Variant classification summary

NM_000551.3:c.241C>T

VHL · NP_000542.1:p.(Pro81Ser) · NM_000551.3

GRCh37: chr3:10183772 C>T · GRCh38: chr3:10142088 C>T

Gene: VHL Transcript: NM_000551.3

Final call

Benign

PS3 supporting PM1 supporting PP3 supporting BA1 stand-alone benign BS1 strong benign BP4 supporting benign BP6 supporting benign

Variant details

Gene

VHL

Transcript

NM_000551.3

Protein

NP_000542.1:p.(Pro81Ser)

gnomAD AF

0.00035259832571862154 (v4.1)

ClinVar

Benign

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000551.3:c.241C>T (p.Pro81Ser) is present in gnomAD v4.1 at an allele frequency of 0.035% (566/1,605,226 alleles, 1 homozygote) with a GroupMax Filtering AF of 0.0428%, exceeding the VHL VCEP BA1 stand-alone benign threshold of 0.0156%.

2

BA1 is met at stand-alone strength, independently establishing this variant as Benign per ACMG/AMP 2015 framework and VHL VCEP specifications. This is concordant with the ClinGen VHL Variant Curation Expert Panel classification of Benign (ClinVar VariationID 2233).

3

The variant also meets BS1 at strong benign strength (grpmax FAF 0.0428% ≥ 0.00156% threshold) and BP4 at supporting benign strength (SpliceAI delta 0.00, no predicted splicing impact).

4

Pathogenic criteria met at supporting strength only: PS3_Supporting (functional data from PMID:23990666 showing VBC complex disruption and HIF1A stabilization; tempered by mild effects in PMID:19228690), PM1_Supporting (located in beta domain at TCEB1/Elongin C binding site), and PP3 (REVEL 0.678 ≥ 0.664). These are insufficient to offset BA1 stand-alone benign evidence.

5

This variant has been observed in COSMIC (n=20 somatic occurrences) and is reported in the literature as a trichloroethylene-associated somatic hotspot in clear cell renal cell carcinoma, but somatic mutation frequency does not alter the germline classification.

Final determination: Rule17 in the ClinGen VHL Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for VHL Version 1.1.0 v1.1.0 criteria-combination framework is satisfied by the adjudicated criteria, so the variant is classified as Benign.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	NM_000551.3:c.241C>T is a missense variant (p.Pro81Ser). PVS1 applies only to null variants (nonsense, frameshift, canonical splice site ±1,2). Per VHL VCEP, PVS1 is reserved for truncating variants after Met54 predicted to undergo NMD, or canonical splice disruptions.	pvs1_gene_context pvs1_variant_assessment cspec
PS1	Not met	No different nucleotide change resulting in the same amino acid substitution (p.Pro81Ser) has been established as pathogenic under VHL VCEP specifications. This exact variant (c.241C>T) has been classified as Benign by the ClinGen VHL Expert Panel, so PS1 does not apply.	clinvar cspec
PS2	Not met	No de novo observation data available for this variant. No proband with confirmed maternity and paternity testing identified in the literature or ClinVar submissions.	clinvar
PS3	Met	Variant-specific functional data from PMID:23990666 demonstrates that P81S VHL disrupts VBC complex interaction (fails to co-immunoprecipitate TCEB1/Elongin C) and stabilizes HIF1A under normoxia in murine ES cells. P81S teratomas showed 3-fold increased volume, reduced apoptosis, and metabolic reprogramming. However, PMID:19228690 found P81S alone has only mild structural effects with preserved HIF-1α regulation in RCC4 cells, indicating partial or context-dependent functional impact. Two independent publications with direct variant testing support PS3 at supporting strength per VCEP rules.	PMID:23990666 PMID:19228690 cspec
PS4	Not met	No proband counting or case-control data available to apply the VHL VCEP PS4 point scoring system. The variant's presence in gnomAD at grpmax FAF 0.0428% (566 alleles, 1 homozygote) argues against significant enrichment in affected individuals.	gnomad_v4 clinvar
PS5	Not assessed	PS5 is a deprecated ACMG criterion; not part of the active VHL VCEP framework.
PM1	Met	The variant is located at codon 81 in the beta domain of VHL (AA 63-155), a key functional domain. Codons 81 and 82 are direct TCEB1 (Elongin C) binding sites critical for VBC E3 ubiquitin ligase complex formation, as confirmed by structural modeling in PMID:23990666. However, cancerhotspots.org does not flag this residue as a statistically significant hotspot, limiting strength to supporting per VCEP rules (PM1_Supporting: <10 instances at the same AA in cancerhotspots.org). COSMIC reports n=20 somatic occurrences, but the VCEP PM1 rule references cancerhotspots.org specifically.	PMID:23990666 cspec
PM2	Not met	gnomAD v4.1 grpmax Filtering AF is 0.00042807 (0.0428%), which exceeds the VHL VCEP PM2_Supporting threshold of ≤0.00000156 (0.000156%). The variant is present in 566 alleles including 1 homozygote in gnomAD v4.	gnomad_v4 cspec
PM5	Not met	No different pathogenic missense variant at the same amino acid residue (P81) has been identified that is classified under VHL VCEP specifications. The PM5 candidate search returned no eligible comparators.	pm5_candidates cspec
PM6	Not met	No de novo observation data (assumed or confirmed) available for this variant. No proband reports in ClinVar submissions or literature indicating de novo occurrence.	clinvar
PP1	Not met	No co-segregation data available for this variant. No family studies with meioses counts identified in the literature or ClinVar submissions.
PP2	N/A	Per VHL VCEP: PP2 is not applicable. VHL is not intolerant to missense variation (gnomAD Z score = -0.39), and there is evidence of benign/common missense variants in VHL.	cspec
PP3	Met	REVEL score 0.678 meets the VHL VCEP PP3 threshold of ≥0.664. This supports a deleterious effect prediction for the missense change p.Pro81Ser.	revel cspec
PP4	N/A	Per VHL VCEP: PP4 is not applicable. The VCEP directs combining phenotype specificity assessment with PS4 to avoid double-counting probands.	cspec
PP5	N/A	Per VHL VCEP: PP5 is not applicable. The ClinGen Sequence Variant Interpretation VCEP Review Committee recommends against use of this criterion.	cspec
BA1	Met	gnomAD v4.1 grpmax Filtering AF is 0.00042807 (0.0428%), which exceeds the VHL VCEP BA1 threshold of ≥0.000156 (0.0156%). The variant is present in 566 of 1,605,226 alleles including 1 homozygote. This allele frequency is incompatible with a highly penetrant autosomal dominant disorder. BA1 at stand-alone strength independently classifies this variant as Benign.	gnomad_v4 cspec
BS1	Met	gnomAD v4.1 grpmax Filtering AF is 0.00042807 (0.0428%), which exceeds the VHL VCEP BS1 threshold of ≥0.0000156 (0.00156%). The variant is too common in the general population to be a cause of VHL disease. Note: BA1 is also met at stand-alone level, which independently establishes benign classification.	gnomad_v4 cspec
BS2	Not met	Although gnomAD v4 contains 1 homozygote for this variant, no phenotype or age data are available for this individual. The VHL VCEP requires at least 3 individuals ≥65 years, unaffected, with full phenotyping and screening (BS2_Strong) or lacking full phenotyping (BS2_Supporting). This threshold is not met.	gnomad_v4 cspec
BS3	Not met	Functional data is conflicting. PMID:23990666 shows P81S disrupts VBC complex interactions and stabilizes HIF1A (supporting a damaging effect), while PMID:19228690 shows that P81S alone preserves near-normal HIF-1α regulation in RCC4 cells with only mild structural perturbation. Net evidence does not clearly demonstrate no damaging effect on protein function, which is required for BS3.	PMID:23990666 PMID:19228690 cspec
BS4	Not met	No lack-of-segregation data available. The VHL VCEP requires observation of lack of segregation in affected members of ≥1 family for BS4_Supporting or ≥2 families for BS4_Strong. No such data were identified.
BP1	N/A	Per VHL VCEP: BP1 is not applicable. Truncating variants account for only a portion of disease-causing variants in VHL; missense variants are a common mechanism of disease.	cspec
BP2	Not met	No evidence of this variant observed in trans with a known pathogenic VHL variant, in homozygous state with phenotype data, or in cis with multiple pathogenic VHL variants. The gnomAD homozygote lacks clinical phenotype data.	gnomad_v4
BP3	N/A	In-frame insertions/deletions in repetitive regions. This is a missense substitution; not applicable per VCEP (BP3 applies only to the 8x GXEEX repeat motif at AA14-AA48 in VHL p30).
BP4	Met	SpliceAI max delta score is 0.00 (≤0.1), indicating no predicted splicing impact. Per VHL VCEP, BP4 can be applied to assess lack of splicing impact with SpliceAI ≤0.1. Missense predictors are explicitly excluded from BP4 per VCEP rules.	spliceai cspec
BP5	Not met	No evidence of co-occurrence with a pathogenic variant in a different gene that fully explains the patient's phenotype, per VHL VCEP BP5 requirements.
BP6	Met	Expert panel ClinGen VHL Variant Curation Expert Panel, ClinGen classified as Benign.	cspec clinvar
BP7	N/A	Missense variant. Per VHL VCEP, BP7 applies only to silent or intronic variants where BP4 is met for lack of splice effect and PhyloP ≤0.2.	cspec

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