NM_000314.8(PTEN):c.783del (p.Asn262fs) AND PTEN hamartoma tumor syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 11, 2019
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:: RCV001050029.5

Allele description

NM_000314.8(PTEN):c.783del (p.Asn262fs)

Gene:

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

Variant type:

Deletion

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.8(PTEN):c.783del (p.Asn262fs)

HGVS:

NC_000010.11:g.87958001del
NG_007466.2:g.99563del
NM_000314.8:c.783delMANE SELECT
NM_001304717.5:c.1302del
NM_001304718.2:c.192del
NP_000305.3:p.Asn262fs
NP_001291646.4:p.Asn435fs
NP_001291647.1:p.Asn65fs
LRG_311t1:c.783del
LRG_311:g.99563del
NC_000010.10:g.89717758del
NM_000314.4:c.783del

Protein change:

N262fs

Links:

dbSNP: rs1860551073

NCBI 1000 Genomes Browser:

rs1860551073

Molecular consequence:

NM_000314.8:c.783del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304717.5:c.1302del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304718.2:c.192del - frameshift variant - [Sequence Ontology: SO:0001589]

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

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Mus musculus RIKEN cDNA A430105I05 gene (A430105I05Rik), mRNA
Mus musculus RIKEN cDNA A430105I05 gene (A430105I05Rik), mRNA
gi|34303974|ref|NM_183306.1|

Nucleotide
Vaccinium fragile internal transcribed spacer 1, partial sequence; 5.8S ribosoma...
Vaccinium fragile internal transcribed spacer 1, partial sequence; 5.8S ribosomal RNA gene, complete sequence; and internal transcribed spacer 2, partial sequence
gi|30408137|gb|AY274579.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001214115	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 11, 2019)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 9467011, 21194675, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001214115

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 11, 2019)

germline

clinical testing

PubMed (3)
[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

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, SCV001214115.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in PTEN are known to be pathogenic (PMID: 9467011, 21194675). This variant has not been reported in the literature in individuals with PTEN-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Asn262Thrfs*4) in the PTEN gene. It is expected to result in an absent or disrupted protein product.

#	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: Feb 20, 2024

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