Is STK11 p.Arg415= (c.1245C>A) pathogenic?

STK11 p.Arg415= (c.1245C>A) is classified Benign/Likely benign in STK11 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-03-31). No allele count reported in gnomAD v4.1 (AN 1,572,314); Associated with hereditary neoplastic syndrome.

What condition is associated with STK11 p.Arg415= (c.1245C>A)?

STK11 p.Arg415= (c.1245C>A) is associated with hereditary neoplastic syndrome, Peutz-Jeghers syndrome (ClinVar).

How common is STK11 p.Arg415= (c.1245C>A) in the general population?

STK11 p.Arg415= (c.1245C>A) is no allele count reported in gnomAD v4.1 (AN 1,572,314) (gnomAD).

STK11 p.Arg415=

c.1245C>A · rs878853985 · VCV1634951

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,572,314)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.016	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.053	GERP -2.5, phastCons 0.88
Overall
CADD	7.874	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,572,314). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: STK11
Protein: p.Arg415=
Coding: c.1245C>A
MANE Select: NM_000455
dbSNP: rs878853985
Type: single nucleotide variant
Location: chr19:1226590 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.27 · 4 PDB
Residue 415: the 'disordered' region

Full STK11 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: Peutz-Jeghers syndrome

Similar variants

STK11 p.Arg415Leu Uncertain significance ★★ ⚠ same residue
STK11 p.Arg415Pro Uncertain significance ★★ ⚠ same residue
STK11 p.Arg415Ser Uncertain significance ★★ ⚠ same residue
STK11 p.Arg415Cys Conflicting classifications of pathogenicity ★ ⚠ same residue
STK11 p.Arg415Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
STK11 p.Arg415His Conflicting classifications of pathogenicity ★ ⚠ same residue
STK11 p.Arg415fs Uncertain significance ★ same residue
STK11 c.290+1G>A 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-arg415 (accessed [today's date]).

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