NM_000314.4(PTEN):c.-1324C>A AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 31, 2014
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV000599225.10

Allele description [Variation Report for NM_000314.4(PTEN):c.-1324C>A]

NM_000314.4(PTEN):c.-1324C>A

Genes:

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
KLLN:killin, p53 regulated DNA replication inhibitor [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.4(PTEN):c.-1324C>A

HGVS:

NC_000010.11:g.87863145C>A
NG_007466.2:g.4708C>A
NG_033079.1:g.5293G>T
NM_001126049.2:c.-658G>TMANE SELECT
LRG_1087t1:c.-658G>T
LRG_311t1:c.-1324C>A
LRG_1087:g.5293G>T
LRG_311:g.4708C>A
NC_000010.10:g.89622902C>A
NM_000314.4:c.-1324C>A

Links:

dbSNP: rs1554889769

NCBI 1000 Genomes Browser:

rs1554889769

Molecular consequence:

NM_001126049.2:c.-658G>T - 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
SCV000709834	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Dec 31, 2014)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000709834

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Dec 31, 2014)

germline

clinical testing

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

Details of each submission

From GeneDx, SCV000709834.2

#	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.-1325C>A, and describes a nucleotide substitution 1325 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 TGCT[C/A]AACG. This variant, also called c.-1324C>A using alternate numbering, has not been published in the literature to our knowledge. One study found that approximately 9% (9/95) of patients with Cowden syndrome (CS) were identified to have a point variant in the PTEN core promoter region (c.-798 to c.-1238) (Zhou 2003). While the c.-1325C>A variant is outside of this core promoter region, it could still have an effect on transcription and, possibly, PTEN protein levels. Based on the currently available information, we consider this 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

Last Updated: Nov 3, 2024

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