Is VHL p.Phe76= (c.228C>T) pathogenic?

VHL p.Phe76= (c.228C>T) is classified Benign/Likely benign in VHL (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-06-10). Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with VHL p.Phe76= (c.228C>T)?

VHL p.Phe76= (c.228C>T) is associated with hereditary neoplastic syndrome, von Hippel-Lindau disease, Chuvash polycythemia (ClinVar).

How common is VHL p.Phe76= (c.228C>T) in the general population?

VHL p.Phe76= (c.228C>T) is absent from gnomAD v4.1 (gnomAD).

VHL p.Phe76=

c.228C>T · rs1575921940 · VCV821039

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.63	GERP -0.35, phastCons 1
Overall
CADD	13.94	PHRED · no single calibrated threshold — expert panels disagree

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.Phe76=
Coding: c.228C>T
MANE Select: NM_000551
dbSNP: rs1575921940
Type: single nucleotide variant
Location: chr3:10142075 (GRCh38)
Gene constraint: LOEUF 0.987 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.45 · 143 PDB
Residue 76: a β-strand; a UniProt-annotated variant site (in vhld; type i)

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.Phe76Tyr Pathogenic/Likely pathogenic ★★ same residue
VHL p.Phe76Cys Uncertain significance ★★ ⚠ same residue
VHL p.Phe76Leu Uncertain significance ★★ ⚠ same residue
VHL p.Phe76Ile Likely pathogenic ★ same residue
VHL p.Phe76Val Likely pathogenic ★ same residue
VHL p.Phe76Ser Conflicting classifications of pathogenicity ★ ⚠ same residue
VHL p.Phe76del Pathogenic/Likely pathogenic ★★ same residue
VHL p.Phe76fs Likely pathogenic same residue

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-phe76 (accessed [today's date]).

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