NM_000314.8(PTEN):c.*5T>C AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: May 10, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV000589303.15

Allele description [Variation Report for NM_000314.8(PTEN):c.*5T>C]

NM_000314.8(PTEN):c.*5T>C

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.*5T>C

Other names:

NM_000314.7(PTEN):c.*5T>C

HGVS:

NC_000010.11:g.87965477T>C
NG_007466.2:g.107039T>C
NM_000314.8:c.*5T>CMANE SELECT
NM_001304717.5:c.*5T>C
NM_001304718.2:c.*5T>C
LRG_311t1:c.*5T>C
LRG_311:g.107039T>C
NC_000010.10:g.89725234T>C
NC_000010.10:g.89725234T>C
NM_000314.4:c.*5T>C
NM_000314.6:c.*5T>C

Links:

dbSNP: rs1006891299

NCBI 1000 Genomes Browser:

rs1006891299

Molecular consequence:

NM_000314.8:c.*5T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001304717.5:c.*5T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001304718.2:c.*5T>C - 3 prime UTR variant - [Sequence Ontology: SO:0001624]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Mus musculus protein phosphatase 4, regulatory subunit 4 (Ppp4r4), mRNA
Mus musculus protein phosphatase 4, regulatory subunit 4 (Ppp4r4), mRNA
gi|141803539|ref|NM_028980.2|

Nucleotide
icPogHisp
icPogHisp
Pogonocherus hispidulus (greater thorn-tipped longhorn beetle), genomic and transcriptomic data

BioProject

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
SCV000566704	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely benign (May 10, 2023)	germline	clinical testing	Citation Link,
SCV000696515	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Mar 30, 2017)	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

SCV000566704

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely benign
(May 10, 2023)

germline

clinical testing

Citation Link,

SCV000696515

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

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Mar 30, 2017)

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, SCV000566704.6

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

Description

See Variant Classification Assertion Criteria.

#	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, SCV000696515.1

#	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 c.*5T>C located in the 3' UTR variant involves the alteration of a conserved nucleotide. One in silico tool predicts a damaging outcome for this variant, although these prediction has yet to be functionally assessed. The variant of interest was observed in the large, broad control population, gnomAD, with an allele frequency of 4/241568 (1/67888), predominantly in the African cohort, 3/23260 (1/7751), which exceeds the estimated maximal expected allele frequency for a pathogenic PTEN variant of 1/158730. Therefore, suggesting this is likely a benign polymorphism found primarily in population(s) of African origin. However, this observation in the gnomAD cohort needs to be cautiously considered due to at this time the LCA VSG has yet to validate this population. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories. Therefore, until additional information becomes available (ie, clinical and functional studies), the variant of interest has been classified as a "Variant of Uncertain Significance - Possibly Benign."

#	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: Nov 10, 2024

ClinVar

Relating variation to medicine