and a maternal cousin had a history of breast cancer. The patient’s parents and a 13-year-old half-brother were healthy.

CasePresentingHPOs:HP:0005584, HP:0000790 ( renal cell carcinoma, hematuria)

CaseHPOFreeText: Computed tomographic scan showed a right renal mass. The tumor was impinging on the renal sinus and extended to the renal capsule. The patient underwent a right nephrectomy. In addition, one of five hilar lymph nodes was positive for metastatic disease.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p. L188V (c.562C>G)

LegacyVariant: N/A

CaseProblemVariantFreeText: N/

ClinVar: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: N/A

gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: L188V (c.562C>G)

MultipleGeneVariants: t(X;1)(p11.2; p34.3)

Study of a German family of 16 family members with cosegregation of the pheochromocytoma-only phenotype with two concurrent germline mutations in the VHL protein alpha and beta domains. These mutations were c.562 C>T (stated as 775C>G in the paper which used the Latif sequence as reference) and c.241C>T (stated as 454C>T in the paper). Patient 1 was unaffected and had the wild-type allele. His spouse, patient 2, presented with pheochromocytoma and had both mutations. They had four children; one had a pheochromocytoma and died, two (patients 5 and 7) had both mutations and presented with pheochromocytomas, and one child (patient 6) was unaffected and carried neither mutation. Patient 7 had a child (patient 9) who also carried both mutations and presented with pheochromocytoma. In the other branch of the family, patient 3 who carried both mutations and presented with pheochromocytoma had a child with patient 4 who was unaffected. Their child (patient 8) carried both mutations and presented with pheochromocytoma. Patient 8 had two children; one who did not carry the mutation and was unaffected (patient 10) and another that carried both mutations but was disease-free (patient 11). DNA was isolated with whole blood and denaturing high-performance liquid chromatography (DHPLC) and dye terminator method on an ABI Prism 310 genetic analyzer (Applied Biosystems, Weiterstadt, Germany) were used for sequencing. Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (ACMG code: PP1).

PatientID: 2

KindredID: 1

Case: F, Age Unknown, German

DiseaseAssertion: VHL

FamilyInfo: This patient and her unaffected spouse (patient 1) had four children; one died and was affected, two (patient 5 and 7) had both mutations and presented with pheochromocytoma, and one child (patient 6) was unaffected and carried neither mutation. Patient 7 had a child (patient 9) who also carried both mutations and presented with pheochromocytoma. Furthermore, this patient's brother (patient 3) carried both mutations and presented with pheochromocytoma. He had a child with patient (4) who was unaffected. Their child (patient 8) carried both mutations and presented with pheochromocytoma. Patient 8 had two children; one that did not carry the mutation and was unaffected (patient 10) and another that carried both mutations but was disease free (patient 11). See Figure 3 for family pedigree.

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 8772572, 7563486

SupplementalData: N/A

Variant: p.L188V (c.562C>G)

LegacyVariant: p.L188V (c.775C>G)

CaseProblemVariantFreeText: N/A

ClinVar: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: CA020488 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.562C%3EG

gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: P81S (c.241C>T) and L188V (c.562C>G)

MultipleGeneVariants: Germline, VHL, c.241C>T (p.Pro81Ser)

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 renalcell 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. There was 1 patient reported with c.562C>G (p.L188V). This member presented with retinal hemangiomas. No family information was provided.

Fourty-four of 389 patients with VHL (between 1988-1999) screened positive for pancreatic neuroendocrine tumors (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 43 was found to have the gemline VHL mutation c.562C>G (stated as 775 C to G in the paper which used the Latif sequence as reference) leading to a Leu to Val change at protein position 188. She presented with four pathologic pancreatic neuroendocrine tumors at age 35. She was also found to harbour the c.241C>T (stated in the paper as 454 C to T) VHL gene mutation leading to a Pro to Ser change at protein position 81. ACMG evidence codes: 'PP4' since the patient presents phenotypes highly specific for a disease with a single genetic etiology.

PatientID: 43

KindredID: 5959

Case: F, 35Y0M, Ethnicity Unknown

DiseaseAssertion: VHL

FamilyInfo: N/A

CasePresentingHPOs: HP:0030405 (pancreatic endocrine tumour)

CaseHPOFreeText: She presented with four pathologic pancreatic neuroendocrine tumors.

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.L188V (c.562C>G)

LegacyVariant: p.L188V (c.775C>G)

CaseProblemVariantFreeText: N/A

ClinVar: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: CA020488 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.562C%3EG

gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: L188V (c.562C>G)

MultipleGeneVariants: Germline, VHL, c.241C>T (p.Prp81Ser)

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 (L188V (c.562C>G)) was taken from the Munich, university of Freiburg and Institute of Pathology database, with an unknown number of members belonging to two family IDs: Family ID 37CE, and 38CE. It was reported in the paper as c.775C>G due to a difference in transcript reference. As reported in Table 4, this mutation is found in VHL families with pheochromocytoma. Other phenotypes are likely, including renal cell carcinoma, however not detailed here.

GroupID/ KindredID: 37CE, 38CE

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 Munich, university of Freiburg and Institute of Pathology database, with an unknown number of members belonging to two family IDs: Family 37CE and 38CE. Table 4 lists all ID and mutations associated with individuals with pheochromocytoma.

GroupPresentingHPOs: HP:0002666 (pheochromocytoma)

GroupHPOFreeText: Described as multiple VHL families with pheochromocytoma. Other phenotypes are likely, including renal cell carcinoma, however not detailed here.

GroupNotHPOs: N/A

GroupNotHPOFreeText: N/A

GroupPreviousTesting: N/A

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.L188V (c.562C>G)

LegacyVariant: p.L188V (c.775C>G)

CaseProblemVariantFreeText: N/A

ClinVarID: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: N/A

gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

VariantEvidence: This paper declares this variant is predicted to compromise the Elongin-binding site by location between codons 157 and 189.

MutationType: missense_variant;transversion

CivicName: L188V (c.562C>G)

MultipleGeneVariants: N/A

PatientID: II,4

KindredID: 1

Case: M, Age Unknown, Ethnicity Unknown

DiseaseAssertion: VHL

FamilyInfo: The patient had significant family history. His mother refused genetic testing but presented with bilateral pohechromocytoma. His father was found to have the same VHL mutation. One of his siblings (patient II,3) was unaffected, while another (patient II,2) was found to have the mutation and presented with bilateral pheochromocytoma. His sibling (patient II,1) passed during childbirth with symptoms and signs of a hypertensive crisis with the autopsy showing a left adrenal and extraadrenal pheochromocytoma. However, cause of death was a cerebral hemorrhage. His half sister (patient II,5) also had the same VHL mutation and presented with bilateral pheochromocytoma. Refer to figure 1 for family pedigree.

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: bilateral pheochromocytoma

CaseNotHPOs: HP:0006737 (Extraadrenal pheochromocytoma)

CaseNotHPOFreeText: Absence of extraadrenal pheochromocytoma. Absence of thyroid disease at age 24.

CasePreviousTesting: RET

PreviouslyPublished: 7563486, 12414898

SupplementalData: N/A

Variant: p.L188V (c.562C>G)

LegacyVariant: p.L259V (c.775C>G)

CaseProblemVariantFreeText: N/A

ClinVar: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: N/A

gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: L188V (c.562C>G)

MultipleGeneVariants: N/A

21 consenting patients treated for pheochromocytoma over a 10-yr period at the University of Freiburg Medical Center were affected by VHL and donated peripheral blood for germline DNA analyses. DNA was sequenced using single-strand conformation polymorphism (SSCP) analysis of all three exons of the VHL gene. Three of these 21 patients had a p.Leu188Val germline mutation, (c.775C>G legacy notation converted to c.562C>G). Patients 19 and 21 had a single benign pheochromocytoma while patient 20 had three benign pheochromocytomas. The three patients were related. No other patient data and demographics was available.

PatientID: 1

KindredID: A

Case: M, 61Y0M, Ethnicity Unknown

DiseaseAssertion: assumed VHL

FamilyInfo: Positive: the patient’s sister also presented with the germline c.562C>G mutation, and metastatic lobular breast carcinoma. In a family pedigree, 10 additional members affected with cancer were displayed. This included both of their parents: father with lung cancer, mother with skin cancer, additional sister with breast cancer, brother with melanoma. Lastly, his two sons presented with skin cancer, however no description of their genotyping. See Fig. 3.

CasePresentingHPOs: HP:0006770; HP:0001028 (Clear cell renal cell carcinoma, hemangioma)

CaseHPOFreeText: He presented in 2012 (52Y) with worsening lower abdominal discomfort (CT scan revealed a right renal solid mass of renal cell carcinoma). A right renal nephrectomy was done, confirming ccRCC. 4 years later, new lung nodules and an enhancing lesion in the L1 vertebral body was found (metastatic ccRCC). Additionally, in 2020, a pancreatic lesion present on his scans was presumed to be a metastatic RCC lesion (consistent with an atypical hemangioma).

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

CaseNotHPOFreeText: N/A

CasePreviousTesting: MAX/NF1/RET/SDHA/SHDB/SHDC/SDHD/SDHAF2/TMEM127 [133 genes evaluated by germline testing - Invitae]

PreviouslyPublished: N/A

SupplementalData: Yes

Variant: p.L188V (c.562C>G)

LegacyVariant: N/A

CaseProblemVariantFreeText: In 2013, somatic next generation sequencing (NGS) testing using a panel of 447 cancer genes (OncoPanel, BWH Pathology, MA, USA) was performed on the resected renal specimen. This revealed the following variants: VHL p.Leu188Val (c.562C>G), CHEK2 p.Val395Leu (c.1183G>C), VHL p.Ala149Thr (c.445G>A) variant, and several copy number losses including a large single-copy deletion in 3p. 6 years later, germline testing revealed a heterozygous germline VHL p.Leu188Val variant, a CHEK2 and ERCC4 mutation.

ClinVarID: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: N/A

gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: L188V (c.562C>G)

MultipleGeneVariants: Somatic, VHL, c.445G>A (p.Ala149Thr)

GroupID: None

DiseaseAssertion: VHL

GroupSize: 9

GroupNumberMales: Unknown

GroupNumberFemales: Unknown

GroupEthnicity: Unknown

GroupAgeRange: Unknown

GroupInfo: Nine individuals from 2 different families initially diagnosed with MEN-IIA were investigated. All were found to have the same (c.562C>G) missense mutation in the VHL gene.

GroupPresentingHPOs: HP:0002666; HP:0006737; HP:0002865; HP:0011781 (pheochromocytoma, extra adrenal pheochromocytoma, medullary thyroid carcinoma, thyroid C cell hyperplasia)

GroupHPOFreeText: All 9 patients had pheochromocytoma, 2 of the 9 patients (unspecified) also had thyroid C-cell tumors, 1 (unspecified) had medullary thyroid carcinoma, and 1 (unspecified) had C-cell hyperplasia. 3 of the 9 patients (unspecified) also developed extra-adrenal pheochromocytoma.

GroupNotHPOs: HP:0000843; HP:0009711; HP:0010797; HP:0000107; HP:0001737 (Hyperparathyroidism, retinal capillary hemangioma, hemangioblastoma, renal cysts, pancreatic cysts.

GroupNotHPOFreeText: None of the patients had any clinical signs of renal cancer. Two patients (unspecified) were screened for retinal, CNS, and abdominal lesions; neither had occult VHL lesions.

GroupPreviousTesting: RET

PreviouslyPublished: N/A

SupplementalData: N/A

Variant: p.L188V (c.562C>G)

LegacyVariant: c.775C>G

CaseProblemVariantFreeText: N/A

ClinVarID: 2225, https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: CA020488

gnomAD: 0.00002121, https://gnomad.broadinstitute.org/variant/3-10191569-C-G?dataset=gnomad_r2_1

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: L188V (c.562C>G)

MultipleGeneVariants: N/A

PatientID: 7

KindredID: 1

Case: M, Age Unknown, German

DiseaseAssertion: VHL

FamilyInfo: The patient's father (patient 1) was unaffected and did not carry the mutation. The patient's mother (patient 2) presented with pheochromocytoma and carried the mutation. The patient had three siblings; one died and was affected, another (patient 5) had both mutations and presented with pheochromocytoma, and the third (patient 6) was unaffected and carried neither mutation. This patient (patient 7) had a child (patient 9) who also carried both mutations and presented with pheochromocytoma. The patient's uncle (patient 3) carried the mutation and was affected. He had a child with patient (4) who was unaffected. Their child (patient 8) carried both mutations and presented with pheochromocytoma. Patient 8 had two children; one that did not carry the mutation and was unaffected (patient 10) and another that carried both mutations but was disease free (patient 11). See Figure 3 for family pedigree.

CasePresentingHPOs: HP:0002666 (pheochromocytoma)

CaseHPOFreeText: N/A

CaseNotHPOs: N/A

CaseNotHPOFreeText: N/A

CasePreviousTesting: N/A

PreviouslyPublished: 8772572, 7563486

SupplementalData: N/A

Variant: p.L188V (c.562C>G)

LegacyVariant: p.L188V (c.775C>G)

CaseProblemVariantFreeText: N/A

ClinVar: 2225 https://www.ncbi.nlm.nih.gov/clinvar/variation/2225/

CAID: CA020488 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/allele?hgvsOrDescriptor=NM_000551.3%3Ac.562C%3EG

gnomAD: 0.00002121 https://gnomad.broadinstitute.org/variant/3-10191569-C-G

VariantEvidence: N/A

MutationType: missense_variant;transversion

CivicName: P81S (c.241C>T) and L188V (c.562C>G)

MultipleGeneVariants: Germline, VHL, c.241C>T (p.Pro81Ser)