About STK11
No gene-level summary was recorded for this case.
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.
Gene-level background from the recorded interpretation.
Words with a dotted underline have a short definition. Hover or tap them.No gene-level summary was recorded for this case.
The recorded framework is Not recorded. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.
The applied criteria and their strengths are shown as assessed under the stated framework.
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.
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.
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.
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.
No benign criterion marked as applied in the recorded assessment.
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.
Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.
gnomAD v4.1: 0 / 1,590,826 alleles. Recorded AF 0. Recorded homozygote count 0.
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
Recorded SpliceAI maximum delta score: 0.520. Refer to the recorded PP3/BP4 rationale for interpretation.
1 Pathogenic · 1 Likely pathogenic. ClinVar API review status: criteria provided, single submitter.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant has previously been reported in somatic cancers (COSMIC; COSV58826710, n = 5 times).
This variant does not lie in a statistically significant hotspot.
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.
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).
No criteria match.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
No further detail was recorded.
Every interpreted variant in STK11, mapped onto the exon structure of NM_000455.5. Select a row to find it on the plot.
| Protein | Location | Classification | Link |
|---|
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).
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
No further detail was recorded.
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.
Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.
The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.
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).
Absent from gnomAD v2.1.
Absent from gnomAD-Canada v1.0.
This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 824343)
SpliceAI predicts possible splice impact for this variant (max delta score = 0.52). BayesDel score = 0.65.
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV58826710, n = 5 times).
This variant does not lie in a statistically significant hotspot.