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Variant interpretation report

VHL c.541G>A, p.(Val181Ile)

NM_000551.4:c.541G>A NP_000542.1:p.(Val181Ile) Missense · exon 3 View identifiers
Classification
Uncertain significance

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is uncertain. Select a step to read what it means.

Uncertain.The recorded classification is uncertain significance.

In plain language

Gene-level background from the recorded interpretation.

About VHL

VHL encodes a protein that tags other proteins for destruction, most notably the hypoxia-inducible factor (HIF), which regulates how cells respond to oxygen levels; it also plays roles in cilia formation, cytokine signaling, and other cellular processes. Inherited changes in this gene cause von Hippel-Lindau syndrome, which predisposes to renal cell carcinoma, pheochromocytoma, hemangioblastomas, and related tumors. The gene acts as a tumor suppressor: when it is lost or inactivated, HIF accumulates and drives blood-vessel growth and tumor formation even under normal oxygen conditions.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is ClinGen VHL VCEP v1.1. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 1 Benign evidence criteria: 0
Pathogenic criteria applied · 1
PM1Moderate
PM1 · moderate

Met (Moderate): codon 181 lies in the pVHL alpha domain (residues 156-192), a key functional domain for Elongin C binding.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Uncertain significance

Only PM1 (moderate) is met; no VHL VCEP v1.1 rule partition is satisfied by a single moderate criterion, yielding VUS.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
5 / 1,614,186 alleles

gnomAD v4.1: 5 / 1,614,186 alleles. Recorded AF 3.09754e-06. Recorded homozygote count 0.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.97744e-06; MAF= 0.00040%, 1/251418 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26669e-05; MAF= 0.00327%, 1/30612 alleles, homozygotes = 0).

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

No screenshot for this evidence
REVEL score
0.431 recorded score

Recorded REVEL score: 0.431. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied
ClinVar submissions
7 reported laboratory submissions

5 Uncertain significance · 1 Uncertain Significance · 1 Likely benign. ClinVar API review status: criteria provided, conflicting classifications.

Context only ClinVar ↗
Functional evidence
Statement recorded

OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. VHL, an E3 ubiquitin ligase, is frequently mutated in renal cell carcinomas.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
1 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV56543552, n = 1 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

ACMG/AMP criteria under ClinGen VHL VCEP v1.1, with the data and sources behind each one.

28 criteria with recorded statuses: 1 met · 5 not met · 12 not assessed · 10 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Met Not met Not assessed Not applicable

Variant NM_000551.4:c.541G>A / NP_000542.1:p.(Val181Ile) is a canonical missense single-nucleotide substitution with no change in protein length, no truncation, and no splice or NMD implication.

The VHL VCEP specification (cspec v1.1) scopes PVS1 to null-variant classes, PM4 to in-frame indels/stop-loss extensions, and BP3 to in-frame indels within a specific N-terminal repeat motif -- none of which describe this substitution, so all three criteria in this group are not_applicable rather than not_met.

Governing framework: ClinGen VHL Expert Panel Specifications v1.1 (cspec), used in preference to generic ACMG/AMP for all five criteria in this group.

PS1 not met: p.(Val181Ile) itself is not an established VCEP-based pathogenic classification (ClinVar VariationID 238111 = Uncertain significance, no expert-panel entry).

PM1 met at Moderate: codon 181 lies within the VCEP-defined alpha domain (AA 156-192, Elongin C binding), a key functional domain, independent of the somatic-hotspot arm which is not met (COSMIC n=1; no cancerhotspots.org hit).

PM5 left not_assessed: automated same-residue comparator search failed (HTTP 429) before completion; genuine absence of a qualifying comparator could not be confirmed.

PP2 and BP1 are both explicitly marked Not Applicable to VHL by the governing VCEP specification and were not assessed further.

No wet-lab functional assay evidence (HIF1/2a degradation, VBC/VCB complex stability, or ECM/fibronectin binding) specific to VHL c.541G>A / p.(V181I) was located in the case bundle's vcep_materials.json, evidence.json, literature_pass.json, or paper_extracts.json.

The only variant-specific literature hit, PMID:18195360, is a computational molecular-dynamics stability simulation of a designed mutant, not an accepted experimental assay type under the VHL VCEP PS3/BS3 specification, and lacks the Brnich et al. control documentation required to weight strength.

Both PS3 and BS3 are therefore returned as not_assessed pending identification of a validated functional assay for this specific variant.

This variant (NM_000551.4:c.541G>A, p.Val181Ile) is a missense substitution, so BP7 (synonymous/intronic-only per VHL VCEP) is not applicable.

PP3 fails on both VCEP-specified paths: missense REVEL=0.431 (<0.664 threshold) and splice SpliceAI max delta=0.014 (<0.5 threshold) -> not_met.

BP4 is withheld pending VarSeak data: the VHL VCEP explicitly forbids using missense predictors (REVEL/BayesDel) for BP4 in this gene, and the sole permitted splice path requires SpliceAI AND VarSeak concordance; only SpliceAI (0.014, satisfying <=0.1) is available in this case's evidence bundle, so BP4 is not_assessed with a flagged gap rather than applied on partial evidence.

BayesDel score (0.0210198) is present in source data but has no verified published calibration threshold available to this pipeline per standing policy, and is independently barred from BP4 use by the VCEP's missense-predictor prohibition for VHL.

Met · 1

PM1 ModerateMet (Moderate): codon 181 lies in the pVHL alpha domain (residues 156-192), a key functional domain for Elongin C binding. Details ▾Hide ▴
Reasoning

VHL VCEP v1.1 PM1 applies at Moderate strength to putative missense variants that are known germline hotspots and/or lie in key functional domains and/or are somatic hotspots with >=10 same-AA instances in cancerhotspots.org. Codon 181 falls within the pVHL alpha (α) domain (AA 156-192), which the same VCEP specification designates a key functional domain responsible for Elongin C binding (critical for VBC complex assembly and HIF regulation). This domain placement alone qualifies for PM1_Moderate under the VCEP wording ('...AND/OR in key functional domains'). The somatic-hotspot arm of the rule is not met: cancerhotspots.org returned no statistically significant hotspot at V181, and COSMIC records only a single somatic occurrence (COSV56543552, n=1), well below the >=10-instance threshold, so the somatic-count pathway does not independently support this criterion.

Rule
VHL VCEP v1.1 PM1_Moderate: applies to missense variants in known germline hotspots and/or key functional domains and/or somatic hotspots with >=10 same-AA cancerhotspots.org instances.
Evidence considered
  • VHL VCEP v1.1 PM1 rule: 'Putative missense variants that are known germline hotspots AND/OR in key functional domains AND/OR somatic variants that have >=10 instances for the same AA in cancerhotspots.org.'
  • VHL VCEP v1.1 domain definitions (cited under PM4/PVS1 sections of the same specification): Alpha (α) domain spans AA 155/156-192 and mediates Elongin C binding, a function critical for VBC complex (VHL-Elongin B-Elongin C-Cullin2-RBX1) assembly; codon 181 (Val181) lies within this alpha domain.
  • cancerhotspots.org query 'VHL V181' returned search_status 'no_result' / found=false, with evidence_sentence: 'This variant does not lie in a statistically significant hotspot.'
  • COSMIC record COSV56543552 shows only 1 somatic occurrence for this variant, far below the VCEP's >=10-instance cancerhotspots.org threshold, so the somatic-hotspot arm of PM1 is not satisfied on its own.
Still missing
  • Confirm with a human reviewer whether the VCEP intends codon-level granularity within the alpha domain (e.g., core Elongin C-binding subregion 157-172 vs the broader 156-192 domain) to qualify for PM1, since V181 lies in the broader alpha domain but outside the narrower 157-172 Elongin C-binding core cited elsewhere in the same specification.
Sources

Not met · 5 · evaluated, threshold not reached

PS1 Not met: ClinVar classifies p.(Val181Ile) itself as uncertain significance, with no VCEP-based pathogenic interpretation of the identical change. Details ▾Hide ▴
Reasoning

VHL VCEP v1.1 restricts PS1 to variants with the identical amino acid change (p.Val181Ile) already interpreted by the VHL VCEP, or established as pathogenic using VHL VCEP specifications. ClinVar (VariationID 238111) shows p.(Val181Ile) itself is currently Uncertain significance with no expert-panel or VCEP-based pathogenic interpretation. No other source (literature, PM5 comparator search) identified a prior VCEP-based pathogenic classification of the same amino acid change. PS1 requirements are therefore not satisfied.

Rule
VHL VCEP v1.1 PS1: Pathogenic Strong when the identical amino-acid change has been interpreted by the VHL VCEP or established as pathogenic using VHL VCEP specifications.
Evidence considered
  • VHL VCEP v1.1 PS1 rule: 'Applied only to variants with interpretation by the VHL VCEP or by a variant with pathogenicity established using VHL VCEP specifications.'
  • ClinVar VariationID 238111 (NM_000551.4(VHL):c.541G>A / p.Val181Ile) is itself classified Uncertain significance by 6 usable submissions, with no VHL VCEP or expert-panel entry, so the same amino-acid change has not been independently established as pathogenic under VCEP specifications.
Sources
PM2 Not met: gnomAD v4 GroupMax FAF is 3.65e-06 (0.000365%), exceeding the permitted PM2 threshold of 0.000156%. Details ▾Hide ▴
Reasoning

PM2 is not met under the VHL Expert Panel specification. PM2 Supporting requires the variant to be absent from gnomAD or to have gnomAD v4 GroupMax Filtering Allele Frequency <=0.00000156 (0.000156%); the variant is present and has GroupMax FAF 3.65e-06 (0.000365%), exceeding the permitted threshold.

Rule
Use PM2 Supporting when the variant is absent from gnomAD or gnomAD v4 GroupMax Filtering Allele Frequency is <=0.00000156 (0.000156%); if no GroupMax FAF is calculated, PM2 Supporting may also apply.
Evidence considered
  • ClinGen VHL Expert Panel Specification v1.1: PM2 Supporting applies when the variant is absent from gnomAD or has gnomAD v4 GroupMax Filtering Allele Frequency <=0.00000156 (0.000156%); if no GroupMax FAF is calculated, PM2 Supporting may also apply.
  • gnomAD v4.1 detects the variant in 5/1,614,186 alleles, with zero homozygotes, and reports GroupMax FAF 3.65e-06 (0.000365%). A GroupMax FAF is available and is greater than the VCEP PM2 threshold.
  • The variant is therefore neither absent nor sufficiently rare under the VCEP-specific PM2 rule; the absence of homozygotes does not rescue PM2.
Sources
PP3 Not met: REVEL scores 0.431, below the required 0.664 threshold, and SpliceAI max delta is 0.014 versus the 0.5 splice threshold. Details ▾Hide ▴
Reasoning

VHL VCEP (cspec v1.1) specifies two independent PP3 paths. Missense path: REVEL >=0.664 required; this variant (NM_000551.4:c.541G>A, p.Val181Ile) scores REVEL=0.431 (local REVEL v1.3 lookup), below threshold, so PP3 is not met via the missense path. Splice path: requires concordance of SpliceAI (>0.5) AND VarSeak (class 4 or 5); SpliceAI max delta score for this variant is 0.014 (SpliceAI Lookup), far below the 0.5 threshold, so the splice path also fails regardless of VarSeak availability. Both VCEP-specified paths for PP3 are unmet.

Rule
PP3_supporting (VHL VCEP cspec v1.1)
Evidence considered
  • VHL VCEP cspec v1.1 PP3 rule: 'For missense variants, use REVEL score >=0.664. For splice variants, concordance of Splice AI (>0.5) and VarSeak (class 4 or class 5).'
  • Local REVEL v1.3 predictor lookup: REVEL score = 0.431 for NM_000551.4:c.541G>A (p.Val181Ile), below the VCEP's 0.664 missense threshold.
  • SpliceAI Lookup: max delta score = 0.014 for this variant, far below the VCEP's 0.5 splice-path threshold for PP3.
Sources
BA1 Not met: gnomAD GroupMax FAF 3.65e-06 (0.000365%) is far below the BA1 threshold of 0.0156%. Details ▾Hide ▴
Reasoning

BA1 is not met. The VHL Expert Panel specifies BA1 at a gnomAD v4 GroupMax Filtering Allele Frequency of >=0.000156 (0.0156%). The observed gnomAD v4 GroupMax FAF is 3.65e-06 (0.000365%), well below the threshold.

Rule
Use BA1 when gnomAD v4 GroupMax Filtering Allele Frequency is >=0.000156 (0.0156%).
Evidence considered
  • ClinGen VHL Expert Panel Specification v1.1: BA1 requires gnomAD v4 GroupMax Filtering Allele Frequency >=0.000156 (0.0156%).
  • gnomAD v4.1 reports GroupMax FAF 3.65e-06 (0.000365%), with total AF 3.09754e-06 from 5/1,614,186 alleles and no homozygotes; the maximum observed population AF is 2.19597e-05 in South Asians, also below BA1.
  • The gnomAD v4 value is far below the BA1 cutoff; no threshold or ancestry artifact supports applying BA1.
Sources
BS1 Not met: gnomAD GroupMax FAF 3.65e-06 (0.000365%) is below the BS1 threshold of 0.00156%. Details ▾Hide ▴
Reasoning

BS1 is not met. The VHL Expert Panel specifies BS1 at a gnomAD v4 GroupMax Filtering Allele Frequency of >=0.0000156 (0.00156%). The observed gnomAD v4 GroupMax FAF is 3.65e-06 (0.000365%), below the threshold.

Rule
Use BS1 when gnomAD v4 GroupMax Filtering Allele Frequency is >=0.0000156 (0.00156%).
Evidence considered
  • ClinGen VHL Expert Panel Specification v1.1: BS1 requires gnomAD v4 GroupMax Filtering Allele Frequency >=0.0000156 (0.00156%).
  • gnomAD v4.1 reports GroupMax FAF 3.65e-06 (0.000365%), below the BS1 cutoff; the highest observed population AF is 2.19597e-05 in South Asians, but the VCEP rule uses GroupMax FAF rather than an unfiltered subgroup AF.
  • The variant is observed at low frequency in multiple ancestry groups and has no homozygotes, but its GroupMax FAF does not reach the VCEP BS1 threshold.
Sources

Not assessed · 12 · no assessment recorded

PS2 Not assessed: no de novo observation, parental confirmation, or family history is documented, so PS2 cannot be assigned. Details ▾Hide ▴
Reasoning

No proband-level de novo observation is documented in the case-evidence bundle. Maternity and paternity confirmation, phenotype classification, and absence of a VHL family history are not available, so PS2 cannot be assigned.

Rule
Use the VHL VCEP PS2 scoring system: 0.5 supporting, 1 moderate, 2 strong, and 4 very strong points; a single proband cannot receive very strong strength, and PS2 requires confirmed maternity and paternity.
Evidence considered
  • The VHL VCEP specification requires de novo scoring using 0.5/1/2/4 points according to phenotype specificity and requires both maternity and paternity confirmation for PS2.
  • The consolidated case-evidence bundle contains no documented proband, parental testing, maternity/paternity confirmation, or de novo observation for NM_000551.4:c.541G>A (p.Val181Ile).
Still missing
  • Proband-level clinical phenotype and VHL Danish-criteria assessment
  • Molecular confirmation that the variant is absent in both parents
  • Independent confirmation of maternity and paternity
  • Documented absence of VHL family history and required negative testing where applicable
Sources
PS3 Not assessed: only an in-silico molecular-dynamics simulation (PMID:18195360) exists; no VCEP-accepted functional assay (HIF degradation, VBC stability, ECM/fibronectin binding) is available. Details ▾Hide ▴
Reasoning

The VHL VCEP specifies PS3 requires acceptable functional assays (HIF1/2a degradation assay, VBC complex stability assay, or ECM formation/fibronectin binding assay), evaluated per the Brnich et al. control workflow (PMID:31892348) to reach PS3_Supporting/Moderate. No such wet-lab functional assay data for VHL c.541G>A (NP_000542.1:p.(V181I)) was found anywhere in the case bundle (evidence.json, literature_pass.json, vcep_materials.json, paper_extracts.json). The only variant-specific literature hit is PMID:18195360, which reports 10-ns molecular-dynamics simulations of unbound pVHL stability for a computationally designed V181I mutant -- this is an in-silico structural stability prediction, not one of the VCEP-accepted experimental assay types (HIF1/2a degradation, VBC complex stability, or ECM/fibronectin binding), and it reports no experimental functional readout, biological replicates, or positive/negative controls as required by the Brnich workflow. It therefore cannot be used to support PS3.

Rule
VHL VCEP cspec v1.1 PS3: Acceptable assays are HIF1/2a degradation, VBC/VCB complex stability, and ECM/fibronectin binding assays, applied via the Brnich et al. (PMID:31892348) control-scoring workflow (10 controls for Supporting, 11 for Moderate).
Evidence considered
  • vcep_materials.json summarizes VBC-complex-form-stability and HIF1/2a-degradation assay tables from the VHL_Functional_Assay_SVI_documentation.xlsx but these catalog general assay/PMID pairs (e.g. Rechsteiner 2011 PMID:21715564, Clifford 2001 PMID:11331613) and do not list p.(V181I)/c.541G>A as a tested variant
  • PMID:18195360 (paper_extracts.json): molecular-dynamics simulation found V181I 'more stable than wild type' pVHL among five designed mutants, but this is a computational stability prediction with no experimental HIF1/2a, VBC, or fibronectin/ECM readout and no Brnich-style controls, so it does not meet the VCEP's accepted PS3 assay definition
Still missing
  • No HIF1/2a degradation assay data for p.(V181I)
  • No VBC/VCB complex stability assay data for p.(V181I)
  • No ECM formation/fibronectin binding assay data for p.(V181I)
  • PMID:18195360 is a computational MD simulation, not an accepted VCEP functional assay type, and lacks documented controls/replicates
Sources
PS4 Not assessed: no scored probands, phenotype details, or case-control enrichment data are available for p.(Val181Ile). Details ▾Hide ▴
Reasoning

PS4 cannot be assigned because the VHL Expert Panel requires cumulative proband-table points, and the available evidence supplies no scored affected probands, phenotype details, or case-control enrichment data for p.(Val181Ile).

Rule
VHL VCEP v1.1 PS4: apply only from the total in the VHL Proband Scoring Tables (Supporting 1 point; Moderate 2-4; Strong 5-15; Very Strong at least 16).
Evidence considered
  • The VHL Expert Panel specifies PS4 by total proband points: 1 point (Supporting), 2-4 points (Moderate), 5-15 points (Strong), and at least 16 points (Very Strong).
  • PMID:18195360 explicitly modeled V181I in molecular-dynamics simulations but reports no patient-level observation; it therefore contributes no VHL PS4 proband points or case-control enrichment data.
Still missing
  • Variant-specific affected-proband data with phenotype assignments sufficient for the VHL PS4 Proband Scoring Tables.
  • A case-control enrichment analysis or other denominator-based enrichment evidence for p.(Val181Ile).
Sources
PM5 Not assessed, flagged for human review: no alternate V181 missense with an established pathogenic classification was confirmed, and the ClinVar comparator search did not complete. Details ▾Hide ▴
Reasoning

VHL VCEP v1.1 PM5 requires a different missense change at the same residue (V181) with pathogenicity established by the VHL VCEP or under VCEP specifications, with the observed change (V181I) at an equal-or-greater Grantham distance than the classified comparator, and splice metapredictors excluding a splicing effect. The automated same-residue comparator search (pm5_candidates.json) targeted this exact logic but failed to complete: it returned 'total_candidates_seen: 5' with 'same_residue_candidates: 0' and an explicit tool error 'HTTP Error 429: Too Many Requests', so the candidate harvesting from ClinVar for alternate V181 missense changes did not run to completion. No same-residue comparator variant (e.g., p.Val181X other than Ile) with an established VCEP pathogenic classification was identified in the bundle. Given the search failure rather than a confirmed negative result, this criterion cannot be reliably called not_met and is left not_assessed pending a manual same-residue ClinVar/literature search.

Rule
VHL VCEP v1.1 PM5_Moderate: same-residue alternate missense change with VCEP-established pathogenicity and Grantham distance >= the comparator variant; splice metapredictors must exclude a splicing effect.
Evidence considered
  • VHL VCEP v1.1 PM5 rule: pathogenicity of the prior variant at the same residue must be established by VHL VCEP interpretation or VCEP specifications; Grantham distance of the variant under consideration must be equal or larger; splice metapredictors should exclude a splicing effect.
  • pm5_candidates.json automated harvest: pm5_mode 'classic_same_residue_missense', eligible_for_classic_pm5_search=true, total_candidates_seen=5, same_residue_candidates=0, recommendation level 'no_useful_candidates_found', with explicit tool error 'HTTP Error 429: Too Many Requests' indicating the search did not fully complete rather than confirming a true absence of comparators.
Still missing
  • PM5 same-residue comparator search (pm5_candidates.json) failed with HTTP 429 (Too Many Requests) before completing; a manual ClinVar/literature query for other pathogenic missense variants at VHL codon 181 (e.g., p.Val181Gly/Glu/Ala/etc.) is needed to properly adjudicate PM5.
  • If a qualifying comparator is found, Grantham distance between the comparator's substituted residue and Val, versus Ile and Val, must be compared per the VCEP rule (Grantham 1974, Table 2) and splice metapredictor results must confirm no splicing effect for c.541G>A.
Sources
pm5_candidatescspec ↗
PM6 Not assessed: no de novo proband or parental-testing result is documented to support a de novo score. Details ▾Hide ▴
Reasoning

No assumed de novo proband or parental testing result is documented in the case-evidence bundle. Therefore, there is no basis to calculate the VHL-specific half-point de novo score for unconfirmed maternity and/or paternity.

Rule
See VHL VCEP PS2 scoring; assumed de novo receives half the points of maternity- and paternity-confirmed de novo evidence, and PM6 strength is determined from the resulting aggregate points.
Evidence considered
  • The VHL VCEP states that assumed de novo observations without confirmed maternity and paternity are scored through PM6 using half the corresponding PS2 points.
  • The consolidated case-evidence bundle contains no documented assumed de novo observation, parental testing, or proband phenotype for this variant.
Still missing
  • A documented de novo proband observation
  • Parental genotypes and whether maternity and paternity were confirmed
  • Proband phenotype specificity under the VHL Danish-criteria framework
  • Number of independent probands if aggregating PM6 evidence
Sources
PP1 Not assessed: no affected relatives, informative meioses, or phenotype-confirmed segregation data are documented. Details ▾Hide ▴
Reasoning

No affected relatives carrying the variant, informative meioses, pedigrees, or phenotype-confirmed VHL segregation data are documented. PP1 cannot be assigned or strength-calibrated.

Rule
VHL VCEP PP1: supporting for 3–4 meioses across at least 1 family, moderate for 5–6 meioses across at least 1 family, and strong for more than 7 meioses across at least 2 families; phenotype must be highly consistent with VHL Danish Criteria.
Evidence considered
  • The VHL VCEP permits PP1 only when the phenotype is highly consistent with VHL and specifies 3–4 meioses for supporting, 5–6 meioses for moderate, and more than 7 meioses across at least 2 families for strong evidence.
  • The consolidated case-evidence bundle contains no pedigree, relative genotypes, segregation observations, or meiosis count for this variant.
Still missing
  • Pedigree with variant status for affected and unaffected relatives
  • VHL Danish-criteria phenotype documentation for affected relatives
  • Count of informative meioses
  • Evidence that segregation observations are independent and not duplicated
Sources
BS2 Not assessed: no three eligible carriers aged 65 or older with absence of VHL-related cancers are documented. Details ▾Hide ▴
Reasoning

BS2 cannot be assessed from the available case evidence. The VHL Expert Panel requires at least 3 individuals, all >=65 years old, unaffected, carrying the same variant, with full phenotyping and screening for absence of VHL-related cancers for BS2 Strong; a Supporting application requires the same age and count criteria without full screening but with no noted VHL-related cancers. The bundle provides gnomAD homozygote counts of zero but does not identify three eligible older carriers or provide their age, phenotype, screening, or cancer histories.

Rule
BS2 Strong: at least 3 unaffected carriers, all >=65 years old, with full phenotyping and screening showing no VHL-related cancers. BS2 Supporting: at least 3 carriers, all >=65 years old, with no noted VHL-related cancers but without full phenotyping and screening.
Evidence considered
  • ClinGen VHL Expert Panel Specification v1.1: BS2 Strong requires at least 3 unaffected individuals all >=65 years old with full phenotyping and screening for absence of VHL-related cancers; BS2 Supporting requires at least 3 individuals all >=65 years old with no noted VHL-related cancers but lacking full phenotyping and screening.
  • gnomAD v4.1 reports zero homozygotes for the variant, but this is not equivalent to three unaffected carriers aged >=65 years and provides no required individual-level clinical screening data.
Still missing
  • No documented set of at least 3 carriers aged >=65 years with the variant.
  • No individual-level phenotype, VHL-related cancer screening, or cancer-history information sufficient to distinguish BS2 Strong from BS2 Supporting.
  • Absence of homozygotes in gnomAD does not establish BS2, which concerns unaffected older individuals carrying the variant.
Sources
BS3 Not assessed: no VCEP-accepted functional assay data exist; only a computational stability simulation (PMID:18195360) is available. Details ▾Hide ▴
Reasoning

The VHL VCEP specifies BS3_Supporting when an HIF1/2a degradation assay replicates WT function, VBC complex stability is unaffected, and/or ECM formation/fibronectin binding is unaffected, following the same Brnich et al. controls framework as PS3. No such wet-lab functional assay data for VHL c.541G>A (NP_000542.1:p.(V181I)) was found in the case bundle. The only variant-specific study, PMID:18195360, is a computational MD stability simulation of a designed V181I mutant reporting increased structural stability relative to wild-type pVHL; this is not one of the VCEP-accepted assay readouts (HIF degradation, VBC stability, ECM/fibronectin binding) and reports no experimental normal-function replication, so it cannot be used to support BS3.

Rule
VHL VCEP cspec v1.1 BS3: BS3_Supporting when HIF1/2a assay replicates WT function and/or VBC complex stability is unaffected and/or ECM formation/fibronectin binding is unaffected, per the Brnich et al. (PMID:31892348) controls framework; for splicing variants RNA assays must show no splicing impact.
Evidence considered
  • vcep_materials.json summarizes VBC-complex-form-stability and HIF1/2a-degradation assay tables from the VHL_Functional_Assay_SVI_documentation.xlsx (e.g. Rechsteiner 2011 PMID:21715564, Clifford 2001 PMID:11331613) but none list p.(V181I)/c.541G>A as a tested variant
  • PMID:18195360 (paper_extracts.json): molecular-dynamics simulation found V181I 'more stable than wild type' pVHL, a computational prediction with no experimental HIF1/2a, VBC, or fibronectin/ECM readout, so it does not meet the VCEP's accepted BS3 assay definition
Still missing
  • No HIF1/2a degradation assay showing WT-like function for p.(V181I)
  • No VBC/VCB complex stability assay showing unaffected stability for p.(V181I)
  • No ECM formation/fibronectin binding assay showing unaffected binding for p.(V181I)
  • PMID:18195360 is a computational MD simulation, not an accepted VCEP functional assay type, and does not report loss-of-function evidence controls
Sources
BS4 Not assessed: no affected relatives lacking the variant or fully phenotyped unaffected carriers are documented for non-segregation. Details ▾Hide ▴
Reasoning

No affected relatives who lack the variant, or fully phenotyped unaffected relatives who carry it, are documented. The VHL-specific requirements for informative non-segregation are therefore not met with available evidence and BS4 cannot be assigned.

Rule
VHL VCEP BS4: supporting for lack of segregation in 1 family and strong for lack of segregation in affected members of at least 2 families; affected members should fulfill Danish Criteria and unaffected relatives require complete phenotyping with appropriate age consideration.
Evidence considered
  • The VHL VCEP requires affected pedigree members to fulfill Danish Criteria and states that BS4 supporting applies to one family with lack of segregation, while BS4 strong requires lack of segregation in affected members of at least two families.
  • The consolidated case-evidence bundle contains no non-segregation observation, affected-relative testing, unaffected-relative phenotyping, or family count for this variant.
Still missing
  • Informative pedigree and genotypes of affected relatives
  • Documentation that affected relatives fulfill VHL Danish Criteria rather than isolated pheochromocytoma or renal cell carcinoma
  • Full VHL phenotyping and age of unaffected relatives, including age at least 65 years where relevant
  • Number of families showing lack of segregation
Sources
BP2 Not assessed: no phase-confirmed trans or cis observations with a pathogenic VHL variant, or qualifying homozygous observation, are documented. Details ▾Hide ▴
Reasoning

The VHL VCEP BP2 rule requires either a phase-confirmed trans observation with a known pathogenic variant and absence of congenital polycythemia, a homozygous observation without personal or family history of VHL disease or congenital polycythemia, or cis/unknown phase with three or more different pathogenic VHL variants for Strong BP2; Supporting BP2 requires cis or unknown phase with a pathogenic VHL variant. The case evidence bundle contains no affected-proband or family-level observation documenting a pathogenic variant in cis or trans with NM_000551.4:c.541G>A (p.Val181Ile), no confirmed homozygous observation, and no qualifying phase or congenital-polycythemia clinical context. BP2 therefore cannot be assigned from the available evidence.

Rule
VHL VCEP Version 1.1 BP2: Strong for phase-confirmed trans with a known pathogenic variant plus absence of congenital polycythemia, or qualifying homozygous/cis-or-unknown-phase observations; Supporting for cis or unknown phase with a pathogenic VHL variant.
Evidence considered
  • The VHL VCEP Version 1.1 BP2 rule requires specified cis/trans or homozygous observations and, for the trans pathway, absence of congenital polycythemia.
  • The case bundle provides population, ClinVar, computational, and gene-level information but does not provide a qualifying affected-proband or family-level allelic observation with phase for this variant.
Still missing
  • No documented cis/trans phase with a known pathogenic variant.
  • No documented homozygous observation with the required negative personal and family history.
  • No documented congenital-polycythemia assessment for a potential trans observation.
  • No documented observation in cis or unknown phase with a pathogenic VHL variant, including the number of distinct pathogenic VHL variants.
Sources
BP4 Not assessed: SpliceAI max delta 0.014 meets its threshold, but no VarSeak result exists to confirm the required two-tool concordance. Details ▾Hide ▴
Reasoning

VHL VCEP (cspec v1.1) explicitly prohibits use of missense in-silico predictors (e.g. REVEL, BayesDel) for BP4 in this gene, citing lack of benign controls and poor accuracy: 'missense predictors should not be used to assign the BP4 evidence code.' The only permitted BP4 path is splicing: concordance of SpliceAI (<=0.1) AND VarSeak (Class 1 or Class 2). SpliceAI max delta = 0.014 satisfies the SpliceAI <=0.1 arm, but no VarSeak result is present anywhere in the case bundle, so the required two-tool concordance cannot be verified. BayesDel score (0.021) exists in source data but has no verified published calibration threshold available to this pipeline and cannot be used for BP4 regardless of the VCEP's missense-predictor prohibition, which independently rules out its use here.

Rule
BP4_supporting (VHL VCEP cspec v1.1)
Evidence considered
  • VHL VCEP cspec v1.1 BP4 rule: 'Due to the lack of benign variants, and the drop in classification accuracy for benign VHL variants, missense predictors should not be used to assign the BP4 evidence code. BP4 can be applied to assess lack of splicing impact, with concordance of Splice AI (<=0.1) and VarSeak (Class 1 or Class 2).'
  • SpliceAI Lookup: max delta score = 0.014, satisfying the VCEP's <=0.1 SpliceAI arm of the BP4 splice-path concordance requirement.
  • No VarSeak record found anywhere in review_manifest.json, source_registry.json, prefetch.json, evidence.json, evidence_brief.json, or vcep_materials.json for this case.
Still missing
  • VarSeak splicing classification is not present in this case's evidence bundle; the VCEP requires concordance of SpliceAI (<=0.1) AND VarSeak (Class 1 or Class 2) to apply BP4 via the splice path, and only the SpliceAI half of that pair is available.
  • Missense predictor path (REVEL/BayesDel) is explicitly disallowed for BP4 by the VHL VCEP specification itself, independent of predictor calibration status.
Sources
BP5 Not assessed: no qualifying co-occurrence with a pathogenic variant in another highly penetrant gene is documented. Details ▾Hide ▴
Reasoning

No qualifying co-occurrence evidence is available. The VHL Expert Panel requires at least two co-occurrences with pathogenic variants in another highly penetrant gene that fully explains the individual's phenotype, with age, tumor type, sex, and personal and family history showing no overlap with VHL features.

Rule
VHL VCEP v1.1 BP5: at least two qualifying co-occurrences with pathogenic variants in a different gene that fully explain the phenotype, with no overlapping VHL features after clinical-context review.
Evidence considered
  • The case bundle contains no co-occurrence, alternate molecular diagnosis, phenotype, or family-history dataset that meets the VHL-specific BP5 requirements.
Still missing
  • At least two independently documented co-occurrences with a pathogenic variant in a different highly penetrant gene.
  • For each co-occurrence, phenotype, age, tumor type, sex, and personal/family history demonstrating that the alternate molecular diagnosis fully explains the phenotype without overlap with VHL-associated features.
Sources
Not applicable · 10· recorded as not applicable Show reasons ▾Hide reasons ▴
PVS1 N/ANot applicable: this is a missense substitution, not a null-variant class (nonsense, frameshift, splice-site disruption, or deletion). Details ▾Hide ▴
Reasoning

NM_000551.4:c.541G>A is a single-nucleotide missense substitution (NP_000542.1:p.(Val181Ile)) confirmed by mutalyzer normalization. It is not a null-variant class (nonsense, frameshift, canonical splice-site disruption, initiation-codon loss, or single/multi-exon/whole-gene deletion) as required for PVS1 entry into the VHL VCEP PVS1 decision tree, which is scoped to truncating and splice-disrupting variant types. No exon skipping, NMD, or protein-truncation evidence applies to a missense substitution, so PVS1 is not applicable to this variant.

Rule
VHL VCEP PVS1 (cspec v1.1): decision tree applies only to predicted null-variant classes (nonsense, frameshift, canonical splice disruption, initiation codon loss, exon/gene deletion); missense substitutions are out of scope.
Evidence considered
  • case_summary.json normalization confirms NM_000551.4:c.541G>A = NP_000542.1:p.(Val181Ile), a missense substitution, not a null/truncating/splice variant class.
  • VHL VCEP cspec PVS1 rule set (v1.1) is scoped to truncating variants (nonsense, frameshift), canonical splice-affecting variants, initiation-codon variants, and single/multi-exon deletions; it does not apply to missense substitutions.
Sources
PM3 VCEPNot applicable: the VHL Expert Panel specification designates PM3 as not applicable for this gene. Details ▾Hide ▴
Reasoning

The ClinGen VHL Expert Panel specification, Version 1.1, designates PM3 as Not Applicable for VHL. Therefore PM3 is not assigned, regardless of the absence or presence of potentially relevant allelic observations in this case.

VCEP rule
VHL VCEP Version 1.1: PM3 applicability = Not Applicable.
Evidence considered
  • The VHL VCEP specification explicitly lists PM3 as Not Applicable.
Sources
PM4 N/ANot applicable: PM4 applies only to in-frame indels and stop-loss variants, but this missense change does not alter protein length. Details ▾Hide ▴
Reasoning

PM4 under the VHL VCEP specification is restricted to in-frame insertions/deletions in the Beta and Alpha domains and to stop-loss variants that add significant additional amino acids to the VHL protein, i.e. variants that change protein length. c.541G>A is a single-nucleotide substitution producing a missense change (Val181Ile) with no alteration to protein length (no insertion, deletion, or stop-loss). PM4 therefore does not apply.

Rule
VHL VCEP PM4 (cspec v1.1): applies only to in-frame indels in Beta/Alpha domains and stop-loss extensions, not to single-residue missense substitutions.
Evidence considered
  • VHL VCEP cspec v1.1 PM4 rule: 'In-frame insertion/deletions in the B and alpha domains and stop-loss variants adding significant additional amino acids to VHL' -- restricted to protein-length-altering variant classes.
  • Variant is a substitution (G>A) producing a single amino-acid substitution (Val181Ile) with no change to protein length, so it does not meet the PM4 variant-class requirement regardless of its location in the Alpha domain (AA156-192).
Sources
PP2 VCEPNot applicable: the VHL Expert Panel specification marks PP2 as not applicable for this gene. Details ▾Hide ▴
Reasoning

The VHL VCEP v1.1 specification explicitly marks PP2 as 'Not Applicable' for this gene, overriding the generic ACMG/AMP PP2 (missense in a gene with low benign missense rate). No PP2 assessment is performed.

VCEP rule
VHL VCEP v1.1: PP2 not applicable to VHL.
Evidence considered
  • VHL VCEP v1.1 specification lists PP2 with applicability: 'Not Applicable'.
Sources
PP4 VCEPNot applicable: the VHL Expert Panel specification designates PP4 as not applicable for this gene. Details ▾Hide ▴
Reasoning

PP4 is designated Not Applicable by the governing VHL Expert Panel specification.

VCEP rule
VHL VCEP v1.1: PP4 Not Applicable.
Evidence considered
  • The VHL Expert Panel specification lists PP4 as Not Applicable.
Sources
PP5 VCEPNot applicable: the ClinVar record has no expert-panel submission, only non-expert laboratory assertions. Details ▾Hide ▴
Reasoning

PP5 is not applicable under the VHL Expert Panel specification. Independently, the exact ClinVar record has no expert-panel submission; its listed assertions are ordinary laboratory or other non-expert submissions and cannot trigger PP5.

VCEP rule
VHL VCEP v1.1: PP5 Not Applicable; exact-variant ClinVar P/LP assertions from non-expert submitters are not eligible for PP5.
Evidence considered
  • The VHL Expert Panel specification lists PP5 as Not Applicable.
  • ClinVar Variation ID 238111 is an exact transcript-HGVS match for c.541G>A (p.Val181Ile), but the available record reports zero expert-panel submissions.
Sources
BP1 VCEPNot applicable: the VHL Expert Panel specification marks BP1 as not applicable for this gene. Details ▾Hide ▴
Reasoning

The VHL VCEP v1.1 specification explicitly marks BP1 as 'Not Applicable' for this gene, overriding the generic ACMG/AMP BP1 (missense in a gene where only truncating variants cause disease). No BP1 assessment is performed.

VCEP rule
VHL VCEP v1.1: BP1 not applicable to VHL.
Evidence considered
  • VHL VCEP v1.1 specification lists BP1 with applicability: 'Not Applicable'.
Sources
BP3 N/ANot applicable: BP3 applies only to in-frame indels in the N-terminal GXEEX repeat (residues 14-48); this is a missense at codon 181. Details ▾Hide ▴
Reasoning

The VHL VCEP restricts BP3 to in-frame indels falling within the 8x GXEEX repeat motif at the VHL N-terminus (AA14-AA48); all other coding regions of VHL lack repeat elements per RepeatMasker, per the specification. c.541G>A is a missense substitution, not an in-frame indel, and codon 181 (Alpha domain) lies far outside the AA14-48 repeat region, so BP3 does not apply on both variant-class and location grounds.

Rule
VHL VCEP BP3 (cspec v1.1): applies only to in-frame indels within the AA14-48 GXEEX repeat motif; not applicable elsewhere in VHL or to non-indel variant classes.
Evidence considered
  • VHL VCEP cspec v1.1 BP3 rule: applicable only to in-frame indels within the GXEEX repeat motif (AA14-AA48); rest of VHL coding sequence has no repeat regions and BP3 is not applicable elsewhere.
  • Variant is a missense substitution (not an in-frame indel) at codon 181, outside the AA14-48 repeat region, failing both the variant-class and location requirements for BP3.
Sources
BP6 VCEPNot applicable: the only likely-benign assertion comes from a single non-expert laboratory, with no expert-panel benign submission. Details ▾Hide ▴
Reasoning

BP6 is not applicable under the VHL Expert Panel specification. The exact ClinVar record has no expert-panel benign or likely benign assertion; the reported likely benign assertion is from a single non-expert laboratory and cannot trigger BP6.

VCEP rule
VHL VCEP v1.1: BP6 Not Applicable; exact-variant ClinVar B/LB assertions from non-expert submitters are not eligible for BP6.
Evidence considered
  • The VHL Expert Panel specification lists BP6 as Not Applicable.
  • ClinVar Variation ID 238111 has zero expert-panel submissions; its likely benign assertion is a single-submitter laboratory assertion.
Sources
BP7 N/ANot applicable: BP7 applies only to synonymous or intronic variants, and this is a missense change. Details ▾Hide ▴
Reasoning

VHL VCEP (cspec v1.1) restricts BP7 to silent (synonymous) or intronic variants where the variant is BP4-met for lack of splice effect and PhyloP <=0.2. NM_000551.4:c.541G>A is a missense variant (p.Val181Ile), not a synonymous or intronic change, so BP7 is not applicable regardless of splicing or conservation data.

Rule
BP7_supporting (VHL VCEP cspec v1.1) - not applicable to missense variants
Evidence considered
  • VHL VCEP cspec v1.1 BP7 rule: applies to 'silent or intronic variants where the PhyloP score is <=0.2', contingent on BP4 being met for lack of splice effect.
  • Variant NM_000551.4:c.541G>A is annotated as NP_000542.1:p.(Val181Ile), a missense substitution, not synonymous or intronic.
Sources

Identifiers

Gene
VHL
Transcript
NM_000551.4
Coding (HGVS c.)
NM_000551.4:c.541G>A
Protein (HGVS p.)
NP_000542.1:p.(Val181Ile)
GRCh38
chr3:10149864 G>A
GRCh37
chr3:10191548 G>A
Location and type
Exon 3 · missense
ClinVar
238111
COSMIC
COSV56543552

Gene diagram

Every interpreted variant in VHL, mapped onto the exon structure of NM_000551.4. Select a row to find it on the plot.

VHLNM_000551.4
Fetching transcript structure from UCSC…
gnomAD v4.1 5 / 1,614,186 alleles AF 3.1e-06 · 0 homozygotes · FAF 3.65e-06
gnomAD v2.1 1 / 251,418 alleles AF 3.98e-06 · 0 homozygotes
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 3.1e-06 · 5 / 1,614,186 alleles · 0 hom · FAF 3.7e-06
South Asian2 / 91,076 2.2e-05
African/African American1 / 75,054 1.3e-05
European (non-Finnish)2 / 1,180,032 1.7e-06
0 alternate alleles recorded in 7 other groups: Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, Ashkenazi Jewish.

gnomAD v2.1

AF 4e-06 · 1 / 251,418 alleles · 0 hom
South Asian1 / 30,612 3.3e-05
0 alternate alleles recorded in 7 other groups: African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 3.09754e-06; MAF= 0.00031%, 5/1614186 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 2.19597e-05; MAF= 0.00220%, 2/91076 alleles, homozygotes = 0); grpmax FAF= 3.65e-06.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.97744e-06; MAF= 0.00040%, 1/251418 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26669e-05; MAF= 0.00327%, 1/30612 alleles, homozygotes = 0).

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -13 bp
0.000
SpliceAI acceptor gainat +5 bp
0.002
SpliceAI donor lossat -160 bp
0.000
SpliceAI donor gainat +145 bp
0.014
Pangolin splice lossmagnitude shown
-0.003
Pangolin splice gain
0.005

Other predictors

REVEL
0.431
BayesDel
0.021

How the predictions were used

PP3 Not met: REVEL scores 0.431, below the required 0.664 threshold, and SpliceAI max delta is 0.014 versus the 0.5 splice threshold. Details ▾Hide ▴
Reasoning

VHL VCEP (cspec v1.1) specifies two independent PP3 paths. Missense path: REVEL >=0.664 required; this variant (NM_000551.4:c.541G>A, p.Val181Ile) scores REVEL=0.431 (local REVEL v1.3 lookup), below threshold, so PP3 is not met via the missense path. Splice path: requires concordance of SpliceAI (>0.5) AND VarSeak (class 4 or 5); SpliceAI max delta score for this variant is 0.014 (SpliceAI Lookup), far below the 0.5 threshold, so the splice path also fails regardless of VarSeak availability. Both VCEP-specified paths for PP3 are unmet.

Rule
PP3_supporting (VHL VCEP cspec v1.1)
Evidence considered
  • VHL VCEP cspec v1.1 PP3 rule: 'For missense variants, use REVEL score >=0.664. For splice variants, concordance of Splice AI (>0.5) and VarSeak (class 4 or class 5).'
  • Local REVEL v1.3 predictor lookup: REVEL score = 0.431 for NM_000551.4:c.541G>A (p.Val181Ile), below the VCEP's 0.664 missense threshold.
  • SpliceAI Lookup: max delta score = 0.014 for this variant, far below the VCEP's 0.5 splice-path threshold for PP3.
Sources
BP4 Not assessed: SpliceAI max delta 0.014 meets its threshold, but no VarSeak result exists to confirm the required two-tool concordance. Details ▾Hide ▴
Reasoning

VHL VCEP (cspec v1.1) explicitly prohibits use of missense in-silico predictors (e.g. REVEL, BayesDel) for BP4 in this gene, citing lack of benign controls and poor accuracy: 'missense predictors should not be used to assign the BP4 evidence code.' The only permitted BP4 path is splicing: concordance of SpliceAI (<=0.1) AND VarSeak (Class 1 or Class 2). SpliceAI max delta = 0.014 satisfies the SpliceAI <=0.1 arm, but no VarSeak result is present anywhere in the case bundle, so the required two-tool concordance cannot be verified. BayesDel score (0.021) exists in source data but has no verified published calibration threshold available to this pipeline and cannot be used for BP4 regardless of the VCEP's missense-predictor prohibition, which independently rules out its use here.

Rule
BP4_supporting (VHL VCEP cspec v1.1)
Evidence considered
  • VHL VCEP cspec v1.1 BP4 rule: 'Due to the lack of benign variants, and the drop in classification accuracy for benign VHL variants, missense predictors should not be used to assign the BP4 evidence code. BP4 can be applied to assess lack of splicing impact, with concordance of Splice AI (<=0.1) and VarSeak (Class 1 or Class 2).'
  • SpliceAI Lookup: max delta score = 0.014, satisfying the VCEP's <=0.1 SpliceAI arm of the BP4 splice-path concordance requirement.
  • No VarSeak record found anywhere in review_manifest.json, source_registry.json, prefetch.json, evidence.json, evidence_brief.json, or vcep_materials.json for this case.
Still missing
  • VarSeak splicing classification is not present in this case's evidence bundle; the VCEP requires concordance of SpliceAI (<=0.1) AND VarSeak (Class 1 or Class 2) to apply BP4 via the splice path, and only the SpliceAI half of that pair is available.
  • Missense predictor path (REVEL/BayesDel) is explicitly disallowed for BP4 by the VHL VCEP specification itself, independent of predictor calibration status.
Sources
BP7 N/ANot applicable: BP7 applies only to synonymous or intronic variants, and this is a missense change. Details ▾Hide ▴
Reasoning

VHL VCEP (cspec v1.1) restricts BP7 to silent (synonymous) or intronic variants where the variant is BP4-met for lack of splice effect and PhyloP <=0.2. NM_000551.4:c.541G>A is a missense variant (p.Val181Ile), not a synonymous or intronic change, so BP7 is not applicable regardless of splicing or conservation data.

Rule
BP7_supporting (VHL VCEP cspec v1.1) - not applicable to missense variants
Evidence considered
  • VHL VCEP cspec v1.1 BP7 rule: applies to 'silent or intronic variants where the PhyloP score is <=0.2', contingent on BP4 being met for lack of splice effect.
  • Variant NM_000551.4:c.541G>A is annotated as NP_000542.1:p.(Val181Ile), a missense substitution, not synonymous or intronic.
Sources

Statement

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.431. BayesDel score = 0.0210198.

8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata.

Recorded publications

  • Allosteric effects in the marginally stable von Hippel-Lindau tumor suppressor protein and allostery-based rescue mutant design.
    Liu J et al. · 2008
    This computational structural-biology paper explicitly models V181I as one of five designed pVHL mutants (G123F, V142P, D143R, D179N, V181I) located in loops of the alpha-domain region, using 10-ns molecular-dynamics simulations of unbound pVHL. V181I was found to be more stable than wild-type pVHL in these simulations, though it was not among the two most-stabilizing mutants (G123F, D179N). The paper reports no experimental functional assay (e.g., HIF degradation, VBC complex stability) and no patient-level clinical or segregation observation for V181I; it is a purely in-silico stability modeling study.
    Names this variant
    PMID 18195360 ↗
    Quoted passage
    Five human pVHL mutants, G123F, V142P, D143R, D179N, and V181I, were generated, located in L6, L7, and L10. Molecular dynamics simulations were performed for these mutants. The rmsd plots are shown in Fig. 4. All five mutants are more stable than the wild type. Among these, the G123F (in L6) and D179N (in L10) mutants stabilize unbound pVHL the most.

    Results and Discussion, "Design of Mutants to Stabilize Unbound pVHL"; Fig. 4; Conclusions

  • Canadian guideline on genetic screening for hereditary renal cell cancers.
    Reaume MN et al. · 2013
    No paper-specific finding is recorded.
    PMID 24319509 ↗
  • ACMG policy statement: updated recommendations regarding analysis and reporting
    No paper-specific finding is recorded.
    PMID 25356965 ↗
  • A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.
    Hampel H et al. · 2015
    No paper-specific finding is recorded.
    PMID 25394175 ↗
  • Standards and guidelines for the interpretation of sequence variants: a joint co
    No paper-specific finding is recorded.
    PMID 25741868 ↗
  • Recommendations for reporting of secondary findings in clinical exome and genome
    No paper-specific finding is recorded.
    PMID 27854360 ↗
  • Sherloc: a comprehensive refinement of the ACMG-AMP variant classification crite
    No paper-specific finding is recorded.
    PMID 28492532 ↗
  • ACMG SF v3.0 list for reporting of secondary findings in clinical exome and geno
    No paper-specific finding is recorded.
    PMID 34012068 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 3.09754e-06; MAF= 0.00031%, 5/1614186 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 2.19597e-05; MAF= 0.00220%, 2/91076 alleles, homozygotes = 0); grpmax FAF= 3.65e-06.

gnomAD v2.1

This variant is present in gnomAD v2.1 (AF= 3.97744e-06; MAF= 0.00040%, 1/251418 alleles, homozygotes = 0) and has highest observed frequency in the South Asian population (AF= 3.26669e-05; MAF= 0.00327%, 1/30612 alleles, homozygotes = 0).

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Uncertain significance (5 clinical laboratories) and as Uncertain Significance (1 clinical laboratory) and as Likely benign (1 clinical laboratory). (ClinVarID = 238111)

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.431. BayesDel score = 0.0210198.

Functional

OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. VHL, an E3 ubiquitin ligase, is frequently mutated in renal cell carcinomas.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV56543552, n = 1 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.