Is STK11 p.Ser232= (c.696C>T) pathogenic?

STK11 p.Ser232= (c.696C>T) is classified Benign/Likely benign in STK11 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-06-01). Very rare (popmax 0.00834%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with STK11 p.Ser232= (c.696C>T)?

STK11 p.Ser232= (c.696C>T) is associated with hereditary neoplastic syndrome, Peutz-Jeghers syndrome (ClinVar).

How common is STK11 p.Ser232= (c.696C>T) in the general population?

STK11 p.Ser232= (c.696C>T) is very rare (popmax 0.00834%, amr) (gnomAD).

STK11 p.Ser232=

c.696C>T · rs566823619 · VCV182883

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00834%, amr)

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 -6.8	GERP -3.1
Overall
CADD	3.3	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00834% Admixed American · 5/59,966 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.00124% 20/1,610,948 alleles · very rare exomes 18/1,458,668 · genomes 2/152,280 · joint denominator

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00834%	11,993
South Asian	0.00549%	18,211
Remaining individualsnot grpmax-eligible	0.00481%	20,784
African / African-American	0.00267%	37,497
Finnishnot grpmax-eligible	0.0016%	62,514
European (non-Finnish)	0.000339%	294,798

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: STK11
Protein: p.Ser232=
Coding: c.696C>T
MANE Select: NM_000455
dbSNP: rs566823619
Type: single nucleotide variant
Location: chr19:1220679 (GRCh38)
Gene constraint: LOEUF 0.364 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 79.27 · 4 PDB
Residue 232: a β-strand; the protein kinase domain; a UniProt-annotated variant site (in sporadic cancer; somatic mutation; no effect heterotrimeric complex assembly with strada and cab39)

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.Ser232Phe Uncertain significance ★ ⚠ same residue
STK11 p.Ser232fs Pathogenic ★ 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.291-1G>A 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-ser232 (accessed [today's date]).

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