NM_000314.8(PTEN):c.1202C>T (p.Thr401Ile) AND PTEN hamartoma tumor syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Oct 24, 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:: RCV001050741.4

Allele description [Variation Report for NM_000314.8(PTEN):c.1202C>T (p.Thr401Ile)]

NM_000314.8(PTEN):c.1202C>T (p.Thr401Ile)

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.1202C>T (p.Thr401Ile)

HGVS:

NC_000010.11:g.87965462C>T
NG_007466.2:g.107024C>T
NM_000314.8:c.1202C>TMANE SELECT
NM_001304717.5:c.1721C>T
NM_001304718.2:c.611C>T
NP_000305.3:p.Thr401Ile
NP_001291646.4:p.Thr574Ile
NP_001291647.1:p.Thr204Ile
LRG_311t1:c.1202C>T
LRG_311:g.107024C>T
NC_000010.10:g.89725219C>T
NM_000314.4:c.1202C>T

Protein change:

T204I

Links:

dbSNP: rs1860740005

NCBI 1000 Genomes Browser:

rs1860740005

Molecular consequence:

NM_000314.8:c.1202C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001304717.5:c.1721C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001304718.2:c.611C>T - 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

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001214862	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Oct 24, 2021)	germline	clinical testing	PubMed (5) [See all records that cite these PMIDs] 10866302, 29117568, 29785012, 30993208, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001214862

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Oct 24, 2021)

germline

clinical testing

PubMed (5)
[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

Functional evaluation of PTEN missense mutations using in vitro phosphoinositide phosphatase assay.

Han SY, Kato H, Kato S, Suzuki T, Shibata H, Ishii S, Shiiba K, Matsuno S, Kanamaru R, Ishioka C.

Cancer Res. 2000 Jun 15;60(12):3147-51.

PubMed [citation]

PMID:: 10866302

PTEN Regulates Glucose Transporter Recycling by Impairing SNX27 Retromer Assembly.

Shinde SR, Maddika S.

Cell Rep. 2017 Nov 7;21(6):1655-1666. doi: 10.1016/j.celrep.2017.10.053.

PubMed [citation]

PMID:: 29117568
PMCID:: PMC5695913

See all PubMed Citations (5)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001214862.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (5)

Description

This sequence change replaces threonine with isoleucine at codon 401 of the PTEN protein (p.Thr401Ile). The threonine residue is moderately conserved and there is a moderate physicochemical difference between threonine and isoleucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals affected with PTEN-related conditions. 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"). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on PTEN function (PMID: 10866302, 29117568, 29785012, 30993208). 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: Sep 29, 2024

ClinVar

Relating variation to medicine