NC_000019.9:g.(?_1218406)_(1219422_?)del AND Peutz-Jeghers syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 18, 2023
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:: RCV001386948.8

Allele description [Variation Report for NC_000019.9:g.(?_1218406)_(1219422_?)del]

NC_000019.9:g.(?_1218406)_(1219422_?)del

Gene:: STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 19p13.3
Genomic location:: Chr19: 1218406 - 1219422 (on Assembly GRCh37)
Preferred name:: NC_000019.9:g.(?_1218406)_(1219422_?)del
HGVS:: NC_000019.9:g.(?_1218406)_(1219422_?)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
SCV001587362	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 18, 2023)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 16287113, 20435009, 20623358, 21118512, 22775437, 25841653, 11389158, 24260271, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001587362

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 18, 2023)

germline

clinical testing

PubMed (9)
[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	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

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

Alu-mediated genomic deletion of the serine/threonine protein kinase 11 (STK11) gene in Peutz-Jeghers syndrome.

De Rosa M, Galatola M, Quaglietta L, Miele E, De Palma G, Rossi GB, Staiano A, Izzo P.

Gastroenterology. 2010 Jun;138(7):2558-60. doi: 10.1053/j.gastro.2010.03.061. No abstract available.

PubMed [citation]

PMID:: 20435009

See all PubMed Citations (9)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001587362.5

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

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 2-3 of the STK11 gene. This variant would be expected to be in-frame, preserving the integrity of the reading frame. A similar copy number variant has been observed in individuals with Peutz‚ÄìJeghers syndrome (PMID: 16287113, 20435009, 20623358, 21118512, 22775437, 25841653). This variant disrupts the p.Met136 amino acid residue in STK11. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11389158, 24260271; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	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

Last Updated: Sep 29, 2024

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