U.S. flag

An official website of the United States government

NM_000314.8(PTEN):c.437_438insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT (p.Leu146delinsPhePhePhePhePhePhePheXaaXaaXaaXaaTer) AND PTEN hamartoma tumor syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Aug 23, 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:
RCV002889281.1

Allele description

NM_000314.8(PTEN):c.437_438insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT (p.Leu146delinsPhePhePhePhePhePhePheXaaXaaXaaXaaTer)

Gene:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
Variant type:
Insertion
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000314.8(PTEN):c.437_438insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT (p.Leu146delinsPhePhePhePhePhePhePheXaaXaaXaaXaaTer)
HGVS:
  • NC_000010.11:g.87933196_87933197insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT
  • NG_007466.2:g.74758_74759insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT
  • NM_000314.8:c.437_438insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTTMANE SELECT
  • NM_001304717.5:c.956_957insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT
  • NM_001304718.2:c.-314_-313insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT
  • NP_000305.3:p.Leu146Phefs
  • NP_000305.3:p.Leu146delinsPhePhePhePhePhePhePheXaaXaaXaaXaaTer
  • NP_001291646.4:p.Leu319delinsPhePhePhePhePhePhePheXaaXaaXaaXaaTer
  • LRG_311t1:c.437_438insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT
  • LRG_311:g.74758_74759insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT
  • LRG_311p1:p.Leu146Phefs
  • NC_000010.10:g.89692936_89692937insCATCGGGGCAAATTTTTTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCC
  • NC_000010.10:g.89692953_89692954insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT
  • NM_000314.4:c.437_438insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT
Molecular consequence:
  • NM_001304718.2:c.-314_-313insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000314.8:c.437_438insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001304717.5:c.956_957insTTTTTTTTTTTTTTTTTTTTNNNNNNNNNNCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCCATCGGGGCAAATTTTT - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
PTEN hamartoma tumor syndrome (PHTS)
Synonyms:
PTEN Hamartomatous Tumour Syndrome; PTEN-related disorders
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

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003233218Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Aug 23, 2022) 		germlineclinical testing

PubMed (7)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Insertion of Alu elements at a PTEN hotspot in Cowden syndrome.

Crivelli L, Bubien V, Jones N, Chiron J, Bonnet F, Barouk-Simonet E, Couzigou P, Sevenet N, Caux F, Longy M.

Eur J Hum Genet. 2017 Sep;25(9):1087-1091. doi: 10.1038/ejhg.2017.81. Epub 2017 May 17.

PubMed [citation]
PMID:
28513612
PMCID:
PMC5558175

The impact of retrotransposons on human genome evolution.

Cordaux R, Batzer MA.

Nat Rev Genet. 2009 Oct;10(10):691-703. doi: 10.1038/nrg2640. Review.

PubMed [citation]
PMID:
19763152
PMCID:
PMC2884099
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV003233218.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

This sequence change inserts a large fragment of DNA, likely a transposable element, in exon 5 of the PTEN gene (c.437_438ins?), causing a frameshift at codon 146 (p.Leu146fs). The exact size and sequence of the insertion cannot be determined by the current assay. However, the insertion is expected to result in an absent or disrupted protein product. This variant is not present in population databases (gnomAD no frequency). A similar variant has been observed in individual(s) with clinical features of Cowden syndrome (PMID: 28513612). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Retrotransposon insertions including LINE1 (L1), Alu, and SVA (SINE-VNTR-Alu) have been reported to be disease-causing through disruption of either a coding region or splice site (PMID: 19763152, 20307669, 22406018) and loss-of-function variants in PTEN are known to be pathogenic (PMID: 9467011, 21194675). For these reasons, this variant has been classified as Pathogenic.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 21, 2023