NM_000314.8(PTEN):c.-838C>T AND not specified

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Oct 28, 2019
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:: RCV000581555.6

Allele description [Variation Report for NM_000314.8(PTEN):c.-838C>T]

NM_000314.8(PTEN):c.-838C>T

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.-838C>T

HGVS:

NC_000010.11:g.87863632C>T
NG_007466.2:g.5195C>T
NG_033079.1:g.4806G>A
NM_000314.8:c.-838C>TMANE SELECT
NM_001304717.5:c.-318C>T
NM_001304718.2:c.-1542C>T
LRG_311t1:c.-837C>T
LRG_1087:g.4806G>A
LRG_311:g.5195C>T
NC_000010.10:g.89623389C>T
NM_000314.4:c.-837C>T
NM_000314.6:c.-837C>T

Links:

dbSNP: rs786201900

NCBI 1000 Genomes Browser:

rs786201900

Molecular consequence:

NM_000314.8:c.-838C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304717.5:c.-318C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304718.2:c.-1542C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

Clear Turn Off Turn On

Homo sapiens non-SMC condensin II complex subunit H2 (NCAPH2), transcript varian...
Homo sapiens non-SMC condensin II complex subunit H2 (NCAPH2), transcript variant 2, mRNA
gi|1519244373|ref|NM_152299.4|

Nucleotide

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000691989	Mayo Clinic Laboratories, Mayo Clinic	no assertion criteria provided	Likely benign	unknown	clinical testing
SCV001363516	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Oct 28, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000691989

Mayo Clinic Laboratories, Mayo Clinic

no assertion criteria provided

Likely benign

unknown

clinical testing

SCV001363516

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Oct 28, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Cowden syndrome-affected patients with PTEN promoter mutations demonstrate abnormal protein translation.

Teresi RE, Zbuk KM, Pezzolesi MG, Waite KA, Eng C.

Am J Hum Genet. 2007 Oct;81(4):756-67. Epub 2007 Aug 15.

PubMed [citation]

PMID:: 17847000
PMCID:: PMC2227925

Details of each submission

From Mayo Clinic Laboratories, Mayo Clinic, SCV000691989.1

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

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	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, SCV001363516.1

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

Description

Variant summary: PTEN c.-838C>T (also known as c.-837C>T) is located in the untranslated mRNA region upstream of the initiation codon. The variant was absent in 31232 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of c.-838C>T in individuals affected with Cowden Syndrome and no experimental evidence demonstrating its impact on protein function have been reported. Two ClinVar submitters (submission after 2014) cite the variant once as uncertain significance and once as likely benign. Based on the evidence outlined above, the variant was classified as uncertain significance.

#	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: May 1, 2024

ClinVar

Relating variation to medicine