ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.113C>T (p.Pro38Leu)

dbSNP: rs1568690036
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000691132 SCV000818875 uncertain significance Peutz-Jeghers syndrome 2022-12-26 criteria provided, single submitter clinical testing This variant is not present in population databases (gnomAD no frequency). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 38 of the STK11 protein (p.Pro38Leu). This variant has not been reported in the literature in individuals affected with STK11-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on STK11 protein function. ClinVar contains an entry for this variant (Variation ID: 570301).
Color Diagnostics, LLC DBA Color Health RCV000777884 SCV000913892 uncertain significance Hereditary cancer-predisposing syndrome 2023-04-06 criteria provided, single submitter clinical testing This missense variant replaces proline with leucine at codon 38 of the STK11 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.
Ambry Genetics RCV000777884 SCV001170129 uncertain significance Hereditary cancer-predisposing syndrome 2023-02-03 criteria provided, single submitter clinical testing The p.P38L variant (also known as c.113C>T), located in coding exon 1 of the STK11 gene, results from a C to T substitution at nucleotide position 113. The proline at codon 38 is replaced by leucine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Genome-Nilou Lab RCV000691132 SCV002057739 uncertain significance Peutz-Jeghers syndrome 2021-07-15 criteria provided, single submitter clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV003320207 SCV004024314 uncertain significance not specified 2023-08-15 criteria provided, single submitter clinical testing
All of Us Research Program, National Institutes of Health RCV000691132 SCV004816314 uncertain significance Peutz-Jeghers syndrome 2023-05-04 criteria provided, single submitter clinical testing This missense variant replaces proline with leucine at codon 38 of the STK11 protein. Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has not been identified in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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