NM_000314.8(PTEN):c.-798A>G AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Apr 10, 2018
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000586431.2

Allele description [Variation Report for NM_000314.8(PTEN):c.-798A>G]

NM_000314.8(PTEN):c.-798A>G

Genes:

LOC130004273:ATAC-STARR-seq lymphoblastoid silent region 2585 [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.-798A>G

HGVS:

NC_000010.11:g.87863672A>G
NG_007466.2:g.5235A>G
NG_033079.1:g.4766T>C
NM_000314.8:c.-798A>GMANE SELECT
NM_001304717.5:c.-278A>G
NM_001304718.2:c.-1502A>G
LRG_311t1:c.-797A>G
LRG_1087:g.4766T>C
LRG_311:g.5235A>G
NC_000010.10:g.89623429A>G
NM_000314.4:c.-797A>G

Links:

dbSNP: rs577569375

NCBI 1000 Genomes Browser:

rs577569375

Molecular consequence:

NM_000314.8:c.-798A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304717.5:c.-278A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304718.2:c.-1502A>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000279159	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Apr 10, 2018)	germline	clinical testing	Citation Link,
SCV000696539	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Apr 25, 2016)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000279159

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Apr 10, 2018)

germline

clinical testing

Citation Link,

SCV000696539

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Apr 25, 2016)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000279159.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant is denoted PTEN c.-798A>G, and describes a nucleotide substitution 798 base pairs upstream of the ATG translational start site in the PTEN promoter region. The surrounding sequence, with the base that is substituted in brackets, is GTTG[A/G]GCCG. This variant, also called c.-797A>G using alternate numbering, has not been published in the literature to our knowledge. Variants within the PTEN promoter have been observed in individuals with features of Cowden syndrome (Zhou 2003). Based on currently available evidence, it is unclear whether PTEN c.-798A>G is a pathogenic or benign variant. We consider it to be a variant of uncertain significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000696539.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant Summary: The PTEN variant c.-797A>G (also known as c.-798A>G) affects a non-conserved nucleotide 798 base pairs upstream of the ATG translational start. The variant falls within PTEN core promoter region. The variant was found in control population dataset of 1000Gs at a frequency 0.04% (2/5008chrs tested). This variant has not, to our knowledge, been reported in HBOC/Cowden Syndrome pts. Neighboring variants, such as c.-799G>C, c.-835C>T, c.-854C>G were identified in pts presented with Cowden Syndrome. Addition clinical and population data needed to classify this variant with confidence. Taking together, the variant was classified as VUS until more information becomes available.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Dec 24, 2023

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