NM_000314.8(PTEN):c.209+5G>A AND PTEN hamartoma tumor syndrome

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Nov 21, 2023
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:: RCV001050316.6

Allele description [Variation Report for NM_000314.8(PTEN):c.209+5G>A]

NM_000314.8(PTEN):c.209+5G>A

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.209+5G>A

HGVS:

NC_000010.11:g.87925562G>A
NG_007466.2:g.67124G>A
NM_000314.8:c.209+5G>AMANE SELECT
NM_001304717.5:c.729+5G>A
NM_001304718.2:c.-541-5484G>A
LRG_311t1:c.209+5G>A
LRG_311:g.67124G>A
NC_000010.10:g.89685319G>A
NM_000314.4:c.209+5G>A
NM_000314.6:c.209+5G>A

Links:

dbSNP: rs1114167650

NCBI 1000 Genomes Browser:

rs1114167650

Molecular consequence:

NM_000314.8:c.209+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001304717.5:c.729+5G>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001304718.2:c.-541-5484G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

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

Recent activity

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uncharacterized protein Dmel_CG31522, isoform B [Drosophila melanogaster]
uncharacterized protein Dmel_CG31522, isoform B [Drosophila melanogaster]
gi|28573238|ref|NP_730841.2|

Protein
CBXT6811.b1 NICHD_XGC_trop_25 Xenopus tropicalis cDNA clone IMAGE:8888642 5', mR...
CBXT6811.b1 NICHD_XGC_trop_25 Xenopus tropicalis cDNA clone IMAGE:8888642 5', mRNA sequence
gi|133812823|gnl|dbEST|45242430|gb| 470.1|

Nucleotide
Mus musculus chromosome 7, clone RP23-421O10, complete sequence
Mus musculus chromosome 7, clone RP23-421O10, complete sequence
gi|77416359|gnl|WIBR|L31051|gb|AC16 2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001214415	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Nov 21, 2023)	germline	clinical testing	PubMed (8) [See all records that cite these PMIDs] 10232405, 20712882, 23695273, 17576681, 9536098, 16014636, 28677221, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001214415

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Nov 21, 2023)

germline

clinical testing

PubMed (8)
[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

Identification of PTEN mutations in five families with Bannayan-Zonana syndrome.

Tok Celebi J, Chen FF, Zhang H, Ping XL, Tsou HC, Peacocke M.

Exp Dermatol. 1999 Apr;8(2):134-9.

PubMed [citation]

PMID:: 10232405

Molecular apocrine differentiation is a common feature of breast cancer in patients with germline PTEN mutations.

Banneau G, Guedj M, MacGrogan G, de Mascarel I, Velasco V, Schiappa R, Bonadona V, David A, Dugast C, Gilbert-Dussardier B, Ingster O, Vabres P, Caux F, de Reynies A, Iggo R, Sevenet N, Bonnet F, Longy M.

Breast Cancer Res. 2010;12(4):R63. doi: 10.1186/bcr2626. Epub 2010 Aug 16.

PubMed [citation]

PMID:: 20712882
PMCID:: PMC2949656

See all PubMed Citations (8)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001214415.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (8)

Description

This sequence change falls in intron 3 of the PTEN gene. It does not directly change the encoded amino acid sequence of the PTEN protein. RNA analysis indicates that this variant induces altered splicing and likely results in a shortened protein product. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with PTEN-related conditions (PMID: 10232405, 20712882, 23695273; Invitae). This variant is also known as IVS3+5G>A. ClinVar contains an entry for this variant (Variation ID: 427614). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant results in skipping of exon 3, but is expected to preserve the integrity of the reading-frame (PMID: 16014636, 28677221). For these reasons, this variant has been classified as Pathogenic.

#	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

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