ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.1286C>G (p.Ala429Gly)

gnomAD frequency: 0.00005  dbSNP: rs757369900
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000197676 SCV000254547 likely benign Peutz-Jeghers syndrome 2024-01-25 criteria provided, single submitter clinical testing
GeneDx RCV000760078 SCV000565601 uncertain significance not provided 2020-07-30 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis supports that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Ambry Genetics RCV000574953 SCV000672336 uncertain significance Hereditary cancer-predisposing syndrome 2023-04-14 criteria provided, single submitter clinical testing The p.A429G variant (also known as c.1286C>G), located in coding exon 9 of the STK11 gene, results from a C to G substitution at nucleotide position 1286. The alanine at codon 429 is replaced by glycine, an amino acid with similar properties. This alteration was detected in a cohort of 37 African American women with breast cancer and 51 family members (McDonald JT et al. PLoS One, 2022 Oct;17:e0273835). This amino acid position is not well 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.
Color Diagnostics, LLC DBA Color Health RCV000574953 SCV000686619 uncertain significance Hereditary cancer-predisposing syndrome 2023-09-07 criteria provided, single submitter clinical testing This missense variant replaces alanine with glycine at codon 429 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 STK11-related disorders in the literature. This variant has been identified in 5/170826 chromosomes 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000760078 SCV000889852 uncertain significance not provided 2018-08-13 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000197676 SCV002058016 uncertain significance Peutz-Jeghers syndrome 2021-07-15 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000574953 SCV002531672 uncertain significance Hereditary cancer-predisposing syndrome 2022-03-12 criteria provided, single submitter curation
All of Us Research Program, National Institutes of Health RCV000197676 SCV004819039 uncertain significance Peutz-Jeghers syndrome 2024-02-05 criteria provided, single submitter clinical testing This missense variant replaces alanine with glycine at codon 429 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). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with hereditary cancer in the literature. This variant has been identified in 5/170826 chromosomes 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.
Mayo Clinic Laboratories, Mayo Clinic RCV000760078 SCV005408639 uncertain significance not provided 2024-09-06 criteria provided, single submitter clinical testing BP4

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