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NM_000314.8(PTEN):c.-765G>A

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Interpretation:
Uncertain significance​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
6 (Most recent: Sep 24, 2021)
Last evaluated:
Apr 6, 2018
Accession:
VCV000007844.4
Variation ID:
7844
Description:
single nucleotide variant
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NM_000314.8(PTEN):c.-765G>A

Allele ID
22883
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.31
Genomic location
10: 87863705 (GRCh38) GRCh38 UCSC
10: 89623462 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_311:g.5268G>A
LRG_1087:g.4733C>T
LRG_311t1:c.-764G>A
... more HGVS
Protein change
-
Other names
-764A-G
Canonical SPDI
NC_000010.11:87863704:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00002
Links
ClinGen: CA000567
OMIM: 601728.0033
dbSNP: rs587776674
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 Apr 6, 2018 RCV000230941.2
Uncertain significance 2 criteria provided, single submitter Apr 21, 2017 RCV000008294.4
Uncertain significance 1 criteria provided, single submitter May 10, 2021 RCV000169801.3
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000763685.1
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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
2001 2243

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Apr 06, 2018)
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: SCV000840498.2
Submitted: (Oct 11, 2018)
Evidence details
Comment:
PTEN c.-764G>A (NC_000010.10:g.89623462G>A) is currently classified as a variant of uncertain significance for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG … (more)
Uncertain significance
(Mar 28, 2016)
criteria provided, single submitter
Method: clinical testing
PTEN hamartoma tumor syndrome
Allele origin: germline
Invitae
Accession: SCV000284573.2
Submitted: (Jun 10, 2016)
Evidence details
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Cowden syndrome 1
Malignant tumor of prostate
VACTERL association with hydrocephalus
None

Macrocephaly/autism syndrome
Meningioma, familial
Glioma susceptibility 2
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000894565.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(May 10, 2021)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000222117.5
Submitted: (Sep 24, 2021)
Evidence details
Comment:
Describes a nucleotide substitution 765 basepairs upstream of the ATG translational start site in the PTEN promoter region; Observed in individuals with breast or endometrial … (more)
Uncertain significance
(Apr 21, 2017)
criteria provided, single submitter
Method: clinical testing
Cowden syndrome 1
Allele origin: unknown
Counsyl
Accession: SCV000785100.2
Submitted: (Jun 20, 2018)
Evidence details
Publications
PubMed (4)
Pathogenic
(Oct 01, 2007)
no assertion criteria provided
Method: literature only
COWDEN SYNDROME 1
Allele origin: germline
OMIM
Accession: SCV000028501.3
Submitted: (Dec 30, 2010)
Evidence details
Publications
PubMed (2)

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
Human gene-centered transcription factor networks for enhancers and disease variants. Fuxman Bass JI Cell 2015 PMID: 25910213
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
RNAsnp: efficient detection of local RNA secondary structure changes induced by SNPs. Sabarinathan R Human mutation 2013 PMID: 23315997
Cowden syndrome-affected patients with PTEN promoter mutations demonstrate abnormal protein translation. Teresi RE American journal of human genetics 2007 PMID: 17847000
Germline PTEN promoter mutations and deletions in Cowden/Bannayan-Riley-Ruvalcaba syndrome result in aberrant PTEN protein and dysregulation of the phosphoinositol-3-kinase/Akt pathway. Zhou XP American journal of human genetics 2003 PMID: 12844284

Text-mined citations for rs587776674...

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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 20, 2021