NM_000314.8(PTEN):c.75G>A (p.Leu25=) AND Malignant tumor of breast

Clinical significance:Likely benign

Review status:(0/4) 0 stars out of maximum of 4 stars

no assertion criteria provided

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000314.8(PTEN):c.75G>A (p.Leu25=)]

NM_000314.8(PTEN):c.75G>A (p.Leu25=)

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000314.8(PTEN):c.75G>A (p.Leu25=)
Other names:
NM_000314.6(PTEN):c.75G>A(p.Leu25=); NM_000314.6(PTEN):c.75G>A
  • NC_000010.11:g.87864544G>A
  • NG_007466.2:g.6106G>A
  • NG_033079.1:g.3894C>T
  • NM_000314.8:c.75G>AMANE SELECT
  • NM_001304717.5:c.594G>A
  • NM_001304718.2:c.-631G>A
  • NP_000305.3:p.Leu25=
  • NP_001291646.4:p.Leu198=
  • LRG_311t1:c.75G>A
  • LRG_1087:g.3894C>T
  • LRG_311:g.6106G>A
  • NC_000010.10:g.89624301G>A
  • NM_000314.4:c.75G>A
  • p.L25L
dbSNP: rs786201506
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001304718.2:c.-631G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000314.8:c.75G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001304717.5:c.594G>A - synonymous variant - [Sequence Ontology: SO:0001819]


Malignant tumor of breast
Breast cancer; Malignant breast neoplasm
MONDO: MONDO:0007254; MedGen: C0006142

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV001554111Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR)

See additional submitters

no assertion criteria providedLikely benignunknownclinical testing

Summary from all submissions

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

Details of each submission

From Department of Pathology and Laboratory Medicine,Sinai Health System - The Canadian Open Genetics Repository (COGR), SCV001554111.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


The PTEN p.Leu25= variant was not identified in the literature nor was it identified in the LOVD 3.0 databases. The variant was identified in dbSNP (rs786201506) as “with likely benign, uncertain significance allele” and ClinVar (classfied as likely benign by Invitae, Color and Ambry Genetics and uncertain significance by ClinGen PTEN variant panel). The variant was not identified in the following control databases: the Exome Aggregation Consortium (August 8th 2016), or the Genome Aggregation Database (Feb 27, 2017). The p.Leu25= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. The variant occurs at a non-highly conserved nucleotide outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 27, 2021

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