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NM_000314.8(PTEN):c.545T>C (p.Leu182Ser) AND PTEN hamartoma tumor syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 1, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
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:
RCV000790887.4

Allele description [Variation Report for NM_000314.8(PTEN):c.545T>C (p.Leu182Ser)]

NM_000314.8(PTEN):c.545T>C (p.Leu182Ser)

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.545T>C (p.Leu182Ser)
Other names:
NM_000314.6(PTEN):c.545T>C
HGVS:
  • NC_000010.11:g.87952170T>C
  • NG_007466.2:g.93732T>C
  • NM_000314.8:c.545T>CMANE SELECT
  • NM_001304717.5:c.1064T>C
  • NM_001304718.2:c.-47T>C
  • NP_000305.3:p.Leu182Ser
  • NP_001291646.4:p.Leu355Ser
  • LRG_311t1:c.545T>C
  • LRG_311:g.93732T>C
  • NC_000010.10:g.89711927T>C
  • NM_000314.1:c.545T>C
  • NM_000314.4:c.545T>C
Protein change:
L182S
Links:
dbSNP: rs794729664
NCBI 1000 Genomes Browser:
rs794729664
Molecular consequence:
  • NM_001304718.2:c.-47T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000314.8:c.545T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304717.5:c.1064T>C - missense variant - [Sequence Ontology: SO:0001583]

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

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000930117Clingen PTEN Variant Curation Expert Panel, Clingen
reviewed by expert panel

(ClinGen PTEN ACMG Specifications V3)		Uncertain significance
(Dec 1, 2023) 		germlinecuration

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From Clingen PTEN Variant Curation Expert Panel, Clingen, SCV000930117.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

PTEN c.545T>C (p.Leu182Ser) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.0.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column). Of note, this variant may be disease-causing when present in the homozygous state (PMID: 26443266), but this expert panel curation is based on presence in the heterozygous state. PM2: Absent in large sequenced populations (PMID 27535533). PP2: PTEN is defined by the PTEN Expert Panel as a gene that has a low rate of benign missense variation and where missense variants are a common mechanism of disease. PP3: REVEL score > 0.7 (score of this variant =0.972)

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

Last Updated: Jun 23, 2024