NM_000314.7(PTEN):c.457G>A (p.Asp153Asn) AND PTEN hamartoma tumor syndrome

Clinical significance:Uncertain significance (Last evaluated: Nov 17, 2016)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_000314.7(PTEN):c.457G>A (p.Asp153Asn)]

NM_000314.7(PTEN):c.457G>A (p.Asp153Asn)

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_000314.7(PTEN):c.457G>A (p.Asp153Asn)
  • NC_000010.11:g.87933216G>A
  • NG_007466.2:g.74778G>A
  • NM_000314.7:c.457G>A
  • NM_001304717.5:c.976G>A
  • NM_001304718.2:c.-294G>A
  • NP_000305.3:p.Asp153Asn
  • NP_001291646.4:p.Asp326Asn
  • LRG_311t1:c.457G>A
  • LRG_311:g.74778G>A
  • NC_000010.10:g.89692973G>A
  • NM_000314.4:c.457G>A
Protein change:
dbSNP: rs9651492
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001304718.2:c.-294G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_000314.7:c.457G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304717.5:c.976G>A - missense variant - [Sequence Ontology: SO:0001583]


PTEN hamartoma tumor syndrome (PHTS)
PTEN Hamartomatous Tumour Syndrome
MONDO: MONDO:0017623; MedGen: C1959582; OMIM: 601728

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000541610Invitaecriteria provided, single submitter
Uncertain significance
(Nov 17, 2016)
germlineclinical testing

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

Summary from all submissions

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



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]

Details of each submission

From Invitae, SCV000541610.2

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


This sequence change replaces aspartic acid with asparagine at codon 153 of the PTEN protein (p.Asp153Asn). The aspartic acid residue is highly conserved and there is a small physicochemical difference between aspartic acid and asparagine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in the literature in individuals affected with breast cancer and it is unclear if this variant was also observed in unaffected control individuals (PMID: 22320991). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies. In summary, this variant is a rare missense change that is not predicted to affect protein function. While it is absent from the population database and reported in affected individuals, the available evidence is currently insufficient to determine its role in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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

Last Updated: Apr 12, 2021

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