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NM_000314.6(PTEN):c.-1059C>G

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Interpretation:
Benign​

Review status:
reviewed by expert panel FDA Recognized Database
Submissions:
3 (Most recent: Oct 11, 2018)
Last evaluated:
Sep 14, 2016
Accession:
VCV000189520.1
Variation ID:
189520
Description:
single nucleotide variant
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NM_000314.6(PTEN):c.-1059C>G

Allele ID
172162
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.31
Genomic location
10: 87863410 (GRCh38) GRCh38 UCSC
10: 89623167 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000010.10:g.89623167C>G
NC_000010.11:g.87863410C>G
NM_001126049.2:c.-923G>C MANE Select 5 prime UTR
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:87863409:C:G
Functional consequence
-
Global minor allele frequency (GMAF)
0.00379 (G)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00493
1000 Genomes Project 0.00379
The Genome Aggregation Database (gnomAD) 0.00405
Links
ClinGen: CA300594
dbSNP: rs144620057
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Benign 1 reviewed by expert panel Sep 14, 2016 RCV000710302.1
Likely benign 1 criteria provided, single submitter Jun 30, 2016 RCV000169909.3
Benign 1 criteria provided, single submitter Feb 1, 2017 RCV000588148.1
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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
1980 2221
KLLN - - GRCh38
GRCh38
GRCh37
7 247

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Benign
(Sep 14, 2016)
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: SCV000840479.2
Submitted: (Oct 11, 2018)
Evidence details
Comment:
PTEN c.-1059C>G (NC_000010.10:g.89623167C>G) meets criteria to be classified as benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester … (more)
Likely benign
(Jun 30, 2016)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000149463.6
Submitted: (Dec 21, 2016)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (more)
Benign
(Feb 01, 2017)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696523.1
Submitted: (Jan 25, 2018)
Evidence details
Publications
PubMed (2)
Comment:
Variant summary: The PTEN variant c.-1059C>G (also known as c.-1060C>G) involves the alteration of a non-conserved nucleotide located in the 5' UTR. The variant of … (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
Missense mutation in the PTEN promoter of a patient with hemifacial hyperplasia. Yamazaki K BoneKEy reports 2015 PMID: 26229595
KLLN epigenotype-phenotype associations in Cowden syndrome. Nizialek EA European journal of human genetics : EJHG 2015 PMID: 25669429

Text-mined citations for rs144620057...

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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 Jul 24, 2021