Variant classification summary

NM_000551.3:c.445G>T

VHL · NP_000542.1:p.(Ala149Ser) · NM_000551.3

GRCh37: chr3:10188302 G>T · GRCh38: chr3:10146618 G>T

Gene: VHL Transcript: NM_000551.3

Final call

Likely Pathogenic

PS4 moderate PM2 supporting PP1 strong PP3 supporting

Variant details

Gene

VHL

Transcript

NM_000551.3

Protein

NP_000542.1:p.(Ala149Ser)

gnomAD AF

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000551.3:c.445G>T (p.Ala149Ser) co-segregates with VHL disease across >7 meioses in two independent multigenerational families with VHL type 2A (PMID:9435426) and type 2B (PMID:23673869) phenotypes, meeting PP1_Strong per VHL VCEP v1.1.0.

2

The variant has been observed in multiple probands with Danish Criteria-meeting VHL phenotypes across two independent families, including pheochromocytoma, renal cell carcinoma, retinal angiomas, spinal hemangioblastoma, and pancreatic neuroendocrine tumors, meeting PS4_Moderate per VHL VCEP.

3

NM_000551.3:c.445G>T is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting per VHL VCEP (threshold: absent or <=0.00000156 GroupMax FAF).

4

REVEL in silico score of 0.896 exceeds the VHL VCEP PP3 threshold of >=0.664, supporting a deleterious effect of the p.Ala149Ser substitution.

5

Applying VHL VCEP v1.1.0 combination rules: PP1_Strong (1 strong) + PS4_Moderate (1 moderate) + PM2_Supporting + PP3 (>=2 supporting) satisfies Rule 12 (1 Strong + >=2 Supporting), resulting in a classification of Likely Pathogenic.

Final determination: Rule11 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 Likely Pathogenic.

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	PVS1 is not applicable to missense variants. NM_000551.3:c.445G>T is a missense substitution (p.Ala149Ser), not a null variant (nonsense, frameshift, or canonical splice). Per the VHL VCEP v1.1.0, PVS1 applies only to truncating variants after codon 54 or variants causing exon skipping.
PS1	Not met	PS1 requires a different nucleotide change at the same amino acid position (Ala149) that has been classified as pathogenic by the VHL VCEP. No VCEP-classified pathogenic comparator at residue 149 with a different nucleotide change was identified. Although p.Ala149Pro (A149P) has been studied as a tumorigenic mutation (PMID:14636579), it has not been formally classified by the VHL VCEP.
PS2	Not met	No de novo occurrence of NM_000551.3:c.445G>T with confirmed or assumed parentage was identified in the reviewed literature. The variant was observed to segregate within multigenerational families, indicating inherited rather than de novo origin.
PS3	Not met	No variant-specific functional studies of p.Ala149Ser (NM_000551.3:c.445G>T) were identified in the available full-text literature. PMID:14636579 (Feldman 2003) characterized p.Ala149Pro (A149P) as disrupting TRiC chaperonin binding and VHL folding, but A149S was not tested. No HIF degradation, VBC complex stability, or fibronectin binding assay data were identified for this specific variant.
PS4	Met	NM_000551.3:c.445G>T (p.Ala149S) has been observed in multiple probands with VHL-defining phenotypes across two independent families. PMID:9435426 (Atuk 1998) reports 7 affected individuals with confirmed mutation in a 4-generation American kindred with pheochromocytoma and retinal angiomas (VHL type 2A). PMID:23673869 (Mete 2014) reports 10 affected patients in a 3-generation Turkish family with pheochromocytoma, renal cell carcinoma, retinal angiomas, spinal hemangioblastoma, and pancreatic neuroendocrine tumors (VHL type 2B). Phenotypes in both families meet Danish Criteria for VHL. Estimated at 2-4 proband-equivalent points per VHL VCEP scoring, consistent with PS4_Moderate.	PMID:9435426 PMID:23673869 clinvar
PS5	N/A	PS5 is not included in the VHL VCEP v1.1.0 criteria framework. The VCEP has elected not to use reputation-based criteria (both PP5 and PS5). The related criterion PP5 is explicitly marked as 'Not Applicable for this VCEP.'
PM1	Not met	The variant is located at codon 149 within the Beta domain (nuclear export region, AA 114-155), which is a key functional domain, and within the TRiC chaperonin binding Box 2 (AA 148-155). However, the residue is not a statistically significant germline or somatic hotspot per cancerhotspots.org data. No COSMIC entries were found for this variant. PM1 per VHL VCEP requires the residue to be a known germline hotspot AND/OR have >=10 somatic instances in cancerhotspots.org, or <10 instances for PM1_Supporting. Neither threshold is met based on available hotspot data.	PMID:14636579
PM2	Met	NM_000551.3:c.445G>T is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0. Per VHL VCEP v1.1.0, PM2_Supporting is applied for variants absent from gnomAD or with GroupMax FAF <= 0.00000156 (0.000156%). Complete absence from large population databases supports pathogenicity.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	Not met	PM5 requires a different pathogenic missense variant at the same amino acid residue (Ala149) classified by the VHL VCEP. Although p.Ala149Pro (A149P) is characterized as a tumorigenic mutation disrupting TRiC binding and VHL folding (PMID:14636579), PM5 candidate screening did not identify any VCEP-classified pathogenic comparator at residue 149. Per VHL VCEP PM5 rules, the comparator must have pathogenicity established using VHL VCEP specifications.
PM6	Not met	No de novo occurrence of NM_000551.3:c.445G>T was identified in the reviewed literature. The variant was observed to segregate in multigenerational families (PMID:9435426, PMID:23673869), consistent with inherited transmission.
PP1	Met	NM_000551.3:c.445G>T (p.Ala149S) co-segregates with VHL disease across >7 meioses in two independent multigenerational families. PMID:9435426 (Atuk 1998): mutation confirmed in 7 affected members across 4 generations of an American kindred, with complete genotype-phenotype concordance. PMID:23673869 (Mete 2014): mutation detected in all 10 symptomatic patients and 7 asymptomatic carriers across 3 generations of a Turkish family. Combined meioses exceed 7 across >=2 families, meeting VHL VCEP threshold for PP1_Strong.	PMID:9435426 PMID:23673869
PP2	N/A	PP2 is not applicable per VHL VCEP v1.1.0. While VHL has known pathogenic missense variants, gnomAD shows VHL is not intolerant to missense variation (Z score = -0.39). The VCEP explicitly states: 'Do not use. Missense variants in VHL will need to achieve pathogenic interpretation via other evidence codes.'
PP3	Met	REVEL score for NM_000551.3:c.445G>T is 0.896, which exceeds the VHL VCEP threshold of >=0.664 for PP3 application. This in silico prediction supports a deleterious effect of the p.Ala149Ser substitution on VHL protein function. SpliceAI delta score is 0.14, indicating no significant splicing impact, so the REVEL score is interpreted in the context of a missense effect.	revel spliceai
PP4	N/A	PP4 is not applicable per VHL VCEP v1.1.0. The VCEP instructs to combine phenotype data with PS4 to avoid double counting probands.
PP5	N/A	PP5 is not applicable per VHL VCEP v1.1.0. The VCEP explicitly marks PP5 as 'Not Applicable for this VCEP' per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.
BA1	Not met	NM_000551.3:c.445G>T is absent from gnomAD v2.1 and v4.1. The VHL VCEP BA1 threshold is >=0.000156 (0.0156%) GroupMax Filtering Allele Frequency. Complete absence from population databases does not meet the BA1 threshold for a stand-alone benign classification.	gnomad_v2 gnomad_v4
BS1	Not met	NM_000551.3:c.445G>T is absent from gnomAD v2.1 and v4.1. The VHL VCEP BS1 threshold is >=0.0000156 (0.00156%) GroupMax Filtering Allele Frequency. Complete absence from population databases does not meet the BS1 threshold for strong benign evidence.	gnomad_v2 gnomad_v4
BS2	Not met	No evidence was identified of >=3 individuals aged >=65 years harboring NM_000551.3:c.445G>T who are unaffected with full or partial phenotyping for VHL-related cancers. The variant has only been reported in affected individuals or young asymptomatic carriers within VHL families.
BS3	Not met	No benign functional evidence was identified for NM_000551.3:c.445G>T (p.Ala149Ser). No studies demonstrating normal HIF degradation, intact VBC complex stability, or preserved fibronectin binding/ECM formation were found for this specific variant. All available functional data in the literature pertain to other variants at the same residue (e.g., A149P).
BS4	Not met	No evidence of lack of segregation in affected family members was identified. On the contrary, the available evidence from two independent families (PMID:9435426, PMID:23673869) demonstrates strong co-segregation of NM_000551.3:c.445G>T with VHL disease phenotypes.
BP1	N/A	BP1 is not applicable per VHL VCEP v1.1.0. The VCEP states: 'This rule code does not apply to this gene, as truncating variants account for only a portion of disease-causing variants.'
BP2	Not met	No evidence was identified of NM_000551.3:c.445G>T observed in trans with a known pathogenic VHL variant, in a homozygous state in an unaffected individual, or in cis with multiple pathogenic VHL variants.
BP4	Not met	Per VHL VCEP v1.1.0, missense predictors are not to be used for BP4 assignment due to poor classification accuracy for benign VHL variants. BP4 can only be applied for splicing assessment with SpliceAI <=0.1 and VarSeak Class 1 or 2. The SpliceAI max delta score for this variant is 0.14, which exceeds the 0.1 threshold. BP4 is not met.	spliceai
BP5	Not met	No evidence was identified of NM_000551.3:c.445G>T co-occurring with a pathogenic variant in a different gene that fully explains the patient's phenotype. VHL VCEP requires two or more such co-occurrences with specific phenotype considerations. No such cases were identified in the reviewed literature.
BP6	N/A	BP6 is not applicable per VHL VCEP v1.1.0. The VCEP explicitly marks BP6 as 'Not Applicable for this VCEP' per ClinGen Sequence Variant Interpretation VCEP Review Committee recommendation.
BP7	N/A	BP7 is not applicable to missense variants. Per VHL VCEP v1.1.0, BP7 can only be applied to silent or intronic variants where BP4 is met for lack of splice effect and PhyloP score <=0.2. NM_000551.3:c.445G>T is a missense substitution (p.Ala149Ser), not a silent or intronic variant.

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