Is VHL p.Pro99Ser (c.295C>T) pathogenic?

VHL p.Pro99Ser (c.295C>T) is classified Conflicting classifications of pathogenicity in VHL (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-07-27). AlphaMissense: likely benign (0.3035); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with VHL p.Pro99Ser (c.295C>T)?

VHL p.Pro99Ser (c.295C>T) is associated with hereditary neoplastic syndrome, von Hippel-Lindau disease, Chuvash polycythemia (ClinVar).

How common is VHL p.Pro99Ser (c.295C>T) in the general population?

VHL p.Pro99Ser (c.295C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about VHL p.Pro99Ser (c.295C>T)?

AlphaMissense predicts likely benign (score 0.3035) — an in-silico prediction, not a clinical call.

VHL p.Pro99Ser

c.295C>T · VCV3753898

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.3035 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.3035	likely benign
REVEL	0.444	indeterminate
SaProt	LLR -6.51	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.1	GERP 1.5, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 8,114 bp · p 0.039 · regional, not allelic
Overall
CADD	19.94	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: VHL
Protein: p.Pro99Ser
Coding: c.295C>T
MANE Select: NM_000551
Type: single nucleotide variant
Location: chr3:10142142 (GRCh38)
Gene constraint: LOEUF 0.987 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.45 · 143 PDB
Residue 99: an α-helix

Full VHL gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: von Hippel-Lindau disease Chuvash polycythemia

Similar variants

VHL p.Pro99= Benign/Likely benign ★★ same residue
VHL p.Pro99Ala Uncertain significance ★ ⚠ same residue
VHL p.Pro99Arg Conflicting classifications of pathogenicity ★ ⚠ same residue
VHL p.Pro99Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
VHL p.Arg64Pro Pathogenic ★★★ same condition
VHL p.Asn78Ser Pathogenic ★★★ ⚠ same condition
VHL p.Glu70Ter Pathogenic ★★★ same condition
VHL p.Pro86Leu Pathogenic ★★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/vhl-p-pro99ser (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown