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NC_000010.11:g.(?_87952108)_(87958029_?)del AND PTEN hamartoma tumor syndrome

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Aug 12, 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:
RCV001033437.5

Allele description

NC_000010.11:g.(?_87952108)_(87958029_?)del

Gene:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
10q23.31
Genomic location:
Chr10: 89711865 - 89717786 (on Assembly GRCh37)
Preferred name:
NC_000010.11:g.(?_87952108)_(87958029_?)del
HGVS:
  • NC_000010.11:g.(?_87952108)_(87958029_?)del
  • NC_000010.10:g.(?_89711865)_(89717786_?)del

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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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001196744Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Aug 12, 2021) 		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

Cowden syndrome and Bannayan Riley Ruvalcaba syndrome represent one condition with variable expression and age-related penetrance: results of a clinical study of PTEN mutation carriers.

Lachlan KL, Lucassen AM, Bunyan D, Temple IK.

J Med Genet. 2007 Sep;44(9):579-85. Epub 2007 May 25.

PubMed [citation]
PMID:
17526800
PMCID:
PMC2597943

The prevalence of PTEN mutations in a clinical pediatric cohort with autism spectrum disorders, developmental delay, and macrocephaly.

Varga EA, Pastore M, Prior T, Herman GE, McBride KL.

Genet Med. 2009 Feb;11(2):111-7. doi: 10.1097/GIM.0b013e31818fd762.

PubMed [citation]
PMID:
19265751
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV001196744.3

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

Description

This variant is a gross deletion of the genomic region encompassing exon(s) 6-7 of the PTEN gene. This variant would be expected to be in-frame, preserving the integrity of the reading frame. This variant has not been reported in the literature in individuals affected with PTEN-related conditions. This variant disrupts the p.Arg173 amino acid residue in PTEN. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 17526800, 19265751, 20533527, 22628360, 23335809, 24778394). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.

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

Last Updated: Feb 13, 2023