NM_000314.8(PTEN):c.800A>C (p.Lys267Thr) AND PTEN hamartoma tumor syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Sep 21, 2021
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:: RCV002024023.4

Allele description [Variation Report for NM_000314.8(PTEN):c.800A>C (p.Lys267Thr)]

NM_000314.8(PTEN):c.800A>C (p.Lys267Thr)

Gene:

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.8(PTEN):c.800A>C (p.Lys267Thr)

HGVS:

NC_000010.11:g.87958018A>C
NG_007466.2:g.99580A>C
NM_000314.8:c.800A>CMANE SELECT
NM_001304717.5:c.1319A>C
NM_001304718.2:c.209A>C
NP_000305.3:p.Lys267Thr
NP_001291646.4:p.Lys440Thr
NP_001291647.1:p.Lys70Thr
LRG_311:g.99580A>C
NC_000010.10:g.89717775A>C

Protein change:

K267T

Links:

dbSNP: rs1554825264

NCBI 1000 Genomes Browser:

rs1554825264

Molecular consequence:

NM_000314.8:c.800A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001304717.5:c.1319A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001304718.2:c.209A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: PTEN hamartoma tumor syndrome (PHTS)
Synonyms:: PTEN Hamartomatous Tumour Syndrome
Identifiers:: MONDO: MONDO:0017623; MeSH: D006223; MedGen: C1959582

Recent activity

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Dendrobium grex Madame Thong-IN homeobox protein OVG2 (ovg2) mRNA, partial cds
Dendrobium grex Madame Thong-IN homeobox protein OVG2 (ovg2) mRNA, partial cds
gi|3929313|gb|AF100326.1|

Nucleotide
DGCR2 [Microcaecilia unicolor]
DGCR2 [Microcaecilia unicolor]
Gene ID:115479505

Gene
ALDH9A1 [Rissa tridactyla]
ALDH9A1 [Rissa tridactyla]
Gene ID:128913600

Gene
LOC120944390 [Rana temporaria]
LOC120944390 [Rana temporaria]
Gene ID:120944390

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002310352	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Sep 21, 2021)	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

SCV002310352

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Sep 21, 2021)

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, SCV002310352.3

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

Description

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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals affected with PTEN-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces lysine with threonine at codon 267 of the PTEN protein (p.Lys267Thr). The lysine residue is moderately conserved and there is a moderate physicochemical difference between lysine and threonine.

#	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: Sep 29, 2024

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