NM_000314.6(PTEN):c.-1338T>A AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Aug 30, 2019
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:: RCV000759331.11

Allele description [Variation Report for NM_000314.6(PTEN):c.-1338T>A]

NM_000314.6(PTEN):c.-1338T>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_000314.6(PTEN):c.-1338T>A

HGVS:

NC_000010.11:g.87863131T>A
NG_007466.2:g.4694T>A
NG_033079.1:g.5307A>T
NM_001126049.2:c.-644A>TMANE SELECT
LRG_1087t1:c.-644A>T
LRG_311t1:c.-1338T>A
LRG_1087:g.5307A>T
LRG_311:g.4694T>A
NC_000010.10:g.89622888T>A
NM_000314.4:c.-1338T>A
NM_000314.6:c.-1338T>A

Links:

dbSNP: rs769351955

NCBI 1000 Genomes Browser:

rs769351955

Molecular consequence:

NM_001126049.2:c.-644A>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Homo sapiens ribosomal protein L24 (RPL24), mRNA
Homo sapiens ribosomal protein L24 (RPL24), mRNA
gi|78190466|ref|NM_000986.3|

Nucleotide
Mycobacterium tuberculosis UT0036
Mycobacterium tuberculosis UT0036
TB-ARC - CDRC Alland

BioProject
Mycobacterium tuberculosis KT-0031
Mycobacterium tuberculosis KT-0031
TB-ARC - CDRC Alland

BioProject
Mycobacterium tuberculosis UT0106
Mycobacterium tuberculosis UT0106
TB-ARC - CDRC Alland

BioProject
Mycobacterium tuberculosis UT0063
Mycobacterium tuberculosis UT0063
TB-ARC CDRC Alland

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000680633	GeneDx	criteria provided, single submitter (GeneDx Variant Classification (06012015))	Uncertain significance (Dec 26, 2017)	germline	clinical testing	Citation Link,
SCV000888589	Quest Diagnostics Nichols Institute San Juan Capistrano	criteria provided, single submitter (Quest Diagnostics criteria)	Uncertain significance (Aug 30, 2019)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000680633

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification (06012015))

Uncertain significance
(Dec 26, 2017)

germline

clinical testing

Citation Link,

SCV000888589

Quest Diagnostics Nichols Institute San Juan Capistrano

criteria provided, single submitter

(Quest Diagnostics criteria)

Uncertain significance
(Aug 30, 2019)

unknown

clinical testing

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

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

Details of each submission

From GeneDx, SCV000680633.1

#	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.-1339T>A, and describes a nucleotide substitution 1339 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 CGAG[T/A]CAGT. This variant, also called c.-1338T>A 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 information, it is unclear whether PTEN c.-1339T>A is pathogenic or benign. 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 Quest Diagnostics Nichols Institute San Juan Capistrano, SCV000888589.2

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

#	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

Last Updated: Nov 3, 2024

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