The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_000551.4(VHL):c.273C>A (p.Phe91Leu)

CA16611270

411978 (ClinVar)

Gene: VHL
Condition: von Hippel-Lindau disease
Inheritance Mode: Autosomal dominant inheritance
UUID: d6ad76b6-e4e0-490b-8d57-e1a11cc12139
Approved on: 2024-06-25
Published on: 2024-06-25

HGVS expressions

NM_000551.4:c.273C>A
NM_000551.4(VHL):c.273C>A (p.Phe91Leu)
NC_000003.12:g.10142120C>A
CM000665.2:g.10142120C>A
NC_000003.11:g.10183804C>A
CM000665.1:g.10183804C>A
NC_000003.10:g.10158804C>A
NG_008212.3:g.5486C>A
ENST00000696142.1:c.273C>A
ENST00000696143.1:c.273C>A
ENST00000696153.1:c.273C>A
ENST00000256474.3:c.273C>A
ENST00000256474.2:c.273C>A
ENST00000345392.2:c.273C>A
NM_000551.3:c.273C>A
NM_198156.2:c.273C>A
NM_001354723.1:c.273C>A
NM_001354723.2:c.273C>A
NM_198156.3:c.273C>A

Uncertain Significance

Met criteria codes 4
PS3_Supporting PP3 PM1 PM2_Supporting
Not Met criteria codes 1
PS4

Evidence Links 1

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_000551.3(VHL):c.273C>A (p.Phe91Leu) variant in VHL is a missense variant predicted to cause substitution of phenylalanine by leucine at amino acid 91. This variant has been reported in 2 unrelated probands. Dolfus et al reports a VHL subject with (c.263 G>C; p.F91L) from a family in the French VHL Registry, the individual did not have renal involvement. No further phenotypic description is provided. (PMID: 15300849). Gallou et al (PMID:15300849) reports a VHL subject with retinal hemangioblastomas and (c.273 C>G and p.F91L). Olschwang et al (1998) is likely the same subject as Gallou et al and is not included in the proband count. Two of three participating commercial laboratories reports 4 cases with this variant, however none have VHL-related cancers. Given the sparse phenotypic descriptions in the two publications, and the 4 samples lacking VHL phenotypes from commercial laboratories, the ClinGen VHL VCEP does not recommend applying this code. (PS4_NOT_MET). This variant is absent from gnomAD v4.1.0 (PM2_Supporting). In Tarade et al, an in vitro pVHL-HIFa binding assay followed by immunoblotting showed the the F91L variant abolished all binding to HIF1a and HIF2a (PMID: 31337753)(PS3_Supporting). This variant resides within a region of VHL that is defined as a critical functional domain (the Beta Domain) (PM1). The computational predictor REVEL gives a score of 0.773, which is above the threshold of >=0.664, evidence that correlates with impact to VHL function (PP3). In summary, this variant meets the criteria to be classified as Uncertain 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
PS3_Supporting
In Tarade et al, an in vitro pVHL-HIFa binding assay followed by immunoblotting showed the the F91L variant abolished all binding to HIF1a and HIF2a (PMID: 31337753)(PS3_Supporting).

PP3
The computational predictor REVEL gives a score of 0.773, which is above the threshold of >=0.664, evidence that correlates with impact to VHL function (PP3).
PM1
This variant resides within a region of VHL that is defined as a critical functional domain (the Beta Domain) (PM1).
PM2_Supporting
This variant is absent from gnomAD v4.1.0 (PM2_Supporting).
Not Met criteria codes
PS4
This variant has been reported in 2 unrelated probands. Dolfus et al reports a VHL subject with (c.263 G>C; p.F91L) from a family in the French VHL Registry, the individual did not have renal involvement. No further phenotypic description is provided. (PMID: 15300849). Gallou et al (PMID:15300849) reports a VHL subject with retinal hemangioblastomas and (c.273 C>G and p.F91L). Olschwang et al (1998) is likely the same subject as Gallou et al and is not included in the proband count. Two of three participating commercial laboratories reports 4 cases with this variant, however none have VHL-related cancers. Given the sparse phenotypic descriptions in the two publications, and the 4 samples lacking VHL phenotypes from commercial laboratories, the ClinGen VHL VCEP does not recommend applying this code. (PS4_NOT_MET)
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