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NC_000019.10:g.(?_1206904)_(1219423_?)del AND Peutz-Jeghers syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 23, 2018
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:
RCV000797480.3

Allele description [Variation Report for NC_000019.10:g.(?_1206904)_(1219423_?)del]

NC_000019.10:g.(?_1206904)_(1219423_?)del

Genes:
  • LOC130062896:ATAC-STARR-seq lymphoblastoid active region 13594 [Gene]
  • LOC130062897:ATAC-STARR-seq lymphoblastoid active region 13595 [Gene]
  • LOC130062898:ATAC-STARR-seq lymphoblastoid active region 13596 [Gene]
  • LOC125371447:Sharpr-MPRA regulatory region 13808 [Gene]
  • LOC121627843:Sharpr-MPRA regulatory region 9448 [Gene]
  • LOC110006317:serine/threonine kinase 11 intron 1 Alu-mediated recombination region [Gene]
  • STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
19p13.3
Genomic location:
Preferred name:
NC_000019.10:g.(?_1206904)_(1219423_?)del
HGVS:
  • NC_000019.10:g.(?_1206904)_(1219423_?)del
  • NC_000019.9:g.(?_1206903)_(1219422_?)del

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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000937039Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 23, 2018) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

LKB1 exonic and whole gene deletions are a common cause of Peutz-Jeghers syndrome.

Volikos E, Robinson J, Aittomäki K, Mecklin JP, Järvinen H, Westerman AM, de Rooji FW, Vogel T, Moeslein G, Launonen V, Tomlinson IP, Silver AR, Aaltonen LA.

J Med Genet. 2006 May;43(5):e18.

PubMed [citation]
PMID:
16648371
PMCID:
PMC2564523

Breakpoint determination of 15 large deletions in Peutz-Jeghers subjects.

Resta N, Giorda R, Bagnulo R, Beri S, Della Mina E, Stella A, Piglionica M, Susca FC, Guanti G, Zuffardi O, Ciccone R.

Hum Genet. 2010 Oct;128(4):373-82. doi: 10.1007/s00439-010-0859-7. Epub 2010 Jul 11.

PubMed [citation]
PMID:
20623358
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000937039.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant is a gross deletion of the genomic region encompassing exons 1-3 of the STK11 gene, which includes the initiator codon. The 5' end of this event is unknown as it extends beyond the assayed region for this gene and therefore may encompass additional genes. The 3' boundary is likely confined to intron 3 of the STK11 gene. This is expected to result in an absent or disrupted protein product. A similar deletion of exons 1-3 has been reported in several individuals affected with Peutz-Jeghers syndrome (PMID: 16648371, 20623358). 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