NC_000019.9:g.(?_1220652)_(1222337_?)del AND Peutz-Jeghers syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jan 30, 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:: RCV004581056.1

Allele description [Variation Report for NC_000019.9:g.(?_1220652)_(1222337_?)del]

NC_000019.9:g.(?_1220652)_(1222337_?)del

Gene:: STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 19p13.3
Genomic location:: Chr19: 1220652 - 1222337 (on Assembly GRCh37)
Preferred name:: NC_000019.9:g.(?_1220652)_(1222337_?)del
HGVS:: NC_000019.9:g.(?_1220652)_(1222337_?)del
This HGVS expression did not pass validation

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
SCV005063600	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 30, 2019)	unknown	clinical testing	PubMed (7) [See all records that cite these PMIDs] 15188174, 16287113, 10408777, 24652667, 26607058, 28185117, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV005063600

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 30, 2019)

unknown

clinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Relative frequency and morphology of cancers in STK11 mutation carriers.

Lim W, Olschwang S, Keller JJ, Westerman AM, Menko FH, Boardman LA, Scott RJ, Trimbath J, Giardiello FM, Gruber SB, Gille JJ, Offerhaus GJ, de Rooij FW, Wilson JH, Spigelman AD, Phillips RK, Houlston RS.

Gastroenterology. 2004 Jun;126(7):1788-94.

PubMed [citation]

PMID:: 15188174

High proportion of large genomic STK11 deletions in Peutz-Jeghers syndrome.

Aretz S, Stienen D, Uhlhaas S, Loff S, Back W, Pagenstecher C, McLeod DR, Graham GE, Mangold E, Santer R, Propping P, Friedl W.

Hum Mutat. 2005 Dec;26(6):513-9.

PubMed [citation]

PMID:: 16287113

See all PubMed Citations (7)

Details of each submission

From Invitae, SCV005063600.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

This variant is a deletion of the genomic region encompassing exons 6-7 and part of exon 5 (c.670_920+332) of the STK11 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with STK11-related conditions. Loss-of-function variants in STK11 are known to be pathogenic (PMID: 15188174, 16287113). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg297 amino acid residue in STK11. Other variant(s) that disrupt this residue have been observed in individuals with STK11-related conditions (PMID:10408777, 24652667, 26607058, 28185117), suggesting that it is a clinically significant residue. As a result, variants that disrupt this residue are likely to be causative of disease.

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

Last Updated: Jul 7, 2024

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