NM_000314.6(PTEN):c.-1059C>G AND not provided

Clinical significance:Benign (Last evaluated: Feb 1, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000588148.1

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)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000696523Women's Health and Genetics/Laboratory Corporation of America, LabCorpcriteria provided, single submitter
Benign
(Feb 1, 2017)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Missense mutation in the PTEN promoter of a patient with hemifacial hyperplasia.

Yamazaki K, Eng C, Kuznetsov SA, Reinisch J, Yamashita DD, Walker J, Cheung C, Robey PG, Yen SL.

Bonekey Rep. 2015;4:654. doi: 10.1038/bonekey.2015.21.

PubMed [citation]
PMID:
26229595
PMCID:
PMC4520444

KLLN epigenotype-phenotype associations in Cowden syndrome.

Nizialek EA, Mester JL, Dhiman VK, Smiraglia DJ, Eng C.

Eur J Hum Genet. 2015 Nov;23(11):1538-43. doi: 10.1038/ejhg.2015.8. Epub 2015 Feb 11.

PubMed [citation]
PMID:
25669429
PMCID:
PMC4613489

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696523.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

Variant summary: The PTEN variant c.-1059C>G (also known as c.-1060C>G) involves the alteration of a non-conserved nucleotide located in the 5' UTR. The variant of interest was observed in 1000 Gs with an allele frequency of 19/5008 (1/270), predominantly in the African cohort, 18/1322 (1/73), which significantly exceeds the estimated maximal expected allele frequency for a pathogenic PTEN variant of 1/158730 for Cowden syndrome and 1/64102 for HBOC. Therefore, suggesting this variant is likely a benign polymorphism found predominantly in population(s) of African origin. Furthermore, another large, broad control population, gnomAD, which is currently only in early beta mode, cites the variant with an allele frequency of 119/8482 (2 homozygotes) in Africans, further supporting the variant being a benign polymorphism. However, of note, the variant has been depicted in ClinVar as c.-1059C>G (the variant's legacy name), with a classification of "likely benign." The variant has been reported in publications and has indicated that it could affect expression. However, due to the high frequency in controls and the supporting classification by a clinical diagnostic laboratory as "likely benign," the variant of interest has been classified as Benign.

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

Last Updated: Jul 24, 2021

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