Is STK11 p.Arg86= (c.258A>G) pathogenic?

STK11 p.Arg86= (c.258A>G) is classified Benign/Likely benign in STK11 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-03-25). Absent from gnomAD v4.1; Associated with Peutz-Jeghers syndrome.

What condition is associated with STK11 p.Arg86= (c.258A>G)?

STK11 p.Arg86= (c.258A>G) is associated with Peutz-Jeghers syndrome (ClinVar).

How common is STK11 p.Arg86= (c.258A>G) in the general population?

STK11 p.Arg86= (c.258A>G) is absent from gnomAD v4.1 (gnomAD).

How is Peutz-Jeghers syndrome inherited?

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

STK11 p.Arg86=

c.258A>G · rs2145405874 · VCV1110527

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Peutz-Jeghers 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 -1.3	GERP -1.8
Overall
CADD	6.413	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: STK11
Protein: p.Arg86=
Coding: c.258A>G
MANE Select: NM_000455
dbSNP: rs2145405874
Type: single nucleotide variant
Location: chr19:1207171 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.27 · 4 PDB
Residue 86: the protein kinase domain; the 'sufficient for interaction with sirt1' region; a UniProt-annotated variant site (in sporadic cancer; somatic mutation; no effect on kinase activity nor in heterotrimeric complex assembly with strada and cab39); an α-helix

Full STK11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Peutz-Jeghers syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Peutz-Jeghers syndrome (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 100 000 (Worldwide)

Similar variants

STK11 p.Arg86Ter Pathogenic ★★ same residue
STK11 p.Arg86Gln Uncertain significance ★★ ⚠ same residue
STK11 p.Arg86Leu Uncertain significance ★ ⚠ same residue
STK11 c.290+1G>A Pathogenic ★★ same condition
STK11 c.290+1G>C Pathogenic ★★ same condition
STK11 c.290+1G>T Pathogenic ★★ same condition
STK11 c.290+2T>A Pathogenic/Likely pathogenic ★★ same condition
STK11 c.291-2A>G 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/stk11-p-arg86 (accessed [today's date]).

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