NM_000455.5(STK11):c.1157T>C (p.Leu386Pro) AND Peutz-Jeghers syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 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:: RCV001053656.7

Allele description

NM_000455.5(STK11):c.1157T>C (p.Leu386Pro)

Gene:

STK11:serine/threonine kinase 11 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_000455.5(STK11):c.1157T>C (p.Leu386Pro)

HGVS:

NC_000019.10:g.1226502T>C
NG_007460.2:g.42096T>C
NM_000455.5:c.1157T>CMANE SELECT
NP_000446.1:p.Leu386Pro
LRG_319t1:c.1157T>C
LRG_319:g.42096T>C
NC_000019.9:g.1226501T>C
NM_000455.4:c.1157T>C

Protein change:

L386P

Links:

dbSNP: rs876658871

NCBI 1000 Genomes Browser:

rs876658871

Molecular consequence:

NM_000455.5:c.1157T>C - missense variant - [Sequence Ontology: SO:0001583]

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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AGENCOURT_54839593 NICHD_XGC_Emb10 Xenopus laevis cDNA clone IMAGE:7982400 5', m...
AGENCOURT_54839593 NICHD_XGC_Emb10 Xenopus laevis cDNA clone IMAGE:7982400 5', mRNA sequence
gi|70899888|gnl|dbEST|30214551|gb|D 76.1|

Nucleotide
BJ070052 NIBB Mochii normalized Xenopus tailbud library Xenopus laevis cDNA clon...
BJ070052 NIBB Mochii normalized Xenopus tailbud library Xenopus laevis cDNA clone XL055g07 5', mRNA sequence
gi|17500065|gnl|dbEST|10526305|dbj| 052.1|

Nucleotide
df20f04.y1 Wellcome CRC pRN3 St13 17 egg animal cap Xenopus laevis cDNA clone IM...
df20f04.y1 Wellcome CRC pRN3 St13 17 egg animal cap Xenopus laevis cDNA clone IMAGE:3557910 5', mRNA sequence
gi|13593483|gnl|dbEST|8303417|gb|BG 9.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001217929	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 30, 2019)	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

SCV001217929

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 30, 2019)

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 Invitae, SCV001217929.6

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The proline amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals with STK11-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces leucine with proline at codon 386 of the STK11 protein (p.Leu386Pro). The leucine residue is moderately conserved and there is a moderate physicochemical difference between leucine and proline. 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: Feb 28, 2024

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