ClinVar Miner

Submissions for variant NM_000455.4(STK11):c.1296G>A (p.Gln432=) (rs587781179)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000213036 SCV000171897 benign not specified 2014-05-09 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Ambry Genetics RCV000128305 SCV000212873 likely benign Hereditary cancer-predisposing syndrome 2014-07-30 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Invitae RCV001079439 SCV000253248 likely benign Peutz-Jeghers syndrome 2020-12-07 criteria provided, single submitter clinical testing
Color Health, Inc RCV000128305 SCV000686620 likely benign Hereditary cancer-predisposing syndrome 2015-12-14 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588407 SCV000696712 benign not provided 2017-07-06 criteria provided, single submitter clinical testing Variant summary: The c.1296G>A (p.Gln432=) in STK11 affects a non-conserved nucleotide and 5/5 programs in Alamut predict that this variant does not affect normal splicing. ESE finder predicts that this variant may affect multiple ESE sites. However, no functional studies confirming these predictions were published at the time of evaluation. This variant is found in 1/11504 control chromosomes of ExAC at a frequency of 0.000086 and 28/157510 chrs tested in gnomAD dataset. These frequencies exceed the maximal expected frequency of a pathogenic allele (0.0000056), suggesting this variant is benign. In addition, multiple clinical laboratories classified this variant as benign/likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant was classified as benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588407 SCV000889853 benign not provided 2018-01-03 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001079439 SCV001287494 uncertain significance Peutz-Jeghers syndrome 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001286690 SCV001473302 likely benign none provided 2020-03-19 criteria provided, single submitter clinical testing

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