ClinVar Miner

Submissions for variant NM_000455.5(STK11):c.310A>T (p.Arg104Trp)

gnomAD frequency: 0.00001  dbSNP: rs587782783
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000132324 SCV000187411 uncertain significance Hereditary cancer-predisposing syndrome 2025-03-13 criteria provided, single submitter clinical testing The p.R104W variant (also known as c.310A>T), located in coding exon 2 of the STK11 gene, results from an A to T substitution at nucleotide position 310. The arginine at codon 104 is replaced by tryptophan, an amino acid with dissimilar properties. This variant was reported in 1/60,466 breast cancer cases and in 0/53,461 controls (Dorling et al. N Engl J Med. 2021 02;384:428-439). This variant has been detected in multiple individuals with no reported features of Peutz-Jeghers syndrome (Ambry internal data). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the available evidence, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV000227082 SCV000284861 likely benign Peutz-Jeghers syndrome 2024-11-26 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000227082 SCV002057767 uncertain significance Peutz-Jeghers syndrome 2021-07-15 criteria provided, single submitter clinical testing
Baylor Genetics RCV003462043 SCV004205596 uncertain significance Melanoma, cutaneous malignant, susceptibility to, 1 2023-05-19 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV005237574 SCV005887363 uncertain significance not specified 2025-01-13 criteria provided, single submitter clinical testing Variant summary: STK11 c.310A>T (p.Arg104Trp) results in a non-conservative amino acid change located in the Protein kinase domain (IPR000719) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 249174 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.310A>T in individuals affected with Peutz-Jeghers Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 142871). Based on the evidence outlined above, the variant was classified as uncertain significance.
Department of Pathology and Laboratory Medicine, Sinai Health System RCV005359301 SCV005915895 uncertain significance Peutz-Jeghers syndrome; Familial pancreatic carcinoma 2022-03-30 criteria provided, single submitter clinical testing

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