NM_000455.4(STK11):c.842C>G (p.Pro281Arg) 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 15, 2016
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:: RCV000228218.2

Allele description

NM_000455.4(STK11):c.842C>G (p.Pro281Arg)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

19p13.3

Genomic location:

Preferred name:

NM_000455.4(STK11):c.842C>G (p.Pro281Arg)

HGVS:

NC_000019.10:g.1221320C>G
NG_007460.2:g.36914C>G
NM_000455.4:c.842C>G
NP_000446.1:p.Pro281Arg
LRG_319t1:c.842C>G
LRG_319:g.36914C>G
LRG_319p1:p.Pro281Arg
NC_000019.9:g.1221319C>G
p.P281R

Protein change:

P281R

Links:

dbSNP: rs121913322

GMAF:

0.0008(T), 121913322

NCBI 1000 Genomes Browser:

rs121913322

Molecular consequence:

NM_000455.4:c.842C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Peutz-Jeghers syndrome (PJS)
Identifiers:: 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
SCV000284876	Invitae,	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 15, 2016)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000284876

Invitae,

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 15, 2016)

germline

clinical testing

Citation Link

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

Details of each submission

From Invitae,, SCV000284876.2

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

Description

This sequence change replaces proline with arginine at codon 281 of the STK11 protein (p.Pro281Arg). The proline residue is moderately conserved and there is a moderate physicochemical difference between proline and arginine. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with an STK11-related disease. ClinVar contains an entry for this variant (Variation ID: 185022). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). In summary, this variant is a rare missense change with uncertain impact on protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. 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: Dec 19, 2017

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