Is VHL p.Arg79= (c.237C>T) pathogenic?

VHL p.Arg79= (c.237C>T) is classified Benign/Likely benign in VHL (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-06-10). Very rare (popmax 0.00879%, sas); Associated with Chuvash polycythemia.

What condition is associated with VHL p.Arg79= (c.237C>T)?

VHL p.Arg79= (c.237C>T) is associated with Chuvash polycythemia, von Hippel-Lindau disease, hereditary neoplastic syndrome (ClinVar).

How common is VHL p.Arg79= (c.237C>T) in the general population?

VHL p.Arg79= (c.237C>T) is very rare (popmax 0.00879%, sas) (gnomAD).

How is Chuvash erythrocytosis inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

VHL p.Arg79=

c.237C>T · rs760899424 · VCV1147379

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00879%, sas)

Conditions

Chuvash polycythemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.85	GERP -0.31, phastCons 1
Overall
CADD	13.87	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00879% South Asian · 8/90,990 alleles

Filtering AF 0.00437% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00312%

Overall 0.000498% 8/1,605,846 alleles · very rare exomes 8/1,453,526 · genomes 0/152,320 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: VHL
Protein: p.Arg79=
Coding: c.237C>T
MANE Select: NM_000551
dbSNP: rs760899424
Type: single nucleotide variant
Location: chr3:10142084 (GRCh38)
Gene constraint: LOEUF 0.987 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 85.45 · 143 PDB
Residue 79: a UniProt-annotated variant site (in vhld)

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

Disease context

Chuvash polycythemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: von Hippel-Lindau disease hereditary neoplastic syndrome

For Chuvash erythrocytosis (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

VHL p.Arg79Cys Uncertain significance ★★ ⚠ same residue
VHL p.Arg79Leu Uncertain significance ★★ ⚠ same residue
VHL p.Arg79Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
VHL p.Arg79His Uncertain significance ★ ⚠ same residue
VHL p.Arg79Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
VHL p.Arg79Ser Uncertain significance ★ ⚠ same residue
VHL p.Arg64Pro Pathogenic ★★★ same condition
VHL p.Asn78Ser 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-arg79 (accessed [today's date]).

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