Starting
Initialising…
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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
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      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.
      Sources & reference links
      7Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      26917230 ↗ A Sensitive NanoString-Based Assay to Score STK11 (LKB1) Pathway Disruption in Lung Adenocarcinoma. ONCOKB
      34849607 ↗ Functional assessment of somatic STK11 variants identified in primary human non-small cell lung cancers. ONCOKB
      10408777 ↗ Novel mutations in the LKB1/STK11 gene in Dutch Peutz-Jeghers families. CLINVAR
      23718779 ↗ 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. CLINVAR
      25645574 ↗ ACG clinical guideline: Genetic testing and management of hereditary gastrointestinal cancer syndromes. CLINVAR
      31672839 ↗ Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium. CLINVAR
      15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
      16582077 ↗ Exonic STK11 deletions are not a rare cause of Peutz-Jeghers syndrome. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR