NM_000314.8(PTEN):c.75G>A (p.Leu25=) AND PTEN hamartoma tumor syndrome

Clinical significance:Uncertain significance (Last evaluated: Jun 25, 2019)

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000553143.4

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

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

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.75G>A (p.Leu25=)
Other names:
NM_000314.6(PTEN):c.75G>A(p.Leu25=); NM_000314.6(PTEN):c.75G>A
HGVS:
  • 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
Links:
dbSNP: rs786201506
NCBI 1000 Genomes Browser:
rs786201506
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]

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
SCV000645620Invitaecriteria provided, single submitter
Likely benign
(Dec 31, 2019)
germlineclinical testing

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

SCV000840466ClinGen PTEN Variant Curation Expert Panelreviewed by expert panel
Uncertain significance
(Jun 25, 2019)
germlinecuration

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

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
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

Analysis of protein-coding genetic variation in 60,706 humans.

Lek M, Karczewski KJ, Minikel EV, Samocha KE, Banks E, Fennell T, O'Donnell-Luria AH, Ware JS, Hill AJ, Cummings BB, Tukiainen T, Birnbaum DP, Kosmicki JA, Duncan LE, Estrada K, Zhao F, Zou J, Pierce-Hoffman E, Berghout J, Cooper DN, Deflaux N, DePristo M, et al.

Nature. 2016 Aug 18;536(7616):285-91. doi: 10.1038/nature19057.

PubMed [citation]
PMID:
27535533
PMCID:
PMC5018207

Details of each submission

From Invitae, SCV000645620.3

#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, SCV000840466.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcuration PubMed (1)

Description

PTEN c.75G>A (p.Leu25=) 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). PM2: Absent in large sequenced populations (PMID 27535533). BP7: Variant is synonymous (silent), nucleotide is not conserved, and no splicing impact is predicted.

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

Last Updated: Nov 6, 2021

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