NM_000455.5(STK11):c.180del (p.Ser59_Tyr60insTer) AND Peutz-Jeghers syndrome

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Nov 9, 2022
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000813229.9

Allele description [Variation Report for NM_000455.5(STK11):c.180del (p.Ser59_Tyr60insTer)]

NM_000455.5(STK11):c.180del (p.Ser59_Tyr60insTer)

Gene:

STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_000455.5(STK11):c.180del (p.Ser59_Tyr60insTer)

HGVS:

NC_000019.10:g.1207093del
NG_007460.2:g.22687del
NM_000455.5:c.180delMANE SELECT
NP_000446.1:p.Ser59_Tyr60insTer
NP_000446.1:p.Ser59_Tyr60insTer
LRG_319t1:c.180del
LRG_319:g.22687del
LRG_319p1:p.Ser59_Tyr60insTer
NC_000019.9:g.1207092del
NM_000455.4:c.180del
NM_000455.4:c.180delC

Links:

dbSNP: rs1555735008

NCBI 1000 Genomes Browser:

rs1555735008

Molecular consequence:

NM_000455.5:c.180del - nonsense - [Sequence Ontology: SO:0001587]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000953577	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 9, 2022)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 9428765, 10353780, 17026623, 22679258, 23718779, 24037887, 15188174, 16287113, 28492532
SCV002057351	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 15, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000953577

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 9, 2022)

germline

clinical testing

PubMed (9)
[See all records that cite these PMIDs]

SCV002057351

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 15, 2021)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A serine/threonine kinase gene defective in Peutz-Jeghers syndrome.

Hemminki A, Markie D, Tomlinson I, Avizienyte E, Roth S, Loukola A, Bignell G, Warren W, Aminoff M, Höglund P, Järvinen H, Kristo P, Pelin K, Ridanpää M, Salovaara R, Toro T, Bodmer W, Olschwang S, Olsen AS, Stratton MR, de la Chapelle A, Aaltonen LA.

Nature. 1998 Jan 8;391(6663):184-7.

PubMed [citation]

PMID:: 9428765

Germline mutations of the LKB1 (STK11) gene in Peutz-Jeghers patients.

Wang ZJ, Churchman M, Avizienyte E, McKeown C, Davies S, Evans DG, Ferguson A, Ellis I, Xu WH, Yan ZY, Aaltonen LA, Tomlinson IP.

J Med Genet. 1999 May;36(5):365-8.

PubMed [citation]

PMID:: 10353780
PMCID:: PMC1734361

See all PubMed Citations (10)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000953577.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 503650). This premature translational stop signal has been observed in individual(s) with Peutz-Jeghers syndrome (PJS) (PMID: 9428765, 10353780, 17026623, 22679258, 23718779, 24037887). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Tyr60*) in the STK11 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in STK11 are known to be pathogenic (PMID: 15188174, 16287113).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002057351.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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