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STK11
Final classification
VUS
STK11 c.580G>C · p.Asp194His
STK11

NM_000455.5:c.580G>C (p.Asp194His) is located in exon 4 of STK11, within the protein kinase domain catalytic loop (DLKPEN motif), a critical functional domain.

Gene
STK11
Transcript
NM_000455.5
HGVS · transcript:coding
NM_000455.5:c.580G>C
Consequence
N/A
GRCh38
chr19:1220488 G>C
GRCh37
chr19:1220487 G>C
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, PP3 supporting; combination = 2 moderate + 1 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 moderate, PM2 moderate, PP3 supporting; combination = 2 moderate + 1 supporting, which maps to VUS.
Classification rationale
PM1PM2PP3 VUS
STK11 c.580G>C

NM_000455.5:c.580G>C (p.Asp194His) is located in exon 4 of STK11, within the protein kinase domain catalytic loop (DLKPEN motif), a critical functional domain. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, representing coverage of over 800,000 alleles (PM2_moderate).1 Asp194 is a statistically significant hotspot residue in the kinase active site, and no benign missense variants are observed at this codon in population databases (PM1_moderate).2 Multiple in silico algorithms predict a deleterious effect: REVEL score 0.943, BayesDel score 0.524 (PP3_supporting).3 SpliceAI predicts no significant splice impact (max delta = 0.02), consistent with a missense mechanism rather than splicing disruption.4 The variant has been observed in somatic cancers (COSMIC COSV99045288, n=3), which is consistent with a potential oncogenic role but does not directly inform germline pathogenicity. ClinVar contains two submissions: Uncertain Significance (Invitae, SCV001518979) and Likely Pathogenic (CeGaT, SCV002498394). Neither is from an expert panel.5 No de novo observations, cosegregation data, or functional studies specific to p.Asp194His were identified in the literature. The absence of variant-specific functional data, segregation evidence, and case-control studies limits the certainty of classification.

PM1 + PM2 + PP3 VUS
Gene diagram · NM_000455.5 · variants mapped to exon structure
STK11 NM_000455.5
Fetching transcript structure from UCSC…
Applied criteria · 3 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Absent from gnomAD v4.1.
      Absent from gnomAD v2.1.
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 1027310)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.943. BayesDel score = 0.524498.
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Hotspot
      COSMIC
      This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV99045288, n = 3 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · 20 PMIDs triaged · 8 high-priority
      20papers screened
      Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.
      26917230 ↗ functional
      A Sensitive NanoString-Based Assay to Score STK11 (LKB1) Pathway Disruption in Lung Adenocarcinoma.
      Serine/threonine kinase 11 gene (STK11), better known as liver kinase β1, is a tumor suppressor that is commonly mutated in lung adenocarcinoma (LUAD). Previous work has shown that mutational inactivation of the STK11 pathway may serve as a predictive biomarker for cancer treatments, including phenformin and cyclooxygenase-2 inhibition. Although immunohistochemical (IHC) staining and diagnos
      BS3PM1PS3
      34849607 ↗ functional
      Functional assessment of somatic STK11 variants identified in primary human non-small cell lung cancers.
      Serine/Threonine Kinase 11 (STK11) encodes an important tumor suppressor that is frequently mutated in lung adenocarcinoma. Clinical studies have shown that mutations in STK11 resulting in loss of function correlate with resistance to anti-PD-1 monoclonal antibody therapy in KRAS-driven non-small cell lung cancer (NSCLC), but the molecular mechanisms responsible remain unclear. Despite this uncert
      BS3PM1PS3
      10408777 ↗ splicing rna
      Novel mutations in the LKB1/STK11 gene in Dutch Peutz-Jeghers families.
      The Peutz-Jeghers syndrome (PJS) is a rare hereditary disorder in which gastrointestinal hamartomatous polyposis, mucocutaneous pigmentation, and a predisposition for developing cancer are transmitted in an autosomal dominant fashion. The recently identified LKB1/STK11 gene located at chromosome 19p13.3 is mutated in a number of PJS pedigrees. We performed mutation analysis in 19, predominantly Du
      BP7PP3PP5PS4PVS1
      23718779 ↗ splicing rna
      High Resolution Melting analysis as a rapid and efficient method of screening for small mutations in the STK11 gene in patients with Peutz-Jeghers syndrome.
      Peutz-Jeghers syndrome (PJS) is a rare hereditary syndrome characterized by the occurrence of hamartomatous polyps in the gastrointestinal tract, mucocutaneous pigmentation and increased risk of cancer in multiple internal organs. Depending on the studied population, its incidence has been estimated to range from 1:200 000 even up to 1:50 000 births. Being an autosomal disease, PJS is caused in mo
      BP7PP3PP5PS4PVS1
      25645574 ↗ splicing rna
      ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes.
      This guideline presents recommendations for the management of patients with hereditary gastrointestinal cancer syndromes. The initial assessment is the collection of a family history of cancers and premalignant gastrointestinal conditions and should provide enough information to develop a preliminary determination of the risk of a familial predisposition to cancer. Age at diagnosis and lineage (ma
      BP7PP3PP5PS4PVS1
      31672839 ↗ splicing rna
      Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium.
      The International Cancer of the Pancreas Screening Consortium met in 2018 to update its consensus recommendations for the management of individuals with increased risk of pancreatic cancer based on family history or germline mutation status (high-risk individuals). A modified Delphi approach was employed to reach consensus among a multidisciplinary group of experts who voted on consensus statement
      BP7PP3PP5PS4PVS1
      15604628 ↗ case observation
      Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors.
      These cancer genetic counseling recommendations describe the medical, psychosocial, and ethical ramifications of identifying at-risk individuals through cancer risk assessment with or without genetic testing. They were developed by members of the Practice Issues Subcommittee of the National Society of Genetic Counselors Cancer Genetic Counseling Special Interest Group. The information contained in
      PP5PS4
      16582077 ↗ case observation
      Exonic STK11 deletions are not a rare cause of Peutz-Jeghers syndrome.
      Peutz-Jeghers syndrome (PJS) is a rare, autosomal dominant cancer predisposition syndrome characterised by oro-facial pigmentation and hamartomatous polyposis of the gastrointestinal tract. A causal germline mutation in STK11 can be identified in 30% to 80% of PJS patients. Here we report the comprehensive mutational analysis of STK11 in 38 PJS probands applying conventional PCR based mutation det
      PP5PS4
      28492532 ↗ background review
      Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
      PP5PS4
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots