ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.1178A>G (p.Asn393Ser)

dbSNP: rs1060499965
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000551124 SCV000629072 uncertain significance Peutz-Jeghers syndrome 2024-01-21 criteria provided, single submitter clinical testing This sequence change replaces asparagine, which is neutral and polar, with serine, which is neutral and polar, at codon 393 of the STK11 protein (p.Asn393Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with breast cancer (PMID: 35264596). ClinVar contains an entry for this variant (Variation ID: 458018). 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) performed at Invitae indicates that this missense variant is not expected to disrupt STK11 protein function with a negative predictive value of 95%. 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.
Mendelics RCV000551124 SCV000839429 uncertain significance Peutz-Jeghers syndrome 2018-07-02 criteria provided, single submitter clinical testing
Color Diagnostics, LLC DBA Color Health RCV000771660 SCV000904284 uncertain significance Hereditary cancer-predisposing syndrome 2022-07-06 criteria provided, single submitter clinical testing This missense variant replaces asparagine with serine at codon 393 of the STK11 protein. Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, 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.
Genome-Nilou Lab RCV000551124 SCV002057956 uncertain significance Peutz-Jeghers syndrome 2021-07-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV000771660 SCV002635179 uncertain significance Hereditary cancer-predisposing syndrome 2022-11-23 criteria provided, single submitter clinical testing The p.N393S variant (also known as c.1178A>G), located in coding exon 9 of the STK11 gene, results from an A to G substitution at nucleotide position 1178. The asparagine at codon 393 is replaced by serine, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx RCV003228944 SCV003926136 uncertain significance not provided 2023-05-17 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; Observed in an individual with breast cancer (Guindalini et al., 2022); This variant is associated with the following publications: (PMID: 28900777, 35264596)
Baylor Genetics RCV003470730 SCV004205593 uncertain significance Melanoma, cutaneous malignant, susceptibility to, 1 2023-06-06 criteria provided, single submitter clinical testing

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