The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computer assertion could be determined for this classification!


Variant: NM_000551.4(VHL):c.194C>G (p.Ser65Trp)

CA020099

43597 (ClinVar)

Gene: VHL
Condition: von Hippel-Lindau disease
Inheritance Mode: Autosomal dominant inheritance
UUID: ae2d00be-c3ab-49cd-a347-b1fd19800735
Approved on: 2024-06-25
Published on: 2024-06-25

HGVS expressions

NM_000551.4:c.194C>G
NM_000551.4(VHL):c.194C>G (p.Ser65Trp)
NC_000003.12:g.10142041C>G
CM000665.2:g.10142041C>G
NC_000003.11:g.10183725C>G
CM000665.1:g.10183725C>G
NC_000003.10:g.10158725C>G
NG_008212.3:g.5407C>G
ENST00000696142.1:c.194C>G
ENST00000696143.1:c.194C>G
ENST00000696153.1:c.194C>G
ENST00000256474.3:c.194C>G
ENST00000256474.2:c.194C>G
ENST00000345392.2:c.194C>G
NM_000551.3:c.194C>G
NM_198156.2:c.194C>G
NM_001354723.1:c.194C>G
NM_001354723.2:c.194C>G
NM_198156.3:c.194C>G

Pathogenic

Met criteria codes 6
PS4 PP3 PM1 PM6 PM2_Supporting PS3_Supporting
Not Met criteria codes 2
BA1 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen VHL Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VHL Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
VHL VCEP
The NM_000551.4(VHL):c.194C>G (p.Ser65Trp) variant in VHL is a missense variant predicted to cause substitution of Ser by Trp at amino acid 65 (p.Ser65Trp).The CIViC database (https://civicdb.org) describes 17 unrelated individuals with clinically diagnosed VHL or cancers in VHL cancer spectrum, many with evidence of VHL in family history. The following PMIDs were used for proband counting (2 unrelated probands or families where noted, all others 1) 28650583(2pt), 17024664, 17392848, 28388566(2pt), 29294023(2pt), 22156657, 23407287, 9829911, 7728151, 18446368, 22357542, 11148816, 21463266, 20518900. In addition, 3 participating laboratories contributed a total of 5 unique subjects. Each subject was evaluated for meeting Danish, Consistent or Nonspecific and a total of 13.5 points was awarded, which constitutes strong evidence. (PS4_Met). A denovo case, 33yo Chinese man presented with Renal Cell Carcinoma, and had a history of urological surgery at the age of 23 years due to an epididymal cyst and an ophthalmologic surgery at 26 years of age for retinal detachment resulting from bilateral retinal angiomatosis. 7 relatives (parents and siblings) were tested for S65W, and it was not identified. The authors do not note confirming maternity/paternity. PMID: 26622630 (PM6_Met). There is one variant present in gnomAD v4.1.0. The GroupMax Filtering Allele Frequency (95% CI) in gnomAD v4.1.0 is not calculated. PM2_Supporting can be applied for variants with <= 0.0000015 (0.00015%) frequency in gnomAD, or if no GroupMax Filtering Allele Frequency is calculated (due to a single variant present) (PM2_Supporting). S65W significantly decreases the VHL protein binding to HIF-1alpha, preventing ubiquitination PMID: 15611064 (PS3_Supporting). This variant resides within the VHL beta domain, a key functional domain. It is also defined as a mutational hotspot in Chinese populations (PMID:31620170) (PM1_Met). The computational predictor REVEL gives a score of 0.943, which is above the threshold of >0.664, evidence that correlates with impact to VHL function (PP3_Met). In summary, this variant meets the criteria to be classified as Pathogenic for autosomal-dominant von Hippel-Lindau disease (VHL disease) based on the ACMG/AMP criteria applied, as specified by the ClinGen VHL VCEP Version 1.0 (Specifications approval date: 02/26/2024. Variant Approval Date 06/25/2024).
Met criteria codes
PS4
The CIViC database (https://civicdb.org) describes 17 unrelated individuals with clinically diagnosed VHL or cancers in VHL cancer spectrum, many with evidence of VHL in family history. The following PMIDs were used for proband counting (2 unrelated probands or families where noted, all others 1) 28650583(2pt), 17024664, 17392848, 28388566(2pt), 29294023(2pt), 22156657, 23407287, 9829911, 7728151, 18446368, 22357542, 11148816, 21463266, 20518900. In addition, 3 participating laboratories contributed a total of 5 unique subjects. Each subject was evaluated for meeting Danish, Consistent or Nonspecific and a total of 13.5 points was awarded, which constitutes strong evidence. (PS4_Met).
PP3
The computational predictor REVEL gives a score of 0.943, which is above the threshold of >0.664, evidence that correlates with impact to VHL function (PP3_Met).
PM1
This variant resides within the VHL beta domain, a key functional domain. It is also defined as a mutational hotspot in Chinese populations (PMID:31620170) (PM1_Met).
PM6
A denovo case, 33yo Chinese man presented with Renal Cell Carcinoma, and had a history of urological surgery at the age of 23 years due to an epididymal cyst and an ophthalmologic surgery at 26 years of age for retinal detachment resulting from bilateral retinal angiomatosis. 7 relatives (parents and siblings) were tested for S65W, and it was not identified. The authors do not note confirming maternity/paternity. PMID: 26622630 (PM6_Met)
PM2_Supporting
There is one variant present in gnomAD v4.1.0. The GroupMax Filtering Allele Frequency (95% CI) in gnomAD v4.1.0 is not calculated. PM2_Supporting can be applied for variants with <= 0.0000015 (0.00015%) frequency in gnomAD, or if no GroupMax Filtering Allele Frequency is calculated (due to a single variant present) (PM2_Supporting).
PS3_Supporting
S65W significantly decreases the VHL protein binding to HIF-1alpha, preventing ubiquitination PMID: 15611064 (PS3_Supporting)
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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