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NM_000455.4(STK11):c.464+4C>T

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Jan 7, 2021)
Last evaluated:
Oct 19, 2020
Accession:
VCV000142377.9
Variation ID:
142377
Description:
single nucleotide variant
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NM_000455.4(STK11):c.464+4C>T

Allele ID
152091
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
19p13.3
Genomic location
19: 1219417 (GRCh38) GRCh38 UCSC
19: 1219416 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000019.10:g.1219417C>T
NC_000019.9:g.1219416C>T
LRG_319t1:c.464+4C>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000019.10:1219416:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD), exomes 0.00001
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00008
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA023012
dbSNP: rs373167735
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts May 22, 2018 RCV000485485.3
Uncertain significance 1 criteria provided, single submitter Oct 19, 2020 RCV000204358.8
Conflicting interpretations of pathogenicity 2 criteria provided, conflicting interpretations Sep 5, 2019 RCV000131463.7
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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
1733 1801

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 29, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
PreventionGenetics,PreventionGenetics
Accession: SCV000806080.1
Submitted: (Jan 29, 2018)
Evidence details
Uncertain significance
(May 22, 2018)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000567046.5
Submitted: (Jan 29, 2019)
Evidence details
Comment:
This variant is denoted STK11 c.464+4C>T or IVS3+4C>T and consists of a C>T nucleotide substitution at the +4 position of intron 3 of the STK11 … (more)
Uncertain significance
(Sep 05, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000686654.3
Submitted: (May 19, 2020)
Comment:
This variant causes a C>T nucleotide substitution at the +4 position of intron 3 of the STK11 gene. Splice site prediction tools predict that this … (more)
Evidence details
Likely benign
(Apr 05, 2019)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000186448.6
Submitted: (Nov 30, 2020)
Evidence details
Comment:
Other data supporting benign classification;RNA Studies
Uncertain significance
(Oct 19, 2020)
criteria provided, single submitter
Method: clinical testing
Peutz-Jeghers syndrome
Allele origin: germline
Invitae
Accession: SCV000260487.8
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change falls in intron 3 of the STK11 gene. It does not directly change the encoded amino acid sequence of the STK11 protein, … (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
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098

Text-mined citations for rs373167735...

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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 23, 2021