NM_000314.8(PTEN):c.54G>A (p.Glu18=) AND PTEN hamartoma tumor syndrome

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Sep 17, 2023
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:: RCV000531245.11

Allele description [Variation Report for NM_000314.8(PTEN):c.54G>A (p.Glu18=)]

NM_000314.8(PTEN):c.54G>A (p.Glu18=)

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.54G>A (p.Glu18=)

HGVS:

NC_000010.11:g.87864523G>A
NG_007466.2:g.6085G>A
NG_033079.1:g.3915C>T
NM_000314.8:c.54G>AMANE SELECT
NM_001304717.5:c.573G>A
NM_001304718.2:c.-652G>A
NP_000305.3:p.Glu18=
NP_001291646.4:p.Glu191=
LRG_311t1:c.54G>A
LRG_1087:g.3915C>T
LRG_311:g.6085G>A
NC_000010.10:g.89624280G>A
NM_000314.4:c.54G>A
NM_000314.6:c.54G>A

Links:

dbSNP: rs1554890388

NCBI 1000 Genomes Browser:

rs1554890388

Molecular consequence:

NM_001304718.2:c.-652G>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000314.8:c.54G>A - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001304717.5:c.573G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

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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PREDICTED: Benincasa hispida zinc transporter 5 (LOC120091147), mRNA
PREDICTED: Benincasa hispida zinc transporter 5 (LOC120091147), mRNA
gi|1955831685|ref|XM_039049019.1|

Nucleotide
Homo sapiens cDNA FLJ42710 fis, clone BRAMY3007609, moderately similar to Homo s...
Homo sapiens cDNA FLJ42710 fis, clone BRAMY3007609, moderately similar to Homo sapiens nuclear RNA export factor 2 (NXF2)
gi|34530560|dbj|AK124700.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000645598	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Oct 28, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004838530	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Sep 17, 2023)	germline	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

SCV000645598

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Oct 28, 2022)

germline

clinical testing

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

SCV004838530

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely Benign
(Sep 17, 2023)

germline

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	unknown	1	not provided	not provided	108544	not provided	clinical testing

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000645598.5

#	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 All of Us Research Program, National Institutes of Health, SCV004838530.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	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	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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