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NM_000314.8(PTEN):c.740T>A (p.Leu247Ter) AND PTEN hamartoma tumor syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 8, 2023
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:
RCV000704056.4

Allele description [Variation Report for NM_000314.8(PTEN):c.740T>A (p.Leu247Ter)]

NM_000314.8(PTEN):c.740T>A (p.Leu247Ter)

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.740T>A (p.Leu247Ter)
HGVS:
  • NC_000010.11:g.87957958T>A
  • NG_007466.2:g.99520T>A
  • NM_000314.8:c.740T>AMANE SELECT
  • NM_001304717.5:c.1259T>A
  • NM_001304718.2:c.149T>A
  • NP_000305.3:p.Leu247Ter
  • NP_001291646.4:p.Leu420Ter
  • NP_001291647.1:p.Leu50Ter
  • LRG_311t1:c.740T>A
  • LRG_311:g.99520T>A
  • NC_000010.10:g.89717715T>A
  • NM_000314.4:c.740T>A
Protein change:
L247*
Links:
dbSNP: rs1057519368
NCBI 1000 Genomes Browser:
rs1057519368
Molecular consequence:
  • NM_000314.8:c.740T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001304717.5:c.1259T>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001304718.2:c.149T>A - 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

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000832989Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jul 8, 2023) 		germlineclinical testing

PubMed (3)
[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

Mutation spectrum and genotype-phenotype analyses in Cowden disease and Bannayan-Zonana syndrome, two hamartoma syndromes with germline PTEN mutation.

Marsh DJ, Coulon V, Lunetta KL, Rocca-Serra P, Dahia PL, Zheng Z, Liaw D, Caron S, Duboué B, Lin AY, Richardson AL, Bonnetblanc JM, Bressieux JM, Cabarrot-Moreau A, Chompret A, Demange L, Eeles RA, Yahanda AM, Fearon ER, Fricker JP, Gorlin RJ, Hodgson SV, et al.

Hum Mol Genet. 1998 Mar;7(3):507-15.

PubMed [citation]
PMID:
9467011

A clinical scoring system for selection of patients for PTEN mutation testing is proposed on the basis of a prospective study of 3042 probands.

Tan MH, Mester J, Peterson C, Yang Y, Chen JL, Rybicki LA, Milas K, Pederson H, Remzi B, Orloff MS, Eng C.

Am J Hum Genet. 2011 Jan 7;88(1):42-56. doi: 10.1016/j.ajhg.2010.11.013. Epub 2010 Dec 30.

PubMed [citation]
PMID:
21194675
PMCID:
PMC3014373
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV000832989.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Leu247*) in the PTEN gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PTEN are known to be pathogenic (PMID: 9467011, 21194675). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with PTEN-related conditions. ClinVar contains an entry for this variant (Variation ID: 580498). 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: May 1, 2024