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NM_000455.4(STK11):c.-1C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(2);Uncertain significance(3)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Nov 30, 2020)
Last evaluated:
Aug 16, 2019
Accession:
VCV000185127.6
Variation ID:
185127
Description:
single nucleotide variant
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NM_000455.4(STK11):c.-1C>T

Allele ID
185459
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.3
Genomic location
19: 1206913 (GRCh38) GRCh38 UCSC
19: 1206912 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.9:g.1206912C>T
NC_000019.10:g.1206913C>T
NM_000455.4:c.-1C>T 5 prime UTR
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:1206912:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Exome Aggregation Consortium (ExAC) 0.00000
The Genome Aggregation Database (gnomAD), exomes 0.00001
Links
ClinGen: CA022704
dbSNP: rs759284466
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 1 criteria provided, single submitter Aug 16, 2019 RCV000986036.1
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Apr 8, 2019 RCV000164494.4
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Dec 7, 2018 RCV000431625.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
STK11 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
1718 1785

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely benign
(Jan 11, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000523220.4
Submitted: (Mar 26, 2018)
Evidence details
Comment:
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 … (more)
Uncertain significance
(Dec 07, 2018)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000920285.1
Submitted: (Apr 24, 2019)
Evidence details
Publications
PubMed (1)
Comment:
Variant summary: STK11 c.-1C>T is located in the untranslated mRNA region upstream of the initiation codon. The variant allele was found at a frequency of … (more)
Uncertain significance
(Aug 16, 2019)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV001134839.2
Submitted: (Mar 06, 2020)
Evidence details
Publications
PubMed (1)
Likely benign
(Apr 13, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV001341888.1
Submitted: (May 19, 2020)
Evidence details
Uncertain significance
(Apr 08, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000215143.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
The c.-1C>T variant is located in the 5' untranslated region (5’ UTR) of the STK11 gene. This variant results from a C to T substitution … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Identification of a Variety of Mutations in Cancer Predisposition Genes in Patients With Suspected Lynch Syndrome. Yurgelun MB Gastroenterology 2015 PMID: 25980754

Text-mined citations for rs759284466...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Jun 14, 2021