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.461C>G (p.Pro154Arg)

CA351754408

560745 (ClinVar)

Gene: VHL
Condition: von Hippel-Lindau disease
Inheritance Mode: Autosomal dominant inheritance
UUID: b1c24a0b-a9ea-40fd-89e4-000a085e03df
Approved on: 2024-06-25
Published on: 2024-06-25

HGVS expressions

NM_000551.4:c.461C>G
NM_000551.4(VHL):c.461C>G (p.Pro154Arg)
NC_000003.12:g.10146634C>G
CM000665.2:g.10146634C>G
NC_000003.11:g.10188318C>G
CM000665.1:g.10188318C>G
NC_000003.10:g.10163318C>G
NG_008212.3:g.10000C>G
ENST00000696142.1:c.*138C>G
ENST00000696143.1:c.600-3153C>G
ENST00000696153.1:c.461C>G
ENST00000256474.3:c.461C>G
ENST00000256474.2:c.461C>G
ENST00000345392.2:c.341-3153C>G
ENST00000477538.1:n.597C>G
NM_000551.3:c.461C>G
NM_198156.2:c.341-3153C>G
NM_001354723.1:c.*18-3153C>G
NM_001354723.2:c.*18-3153C>G
NM_198156.3:c.341-3153C>G

Uncertain Significance

Met criteria codes 2
PP3 PM1
Not Met criteria codes 3
BS1 PS4 PM5

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 variant NM_000551.3(VHL):c.461C>G (p.Pro154Arg) is a missense variant predicted to cause substitution of Proline by Arginine. This variant is in the nuclear export domain, a critical functional domain of VHL (PM1). The computational predictor REVEL gives a score of 0.942, which is above the threshold of >0.664, evidence that correlates with impact to VHL function (PP3). One subject age 40-45 is reported with paraganglioma (0.5 points). Of three commercial laboratories, two report no subjects with this variant. One laboratory reports two women in 60s and 70s with breast cancer (non-VHL related cancers), both having had multi-cancer and common cancer panels run. There is no further detail on phenotype/screening for VHL related phenotypes. Therefore the PS4 code is not met. The GroupMax Filtering Allele Frequency (95% CI) in gnomAD v4.1.0 is 0.00001425 (4/86248 from South Asian Population). This is lower than the ClinGen VHL VCEP threshold expected for VHL disease, of >=0.0000156 (0.00156%) for BS1, and therefore does not meet any criterion (BS1, BA1, PM2_Supporting are not met). Three other variants are reported in ClinVar at this position: Pro154Ala, Pro154Ser and Pro154Leu. All have Chuvash polycythemia and VHL as listed conditions. However, only Pro154Leu is reported as Pathogenic. Proline to Leucine is a distance of 98 and Proline to Arginine is a distance of 103 based on Grantham's table (1974). The Arginine substitution has a larger Grantham distance than Leucine. At this time the VHL VCEP has not classified Pro154Leu, and PM5 is not met. In summary, this variant meets the criteria to be classified as Uncertain for autosomal-dominant von Hippel Lindau syndrome (VHL syndrome) 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
PP3
The computational predictor REVEL gives a score of 0.942, which is above the threshold of >0.664, evidence that correlates with impact to VHL function (PP3).
PM1
This variant is in the nuclear export domain, a critical functional domain of VHL.
Not Met criteria codes
BS1
The GroupMax Filtering Allele Frequency (95% CI) in gnomAD v4.1.0 is 0.00001425 (4/86248 from South Asian Population). This is lower than the ClinGen VHL VCEP threshold expected for VHL disease, of >=0.0000156 (0.00156%) for BS1, and therefore does not meet any criterion (BS1, BA1, PM2_Supporting are not met).
PS4
One subject age 40-45 reported with paraganglioma (0.5 points). Of three commercial laboratories, two report no subjects with this variant. One laboratory two women in 60s and 70s with breast cancer (non-VHL related cancers), both having had multi-cancer and common cancer panels run. There is no further detail on phenotype/screening for VHL related phenotypes.
PM5
Proline to Leucine is a distance of 98 and Proline to Arginine is a distance of 103 based on Grantham's table (1974). The Arginine substitution has a larger grantham distance than Leucine, and P154L is a pathogenic variant in ClinVar. However, it has not been interpreted by the VHL VCEP at this time.
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