NM_000314.8(PTEN):c.-799G>C AND PTEN hamartoma tumor syndrome

Clinical significance:Uncertain significance (Last evaluated: Apr 6, 2018)

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
3 submissions [Details]
Record status:
current
Accession:
RCV000232535.3

Allele description [Variation Report for NM_000314.8(PTEN):c.-799G>C]

NM_000314.8(PTEN):c.-799G>C

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.-799G>C
HGVS:
  • NC_000010.11:g.87863671G>C
  • NG_007466.2:g.5234G>C
  • NG_033079.1:g.4767C>G
  • NM_000314.8:c.-799G>CMANE SELECT
  • NM_001304717.5:c.-279G>C
  • NM_001304718.2:c.-1503G>C
  • LRG_311t1:c.-798G>C
  • LRG_1087:g.4767C>G
  • LRG_311:g.5234G>C
  • NC_000010.10:g.89623428G>C
  • NM_000314.4:c.-798G>C
  • c.-799G>C[hg19]
Links:
dbSNP: rs587779992
NCBI 1000 Genomes Browser:
rs587779992
Molecular consequence:
  • NM_000314.8:c.-799G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001304717.5:c.-279G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_001304718.2:c.-1503G>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000284574Invitaecriteria provided, single submitter
Likely benign
(Mar 7, 2016)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000863481ClinGen PTEN Variant Curation Expert Panelreviewed by expert panel
Uncertain significance
(Apr 6, 2018)
germlinecuration

ClinGen_PTEN_ACMG_Specifications_v1.pdf,

Citation Link,

SCV001138120Mendelicscriteria provided, single submitter
Benign
(May 28, 2019)
unknownclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000284574.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From ClinGen PTEN Variant Curation Expert Panel, SCV000863481.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

PTEN c.-798G>C (NC_000010.10:g.89623428G>C) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (PMID 30311380). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). No criteria currently apply to this variant.

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

From Mendelics, SCV001138120.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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