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Variant interpretation report

STK11 c.388G>T, p.(Glu130Ter)

NM_000455.5:c.388G>T NP_000446.1:p.(Glu130Ter) View identifiers
Classification
Pathogenic

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. This variant is pathogenic. Select a step to read what it means.

Pathogenic.A pathogenic classification under the recorded framework.

In plain language

Gene-level background from the recorded interpretation.

About STK11

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 4 Benign evidence criteria: 0
Pathogenic criteria applied · 4
PVS1Very strong
PVS1 · very strong

This variant is a nonsense change (NP_000446.1:p.(Glu130Ter)) predicted to undergo nonsense-mediated decay. STK11 loss of function is an established mechanism for Peutz-Jeghers syndrome. Under the ClinGen SVI PVS1 decision framework (PMC6185798), nonsense variants in genes with an established loss-of-function disease mechanism are assigned PVS1 at very strong strength. The premature termination codon at position 130 lies well upstream of the last exon-exon junction, meeting NMD prediction criteria.

PM1Moderate
PM1 · moderate

This variant introduces a premature termination at codon 130 within the protein kinase domain of STK11 (spanning approximately aa49-309). Truncation at this position removes the majority of the kinase domain including subdomains I-XI and the C-terminal regulatory region. The kinase domain of STK11 is a well-characterized critical functional domain essential for LKB1 catalytic activity and tumor suppressor function.

PM2Supporting
PM2 · supporting

This variant is absent from gnomAD v4.1 (0/1,590,826 alleles; AF=0.00000%) and absent from gnomAD v2.1. The allele frequency is well below the 0.1% threshold for PM2 application.

PP3Supporting
PP3 · supporting

In silico tools support a deleterious effect: SpliceAI predicts a possible splice impact with a max delta score of 0.52 (acceptor loss delta 0.52), and BayesDel predicts a damaging effect with a score of 0.65. The SpliceAI prediction reflects potential cryptic splice effects from the nucleotide change beyond the primary nonsense mechanism.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Pathogenic

gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PVS1 very strong, PM1 moderate, PM2 supporting, PP3 supporting; combination = 1 very strong + 1 moderate + 2 supporting, which maps to Pathogenic.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

SpliceAI score
0.520 maximum delta

Recorded SpliceAI maximum delta score: 0.520. Refer to the recorded PP3/BP4 rationale for interpretation.

ClinVar submissions
2 reported laboratory submissions

1 Pathogenic · 1 Likely pathogenic. ClinVar API review status: criteria provided, single submitter.

Context only ClinVar ↗
Functional evidence
Statement recorded

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
5 recorded samples

This variant has previously been reported in somatic cancers (COSMIC; COSV58826710, n = 5 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.

For specialists

Technical detail

ACMG/AMP criteria under Not recorded, with the data and sources behind each one.

29 criteria with recorded statuses: 4 met · 17 not met · 0 not assessed · 8 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Met Not met Not assessed Not applicable

NM_000455.5:c.388G>T is a nonsense variant predicted to produce a premature termination codon at position 130 (p.Glu130Ter). This null variant in STK11, a gene where loss of function is a well-established mechanism for Peutz-Jeghers syndrome, meets PVS1 at very strong strength under the ClinGen SVI PVS1 decision framework.

The truncation at codon 130 removes the majority of the protein kinase domain and the entire C-terminal regulatory region of STK11. The kinase domain is a well-characterized critical functional domain essential for LKB1 catalytic activity and tumor suppressor function, satisfying PM1 at moderate strength.

This variant is absent from gnomAD v4.1 with 0 alleles observed across 1,590,826 alleles, meeting the PM2 threshold of <0.1% population frequency.

In silico predictions support a deleterious effect: SpliceAI predicts possible splice impact with a max delta score of 0.52 (acceptor loss), and BayesDel predicts a damaging score of 0.65, satisfying PP3 at supporting strength.

Overall classification: PATHOGENIC. The combination of PVS1 (very strong), PM1 (moderate), PM2 (supporting), and PP3 (supporting) meets the ACMG/AMP 2015 classification threshold for Pathogenic (1 Very Strong + 1 Moderate + >=1 Supporting).

Met · 4

PVS1 Very strongThis variant is a nonsense change (NP_000446.1:p.(Glu130Ter)) predicted to undergo nonsense-mediated decay. STK11 loss of function is an established mechanism for Peutz-Jeghers syndrome. Under the ClinGen SVI PVS1 decision framework (PMC6185798), nonsense variants in genes with an established loss-of-function disease mechanism are assigned PVS1 at very strong strength. The premature termination codon at position 130 lies well upstream of the last exon-exon junction, meeting NMD prediction criteria. Details ▾Hide ▴
Evidence considered
  • Nonsense variant c.388G>T producing p.(Glu130Ter) in exon 3 of 9
  • STK11 loss of function is an established germline disease mechanism for Peutz-Jeghers syndrome
  • Premature termination at codon 130 predicted to trigger NMD under PVS1 decision framework PMC6185798
Sources
PM1 ModerateThis variant introduces a premature termination at codon 130 within the protein kinase domain of STK11 (spanning approximately aa49-309). Truncation at this position removes the majority of the kinase domain including subdomains I-XI and the C-terminal regulatory region. The kinase domain of STK11 is a well-characterized critical functional domain essential for LKB1 catalytic activity and tumor suppressor function. Details ▾Hide ▴
Evidence considered
  • Truncation at codon 130 removes most of the kinase domain (aa130-309) and the entire C-terminal region
  • The STK11 kinase domain is a well-established critical functional domain characterized in structural studies
  • PMID:24652667 demonstrates domain-specific genotype-phenotype correlations in STK11
Sources
PM2 SupportingThis variant is absent from gnomAD v4.1 (0/1,590,826 alleles; AF=0.00000%) and absent from gnomAD v2.1. The allele frequency is well below the 0.1% threshold for PM2 application. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1: 0/1
  • 590
  • 826 alleles
  • AF=0.0
  • gnomAD v2.1: absent
  • All subpopulation frequencies at 0.0
Sources
PP3 SupportingIn silico tools support a deleterious effect: SpliceAI predicts a possible splice impact with a max delta score of 0.52 (acceptor loss delta 0.52), and BayesDel predicts a damaging effect with a score of 0.65. The SpliceAI prediction reflects potential cryptic splice effects from the nucleotide change beyond the primary nonsense mechanism. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta score: 0.52 (acceptor loss = 0.52
  • above the 0.2 threshold)
  • BayesDel score: 0.65 (above typical deleterious threshold of ~0.5)
Sources
spliceai ↗bayesdel

Not met · 17 · evaluated, threshold not reached

PS2 No de novo occurrence of NM_000455.5:c.388G>T has been reported in the available literature or case materials. Details ▾Hide ▴
Still missing
  • No de novo observation available for this variant
PS3 No variant-specific functional data was identified for NM_000455.5:c.388G>T (p.Glu130Ter) in the seven publications reviewed. The OncoKB-curated literature provides general functional characterization of LKB1/STK11 biology but does not include experimental testing of the E130* variant or systematic range characterization spanning codon 130. Details ▾Hide ▴
Evidence considered
  • OncoKB annotated as Likely Loss-of-function and Likely Oncogenic
  • but no variant-specific experimental data cited
  • COSMIC reports 5 somatic occurrences (COSV58826710)
  • but somatic observation does not constitute experimental functional evidence
Still missing
  • No experimental functional studies of p.(Glu130Ter) or systematically characterized range including codon 130
PS4 No published case-control or case series data confirming this variant in affected individuals was identified. The ClinVar submission (Ambry Genetics, SCV001182975) classifies the variant as Pathogenic based on clinical testing, but no published clinical details or variant-specific case counts are available for independent review. A ClinVar-associated image (PMID:18846624) could not be assessed as no full text or abstract is available. Details ▾Hide ▴
Evidence considered
  • ClinVar variation ID 824343: Pathogenic (Ambry Genetics
  • criteria provided single submitter) and Likely pathogenic (PreventionGenetics)
  • No published case counts or cohort statistics for this variant
Still missing
  • No published case series or case-control data with variant-specific counts
Sources
PM6 No de novo observation of this variant has been reported. PM6 requires a de novo occurrence with or without confirmed maternity and paternity. Details ▾Hide ▴
Still missing
  • No de novo observation available
PP1 No cosegregation data is available for this variant. Details ▾Hide ▴
Still missing
  • No cosegregation data available
PP4 No proband phenotype or family history information is available for assessment. PP4 requires a highly specific patient phenotype or family history for a disease with a single genetic etiology. Details ▾Hide ▴
Still missing
  • No proband phenotype or family history available
PP5 The ClinVar entry (variation ID 824343) has a review status of 'criteria provided, single submitter,' which is not a 3-star expert panel review. Under the adjudication framework, PP5 is applied at supporting strength only when the ClinVar classification comes from a 3-star expert panel. The ACMG/NSGC referral guideline (PMID:25394175) does not mention this specific variant. Details ▾Hide ▴
Evidence considered
  • ClinVar classification: Pathogenic (Ambry Genetics
  • criteria provided single submitter) and Likely pathogenic (PreventionGenetics)
  • Review status is 'criteria provided
  • single submitter' — not 3-star expert panel
  • PMID:25394175 is a referral guideline
  • not variant-specific evidence
Still missing
  • No 3-star expert panel ClinVar classification available
Sources
BA1 This variant is absent from gnomAD (0/1,590,826 alleles; AF=0.0). BA1 requires an allele frequency greater than 1% in population databases. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1: 0/1
  • 590
  • 826 alleles
  • AF=0.0
Sources
BS1 This variant is absent from gnomAD (0/1,590,826 alleles; AF=0.0). BS1 requires an allele frequency greater than 0.3% in population databases. Details ▾Hide ▴
Evidence considered
  • gnomAD v4.1: 0/1
  • 590
  • 826 alleles
  • AF=0.0
Sources
BS2 This variant is absent from all population databases. No evidence exists of healthy adult homozygotes or heterozygotes carrying this variant. BS2 requires observation in a healthy adult individual for a fully penetrant disorder. Details ▾Hide ▴
Evidence considered
  • Absent from gnomAD and all population databases
BS3 No well-established functional studies demonstrate no deleterious effect for this variant. Available evidence from OncoKB suggests likely loss-of-function, consistent with a pathogenic mechanism rather than a benign one. Reviewed functional literature (structural studies, reviews, TCGA profiling) provides general LKB1 biology context but no variant-specific benign functional data. Details ▾Hide ▴
Evidence considered
  • OncoKB: Likely Loss-of-function
  • Likely Oncogenic — supports deleterious effect
  • No experimental studies show normal function for p.(Glu130Ter)
BS4 No cosegregation data is available demonstrating lack of segregation with disease. Details ▾Hide ▴
Still missing
  • No cosegregation data available
BP2 No observation of this variant in trans with a known pathogenic STK11 variant has been reported. Details ▾Hide ▴
Still missing
  • No observation in trans with a pathogenic variant
BP4 Multiple lines of computational evidence suggest a deleterious effect rather than a benign one. SpliceAI predicts possible splice impact (max delta 0.52) and BayesDel predicts a damaging score of 0.65. BP4 requires multiple lines of computational evidence suggesting no impact. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta: 0.52 — predicts potential splice impact
  • BayesDel: 0.65 — predicts damaging effect
Sources
spliceai ↗bayesdel
BP5 No observation of this variant in a case with an alternate molecular basis for disease has been reported. Details ▾Hide ▴
Still missing
  • No observation with alternate molecular basis
BP6 The ClinVar classification for this variant is Pathogenic/Likely pathogenic, not benign. BP6 requires a reputable source to classify the variant as benign. Details ▾Hide ▴
Evidence considered
  • ClinVar: Pathogenic (1 submitter) and Likely pathogenic (1 submitter)
Sources
PS5 PS5 requires the same amino acid change as a previously established pathogenic variant from a different nucleotide change. No alternative nucleotide change creating p.(Glu130Ter) has been reported as pathogenic. Details ▾Hide ▴

No further detail was recorded.

Not applicable · 8· recorded as not applicable Show reasons ▾Hide reasons ▴
PS1 N/APS1 applies when the same amino acid change has been established as pathogenic from a different nucleotide change. This is a nonsense variant and PS1 is not applicable to truncating variants. Details ▾Hide ▴

No further detail was recorded.

PM3 N/APM3 applies to recessive disorders where a pathogenic variant is detected in trans. STK11-related Peutz-Jeghers syndrome is autosomal dominant. Details ▾Hide ▴

No further detail was recorded.

PM4 N/APM4 applies to in-frame deletions/insertions or stop-loss variants. This is a nonsense (stop-gain) substitution. Details ▾Hide ▴

No further detail was recorded.

PM5 N/APM5 applies to novel missense variants at residues where a different missense change is known to be pathogenic. This is a nonsense variant. Details ▾Hide ▴

No further detail was recorded.

PP2 N/APP2 applies to missense variants in genes with a low rate of benign missense variation where missense variants are a common disease mechanism. This is a nonsense variant. Details ▾Hide ▴

No further detail was recorded.

BP1 N/ABP1 applies to missense variants in genes for which primarily truncating variants are known to cause disease. This is a nonsense (truncating) variant. Details ▾Hide ▴

No further detail was recorded.

BP3 N/ABP3 applies to in-frame deletions/insertions in a repetitive region without known function. This is a nonsense substitution. Details ▾Hide ▴

No further detail was recorded.

BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. This is a nonsense variant. Details ▾Hide ▴

No further detail was recorded.

Identifiers

Gene
STK11
Transcript
NM_000455.5
Coding (HGVS c.)
NM_000455.5:c.388G>T
Protein (HGVS p.)
NP_000446.1:p.(Glu130Ter)
GRCh38
chr19:1219337 G>T
GRCh37
chr19:1219336 G>T
ClinVar
824343
COSMIC
COSV58826710

Gene diagram

Every interpreted variant in STK11, mapped onto the exon structure of NM_000455.5. Select a row to find it on the plot.

STK11NM_000455.5
Fetching transcript structure from UCSC…
gnomAD v4.1 0 / 1,590,826 alleles AF 0 · 0 homozygotes
gnomAD v2.1 Allele count data not recorded
gnomAD-Canada v1.0 Allele count data not recorded

By genetic ancestry

gnomAD v4.1

AF 0 · 0 / 1,590,826 alleles · 0 hom
No alternate alleles recorded in the displayed ancestry groups.

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0; MAF= 0.00000%, 0/1590826 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74650 alleles, homozygotes = 0).

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

SpliceAI and Pangolin

SpliceAI acceptor lossat -21 bp
0.520
SpliceAI acceptor gainat +3 bp
0.230
SpliceAI donor lossat +76 bp
0.110
SpliceAI donor gainat -58 bp
0.000
Pangolin splice lossmagnitude shown
-0.460
Pangolin splice gain
0.070

Other predictors

REVEL
Not available
BayesDel
0.650

How the predictions were used

PP3 SupportingIn silico tools support a deleterious effect: SpliceAI predicts a possible splice impact with a max delta score of 0.52 (acceptor loss delta 0.52), and BayesDel predicts a damaging effect with a score of 0.65. The SpliceAI prediction reflects potential cryptic splice effects from the nucleotide change beyond the primary nonsense mechanism. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta score: 0.52 (acceptor loss = 0.52
  • above the 0.2 threshold)
  • BayesDel score: 0.65 (above typical deleterious threshold of ~0.5)
Sources
spliceai ↗bayesdel
BP4 Multiple lines of computational evidence suggest a deleterious effect rather than a benign one. SpliceAI predicts possible splice impact (max delta 0.52) and BayesDel predicts a damaging score of 0.65. BP4 requires multiple lines of computational evidence suggesting no impact. Details ▾Hide ▴
Evidence considered
  • SpliceAI max delta: 0.52 — predicts potential splice impact
  • BayesDel: 0.65 — predicts damaging effect
Sources
spliceai ↗bayesdel
BP7 N/ABP7 applies to synonymous variants with no predicted splice impact. This is a nonsense variant. Details ▾Hide ▴

No further detail was recorded.

Statement

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.52). BayesDel score = 0.65.

7 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

  • Somatic LKB1 mutations promote cervical cancer progression.
    Reports somatic LKB1 mutations in cervical cancer. Describes germline STK11 mutations causing Peutz-Jeghers syndrome and somatic inactivation in cervical tumors. NM_000455.5:c.388G>T (p.Glu130Ter) was not identified in this paper.
    Does not name this variant
    PMID 19340305 ↗
  • Structure of the LKB1-STRAD-MO25 complex reveals an allosteric mechanism of kinase activation.
    Describes the crystal structure of the LKB1-STRAD-MO25 heterotrimeric complex and the allosteric mechanism of kinase activation. Provides structural characterization of the LKB1 kinase domain. NM_000455.5:c.388G>T (p.Glu130Ter) was not identified in this paper.
    Does not name this variant
    PMID 19892943 ↗
  • The role of LKB1 in lung cancer.
    Review article describing the role of LKB1 in lung cancer, including mutation patterns, functional pathways (AMPK, cell polarity, EMT), and therapeutic implications. Notes that most LKB1 mutations in lung cancer are nonsense, frameshift, or large deletions giving rise to truncated proteins. NM_000455.5:c.388G>T (p.Glu130Ter) was not identified in this paper.
    Does not name this variant
    PMID 21516316 ↗
  • STK11 domain XI mutations: candidate genetic drivers leading to the development of dysplastic polyps in Peutz-Jeghers syndrome.
    Reports STK11 mutation spectrum in 116 Chinese PJS patients. Describes a genotype-phenotype correlation wherein mutations in kinase domain XI (aa277-309) are associated with a 90% incidence of GI polyp dysplasia. NM_000455.5:c.388G>T (p.Glu130Ter) is outside domain XI and was not identified in this cohort.
    Does not name this variant
    PMID 24652667 ↗
  • Comprehensive molecular profiling of lung adenocarcinoma.
    TCGA comprehensive molecular profiling of 230 lung adenocarcinomas. Reports STK11 as one of 18 statistically significantly mutated genes. NM_000455.5:c.388G>T (p.Glu130Ter) was not identified in this paper.
    Does not name this variant
    PMID 25079552 ↗
  • Gene symbol: STK11. Disease: Peutz-Jeghers Syndrome.
    Scott R et al. · 2008
    Short journal letter titled 'Gene symbol: STK11. Disease: Peutz-Jeghers Syndrome.' Full text not available in text format; only a screenshot image exists in the case materials. Abstract is empty in PubMed metadata. The variant NM_000455.5:c.388G>T could not be confirmed as mentioned in this publication.
    Does not name this variant
    PMID 18846624 ↗
  • A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment.
    Hampel H et al. · 2015
    ACMG/NSGC practice guideline providing referral indications for cancer predisposition assessment. Lists criteria for referral to cancer genetic consultation for multiple hereditary cancer syndromes including Peutz-Jeghers syndrome. Does not discuss any specific STK11 variants. NM_000455.5:c.388G>T (p.Glu130Ter) was not identified in this paper.
    Does not name this variant
    PMID 25394175 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0; MAF= 0.00000%, 0/1590826 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/74650 alleles, homozygotes = 0).

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 824343)

In silico

SpliceAI predicts possible splice impact for this variant (max delta score = 0.52). BayesDel score = 0.65.

Functional

OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.

Somatic

This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV58826710, n = 5 times).

Cancer Hotspots

This variant does not lie in a statistically significant hotspot.