NM_000455.5(STK11):c.1045GAGGAC[3] (p.349ED[3]) AND Peutz-Jeghers syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 30, 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:: RCV001234124.16

Allele description [Variation Report for NM_000455.5(STK11):c.1045GAGGAC[3] (p.349ED[3])]

NM_000455.5(STK11):c.1045GAGGAC[3] (p.349ED[3])

Genes:

LOC130062899:ATAC-STARR-seq lymphoblastoid active region 13597 [Gene]
STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_000455.5(STK11):c.1045GAGGAC[3] (p.349ED[3])

HGVS:

NC_000019.10:g.1223109GAGGAC[3]
NG_007460.2:g.38703GAGGAC[3]
NM_000455.4:c.1051_1056dupGAGGAC
NM_000455.5:c.1045GAGGAC[3]MANE SELECT
NP_000446.1:p.349ED[3]
LRG_319t1:c.1051_1056dup
LRG_319:g.38703GAGGAC[3]
NC_000019.9:g.1223103_1223104insGGACGA
NC_000019.9:g.1223108GAGGAC[3]
NM_000455.4:c.1045_1050dupGAGGAC
NM_000455.4:c.1051_1056dup
NM_000455.4:c.1051_1056dupGAGGAC

Links:

dbSNP: rs762810203

NCBI 1000 Genomes Browser:

rs762810203

Molecular consequence:

NM_000455.5:c.1045GAGGAC[3] - inframe_insertion - [Sequence Ontology: SO:0001821]

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

Recent activity

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dai44d06.x1 NICHD_XGC_Sp1 Xenopus laevis cDNA clone IMAGE:4964411 3', mRNA seque...
dai44d06.x1 NICHD_XGC_Sp1 Xenopus laevis cDNA clone IMAGE:4964411 3', mRNA sequence
gi|17403556|gnl|dbEST|10489832|gb|B 96.1|

Nucleotide
JGI_XZT9866.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587790 5',...
JGI_XZT9866.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7587790 5', mRNA sequence
gi|57045030|gnl|dbEST|26936319|gb|C 55.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001406753	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 30, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 34326862, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001406753

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 30, 2023)

germline

clinical testing

PubMed (2)
[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

Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach.

Bhai P, Levy MA, Rooney K, Carere DA, Reilly J, Kerkhof J, Volodarsky M, Stuart A, Kadour M, Panabaker K, Schenkel LC, Lin H, Ainsworth P, Sadikovic B.

Front Genet. 2021;12:698595. doi: 10.3389/fgene.2021.698595.

PubMed [citation]

PMID:: 34326862
PMCID:: PMC8314385

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, SCV001406753.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant, c.1051_1056dup, results in the insertion of 2 amino acid(s) of the STK11 protein (p.Glu351_Asp352dup), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has been observed in individual(s) with ovarian cancer (PMID: 34326862). ClinVar contains an entry for this variant (Variation ID: 422813). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Nov 3, 2024

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