NM_000314.8(PTEN):c.980_981del (p.Lys327fs) AND PTEN hamartoma tumor syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 21, 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:: RCV003510178.2

Allele description [Variation Report for NM_000314.8(PTEN):c.980_981del (p.Lys327fs)]

NM_000314.8(PTEN):c.980_981del (p.Lys327fs)

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.980_981del (p.Lys327fs)

HGVS:

NC_000010.11:g.87961072_87961073del
NG_007466.2:g.102634_102635del
NM_000314.8:c.980_981delMANE SELECT
NM_001304717.5:c.1499_1500del
NM_001304718.2:c.389_390del
NP_000305.3:p.Lys327Serfs
NP_000305.3:p.Lys327fs
NP_001291646.4:p.Lys500fs
NP_001291647.1:p.Lys130fs
LRG_311t1:c.980_981del
LRG_311:g.102634_102635del
LRG_311p1:p.Lys327Serfs
NC_000010.10:g.89720828_89720829del
NC_000010.10:g.89720829_89720830del
NM_000314.4:c.980_981delAA

Protein change:

K130fs

Molecular consequence:

NM_000314.8:c.980_981del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304717.5:c.1499_1500del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001304718.2:c.389_390del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004324854	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Sep 21, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 20223021, 29273943, 31336731, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004324854

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Sep 21, 2023)

germline

clinical testing

PubMed (4)
[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

Germline PTEN mutations are rare and highly penetrant.

Rustad CF, Bjørnslett M, Heimdal KR, Mæhle L, Apold J, Møller P.

Hered Cancer Clin Pract. 2006 Dec 15;4(4):177-85. doi: 10.1186/1897-4287-4-4-177.

PubMed [citation]

PMID:: 20223021
PMCID:: PMC2837306

Thyroid disease in children and adolescents with PTEN hamartoma tumor syndrome (PHTS).

Plamper M, Schreiner F, Gohlke B, Kionke J, Korsch E, Kirkpatrick J, Born M, Aretz S, Woelfle J.

Eur J Pediatr. 2018 Mar;177(3):429-435. doi: 10.1007/s00431-017-3067-9. Epub 2017 Dec 22.

PubMed [citation]

PMID:: 29273943

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004324854.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Lys327Serfs*3) in the PTEN gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 77 amino acid(s) of the PTEN protein. 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. This variant disrupts a region of the PTEN protein in which other variant(s) (p.Tyr336*) have been determined to be pathogenic (PMID: 20223021, 29273943, 31336731). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

#	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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