NM_000314.6(PTEN):c.-1059C>G AND PTEN hamartoma tumor syndrome

Clinical significance:Benign (Last evaluated: Sep 14, 2016)

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000710302.1

Allele description [Variation Report for NM_000314.6(PTEN):c.-1059C>G]

NM_000314.6(PTEN):c.-1059C>G

Genes:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
KLLN:killin, p53 regulated DNA replication inhibitor [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000314.6(PTEN):c.-1059C>G
HGVS:
  • NC_000010.11:g.87863410C>G
  • NG_007466.2:g.4973C>G
  • NG_033079.1:g.5028G>C
  • NM_001126049.2:c.-923G>CMANE SELECT
  • LRG_1087t1:c.-923G>C
  • LRG_311t1:c.-1059C>G
  • LRG_1087:g.5028G>C
  • LRG_311:g.4973C>G
  • NC_000010.10:g.89623167C>G
  • NM_000314.4:c.-1059C>G
  • NM_001126049.1:c.-923G>C
  • c.-1060C>G[hg19]
Links:
dbSNP: rs144620057
NCBI 1000 Genomes Browser:
rs144620057
Molecular consequence:
  • NM_001126049.2:c.-923G>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
SCV000840479ClinGen PTEN Variant Curation Expert Panelreviewed by expert panel
Benign
(Sep 14, 2016)
germlinecuration

ClinGen_PTEN_ACMG_Specifications_v1.pdf

Citation Link

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, SCV000840479.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

PTEN c.-1059C>G (NC_000010.10:g.89623167C>G) meets criteria to be classified as benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the 'PTEN ACMG Specifications Summary' document (assertion method column). BA1: Allele frequency of 0.0138 (1.38%, 120/8698 alleles) in the African subpopulation of the gnomAD cohort. (PMID 27535533)

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

Last Updated: Jul 24, 2021

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