NM_000455.5(STK11):c.921-9del AND Peutz-Jeghers syndrome

Germline classification:: Likely benign (1 submission)
Last evaluated:: Sep 20, 2022
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:: RCV002532788.3

Allele description [Variation Report for NM_000455.5(STK11):c.921-9del]

NM_000455.5(STK11):c.921-9del

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.921-9del

HGVS:

NC_000019.10:g.1222976del
NG_007460.2:g.38570del
NM_000455.5:c.921-9delMANE SELECT
LRG_319:g.38570del
NC_000019.9:g.1222975del
NM_000455.4:c.921-9delC

Links:

dbSNP: rs1555739151

NCBI 1000 Genomes Browser:

rs1555739151

Molecular consequence:

NM_000455.5:c.921-9del - intron variant - [Sequence Ontology: SO:0001627]

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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cytochrome c oxidase subunit I, partial (mitochondrion) [Phakellia robusta]
cytochrome c oxidase subunit I, partial (mitochondrion) [Phakellia robusta]
gi|1844481474|gb|QJX68341.1|

Protein
cytochrome c oxidase subunit I, partial (mitochondrion) [Axinella rugosa]
cytochrome c oxidase subunit I, partial (mitochondrion) [Axinella rugosa]
gi|1844482505|gb|QJX68743.1|

Protein
Erythropodium caribaeorum AT1, TPS1, and CYP1 genes, complete cds
Erythropodium caribaeorum AT1, TPS1, and CYP1 genes, complete cds
gi|2229018483|gb|OK081311.1|

Nucleotide
Erythropodium caribaeorum TPS7 mRNA, partial cds
Erythropodium caribaeorum TPS7 mRNA, partial cds
gi|2229018970|gb|OK081318.1|

Nucleotide
Paracoccus pantotrophus strain NKNCYSA putative GntR type regulator of taurine d...
Paracoccus pantotrophus strain NKNCYSA putative GntR type regulator of taurine degradation (tauR) gene, partial cds; putative ABC transporter periplasmic binding protein (tauA), putative ABC transporter ATP binding protein (tauB), putative ABC transporter permease component (tauC), putative taurine dehydrogenase small subunit (tauX), putative taurine dehydrogenase large subunit (tauY), and sulfoacetaldehyde acetyltransferase (xsc) genes, complete cds; and putative sulfate exporter (tauZ) gene, partial cds
gi|61742864|gb|AY498615.3|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003029477	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Sep 20, 2022)	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

SCV003029477

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Sep 20, 2022)

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

Citations

PubMed

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, SCV003029477.2

#	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	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 8, 2024

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