NM_000314.7(PTEN):c.-9C>G AND PTEN hamartoma tumor syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Benign (3 submissions)
Last evaluated:: Nov 9, 2016
Review status:: 3 stars out of maximum of 4 stars
reviewed by expert panel

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:: RCV000203697.3

Allele description

NM_000314.7(PTEN):c.-9C>G

Gene:

PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q23.31

Genomic location:

Preferred name:

NM_000314.7(PTEN):c.-9C>G

HGVS:

NC_000010.11:g.87864461C>G
NG_007466.2:g.6023C>G
NG_033079.1:g.3977G>C
NM_000314.7:c.-9C>G
NM_001304717.5:c.511C>G
NM_001304718.2:c.-714C>G
NP_001291646.4:p.Leu171Val
LRG_311t1:c.-9C>G
LRG_311:g.6023C>G
NC_000010.10:g.89624218C>G
NM_000314.4:c.-9C>G

Protein change:

L171V

Links:

dbSNP: rs11202592

NCBI 1000 Genomes Browser:

rs11202592

Molecular consequence:

NM_000314.7:c.-9C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304718.2:c.-714C>G - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001304717.5:c.511C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: PTEN hamartoma tumor syndrome (PHTS)
Synonyms:: PTEN Hamartomatous Tumour Syndrome
Identifiers:: MONDO: MONDO:0017623; MedGen: C1959582; OMIM: 601728

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000261850	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Mar 29, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000365735	Illumina Clinical Services Laboratory,Illumina	criteria provided, single submitter (ICSL Variant Classification 20161018)	Likely benign (Jun 14, 2016)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] ICSL_Variant_Classification_20161018.pdf, Citation Link,
SCV000840463	ClinGen PTEN Variant Curation Expert Panel	reviewed by expert panel (ClinGen PTEN ACMG Specifications v1)	Benign (Nov 9, 2016)	germline	curation	ClinGen_PTEN_ACMG_Specifications_v1.pdf Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000261850

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Benign
(Mar 29, 2016)

germline

clinical testing

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

SCV000365735

Illumina Clinical Services Laboratory,Illumina

criteria provided, single submitter

(ICSL Variant Classification 20161018)

Likely benign
(Jun 14, 2016)

germline

clinical testing

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

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV000840463

ClinGen PTEN Variant Curation Expert Panel

reviewed by expert panel

(ClinGen PTEN ACMG Specifications v1)

Benign
(Nov 9, 2016)

germline

curation

ClinGen_PTEN_ACMG_Specifications_v1.pdf

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, curation

Citations

PubMed

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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Association of the polymorphisms in the 5'-untranslated region of PTEN gene with type 2 diabetes in a Japanese population.

Ishihara H, Sasaoka T, Kagawa S, Murakami S, Fukui K, Kawagishi Y, Yamazaki K, Sato A, Iwata M, Urakaze M, Ishiki M, Wada T, Yaguchi S, Tsuneki H, Kimura I, Kobayashi M.

FEBS Lett. 2003 Nov 20;554(3):450-4.

PubMed [citation]

PMID:: 14623110

Details of each submission

From Invitae, SCV000261850.3

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Illumina Clinical Services Laboratory,Illumina, SCV000365735.2

#	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	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From ClinGen PTEN Variant Curation Expert Panel, SCV000840463.2

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

Description

PTEN c.-9C>G (NC_000010.10:g.89624218C>G) meets criteria to be classified as benign for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (Mester et al. 2018; manuscript in preparation). Please see a summary of the rules and criteria codes in the 'PTEN ACMG Specifications Summary' document (assertion method column). BA1: Allele frequency of 0.048 (4.8%, 903/18,870 alleles) in the East Asian subpopulation of the gnomAD cohort. (PMID 27535533)

#	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: Apr 18, 2020

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