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

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Interpretation:
Uncertain significance​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
6 (Most recent: Nov 3, 2021)
Last evaluated:
Jun 25, 2019
Accession:
VCV000184505.8
Variation ID:
184505
Description:
single nucleotide variant
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NM_000314.8(PTEN):c.75G>A (p.Leu25=)

Allele ID
183008
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.31
Genomic location
10: 87864544 (GRCh38) GRCh38 UCSC
10: 89624301 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.89624301G>A
NC_000010.11:g.87864544G>A
NG_007466.2:g.6106G>A
... more HGVS
Protein change
-
Other names
NM_000314.6(PTEN):c.75G>A(p.Leu25=)
NM_000314.6(PTEN):c.75G>A
Canonical SPDI
NC_000010.11:87864543:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA000197
dbSNP: rs786201506
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 reviewed by expert panel Jun 25, 2019 RCV000553143.4
Likely benign 2 criteria provided, multiple submitters, no conflicts Aug 11, 2015 RCV000163772.2
Uncertain significance 1 criteria provided, single submitter Oct 3, 2019 RCV001753554.1
Likely benign 1 no assertion criteria provided - RCV001358393.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PTEN Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
2003 2245

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Jun 25, 2019)
reviewed by expert panel
Method: curation
PTEN hamartoma tumor syndrome
(Autosomal dominant inheritance)
Allele origin: germline
ClinGen PTEN Variant Curation Expert Panel
FDA Recognized Database
Accession: SCV000840466.3
Submitted: (Jul 23, 2019)
Evidence details
Publications
PubMed (1)
Other databases
https://erepo.clinicalgenome.org…
Comment:
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 … (more)
Likely benign
(Oct 08, 2014)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Ambry Genetics
Accession: SCV000214353.5
Submitted: (Nov 30, 2020)
Evidence details
Comment:
This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, … (more)
Likely benign
(Aug 11, 2015)
criteria provided, single submitter
Method: clinical testing
Hereditary cancer-predisposing syndrome
Allele origin: germline
Color Health, Inc
Accession: SCV000686302.1
Submitted: (Oct 26, 2017)
Evidence details
Likely benign
(Dec 31, 2019)
criteria provided, single submitter
Method: clinical testing
PTEN hamartoma tumor syndrome
Allele origin: germline
Invitae
Accession: SCV000645620.3
Submitted: (Jan 29, 2020)
Evidence details
Uncertain significance
(Oct 03, 2019)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV002007349.1
Submitted: (Nov 03, 2021)
Evidence details
Comment:
Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016); In-silico analysis, which … (more)
Likely benign
(-)
no assertion criteria provided
Method: clinical testing
Malignant tumor of breast
Allele origin: unknown
Department of Pathology and Laboratory Medicine,Sinai Health System
Additional submitter:
Franklin by Genoox
Study: The Canadian Open Genetics Repository (COGR)
Accession: SCV001554111.1
Submitted: (Mar 31, 2021)
Evidence details
Comment:
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 … (more)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Analysis of protein-coding genetic variation in 60,706 humans. Lek M Nature 2016 PMID: 27535533
https://erepo.clinicalgenome.org/evrepo/ui/interpretation/e5e35031-cdfe-44ec-ad5e-0f3892c0a7b1 - - - -

Text-mined citations for rs786201506...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 27, 2021