NC_000010.10:g.(?_89717600)_(89720885_?)del AND PTEN hamartoma tumor syndrome

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

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Aug 29, 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:: RCV001956222.2

Allele description

NC_000010.10:g.(?_89717600)_(89720885_?)del

Gene:: PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
Variant type:: Deletion
Cytogenetic location:: 10q23.31
Genomic location:: Chr10: 89717600 - 89720885 (on Assembly GRCh37)
Preferred name:: NC_000010.10:g.(?_89717600)_(89720885_?)del
HGVS:: NC_000010.10:g.(?_89717600)_(89720885_?)del
This HGVS expression did not pass validation

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
SCV002245905	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Aug 29, 2021)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 10468583, 10866658, 11035045, 12297295, 24905788, 25336918, 25448482, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002245905

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Aug 29, 2021)

germline

clinical testing

PubMed (8)
[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

The tumor-suppressor activity of PTEN is regulated by its carboxyl-terminal region.

Georgescu MM, Kirsch KH, Akagi T, Shishido T, Hanafusa H.

Proc Natl Acad Sci U S A. 1999 Aug 31;96(18):10182-7.

PubMed [citation]

PMID:: 10468583
PMCID:: PMC17863

Phosphorylation of the PTEN tail regulates protein stability and function.

Vazquez F, Ramaswamy S, Nakamura N, Sellers WR.

Mol Cell Biol. 2000 Jul;20(14):5010-8.

PubMed [citation]

PMID:: 10866658
PMCID:: PMC85951

See all PubMed Citations (8)

Details of each submission

From Invitae, SCV002245905.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 7-8 of the PTEN gene. While this deletion is not anticipated to lead to nonsense mediated decay, it is expected to disrupt the C-terminus of the protein. 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.Glu390*) have been determined to be pathogenic (PMID: 10468583, 10866658, 11035045, 12297295, 24905788, 25336918, 25448482; Invitae). 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: Feb 13, 2023

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