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NM_000455.5(STK11):c.954_956delinsCCAGGTGGGA (p.Pro319fs) AND Peutz-Jeghers syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 21, 2019
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV001239930.2

Allele description [Variation Report for NM_000455.5(STK11):c.954_956delinsCCAGGTGGGA (p.Pro319fs)]

NM_000455.5(STK11):c.954_956delinsCCAGGTGGGA (p.Pro319fs)

Gene:
STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]
Variant type:
Indel
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NM_000455.5(STK11):c.954_956delinsCCAGGTGGGA (p.Pro319fs)
HGVS:
  • NC_000019.10:g.1223018_1223020delinsCCAGGTGGGA
  • NG_007460.2:g.38612_38614delinsCCAGGTGGGA
  • NM_000455.5:c.954_956delinsCCAGGTGGGAMANE SELECT
  • NP_000446.1:p.Pro319fs
  • LRG_319t1:c.954_956delinsCCAGGTGGGA
  • LRG_319:g.38612_38614delinsCCAGGTGGGA
  • NC_000019.9:g.1223017_1223019delinsCCAGGTGGGA
  • NM_000455.4:c.954_956delinsCCAGGTGGGA
Protein change:
P319fs
Links:
dbSNP: rs2080796043
NCBI 1000 Genomes Browser:
rs2080796043
Molecular consequence:
  • NM_000455.5:c.954_956delinsCCAGGTGGGA - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Name:
Peutz-Jeghers syndrome (PJS)
Synonyms:
Polyposis, hamartomatous intestinal; Polyps-and-spots syndrome; Peutz-Jeghers polyposis; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0008280; MeSH: D010580; MedGen: C0031269; Orphanet: 2869; OMIM: 175200

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001412834Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Oct 21, 2019)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001412834.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This sequence change creates a premature translational stop signal (p.Pro319Glnfs*43) in the STK11 gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with STK11-related conditions. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Loss-of-function variants in STK11 are known to be pathogenic (PMID: 15188174, 16287113). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024