NM_000314.8(PTEN):c.-844T>C AND PTEN hamartoma tumor syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 27, 2022
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:: RCV001854554.3

Allele description [Variation Report for NM_000314.8(PTEN):c.-844T>C]

NM_000314.8(PTEN):c.-844T>C

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.-844T>C

HGVS:

NC_000010.11:g.87863626T>C
NG_007466.2:g.5189T>C
NG_033079.1:g.4812A>G
NM_000314.8:c.-844T>CMANE SELECT
NM_001304717.5:c.-324T>C
NM_001304718.2:c.-1548T>C
LRG_311t1:c.-843T>C
LRG_1087:g.4812A>G
LRG_311:g.5189T>C
NC_000010.10:g.89623383T>C
NM_000314.4:c.-843T>C
c.-844T>C[hg19]

Links:

dbSNP: rs587779995

NCBI 1000 Genomes Browser:

rs587779995

Molecular consequence:

NM_000314.8:c.-844T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304717.5:c.-324T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304718.2:c.-1548T>C - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Name:: PTEN hamartoma tumor syndrome (PHTS)
Synonyms:: PTEN Hamartomatous Tumour Syndrome
Identifiers:: MONDO: MONDO:0017623; MeSH: D006223; MedGen: C1959582

Recent activity

Clear Turn Off Turn On

Hydnocarpus hainanensis
Hydnocarpus hainanensis
Hydnocarpus hainanensis RefSeq Genome

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
SCV002230163	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 27, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 16773562, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002230163

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 27, 2022)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Citations

PubMed

Distinct expression profiles for PTEN transcript and its splice variants in Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome.

Sarquis MS, Agrawal S, Shen L, Pilarski R, Zhou XP, Eng C.

Am J Hum Genet. 2006 Jul;79(1):23-30. Epub 2006 May 22.

PubMed [citation]

PMID:: 16773562
PMCID:: PMC1474112

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002230163.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

This variant occurs in a non-coding region of the PTEN gene. It does not change the encoded amino acid sequence of the PTEN protein. This variant is present in population databases (rs587779995, gnomAD 0.007%). This variant has been observed in individual(s) with clinical features of Cowden syndrome (PMID: 16773562). This variant is also known as -843C/T. Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of 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: Sep 29, 2024

ClinVar

Relating variation to medicine