NM_000314.8(PTEN):c.517C>A (p.Arg173Ser) AND PTEN hamartoma tumor syndrome

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 14, 2016
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:: RCV000460834.6

Allele description [Variation Report for NM_000314.8(PTEN):c.517C>A (p.Arg173Ser)]

NM_000314.8(PTEN):c.517C>A (p.Arg173Ser)

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.517C>A (p.Arg173Ser)

HGVS:

NC_000010.11:g.87952142C>A
NG_007466.2:g.93704C>A
NM_000314.8:c.517C>AMANE SELECT
NM_001304717.5:c.1036C>A
NM_001304718.2:c.-75C>A
NP_000305.3:p.Arg173Ser
NP_001291646.4:p.Arg346Ser
LRG_311t1:c.517C>A
LRG_311:g.93704C>A
NC_000010.10:g.89711899C>A
NM_000314.4:c.517C>A

Protein change:

R173S

Links:

dbSNP: rs121913293

NCBI 1000 Genomes Browser:

rs121913293

Molecular consequence:

NM_001304718.2:c.-75C>A - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_000314.8:c.517C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001304717.5:c.1036C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000541584	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 14, 2016)	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

SCV000541584

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 14, 2016)

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	not provided	not provided	not provided	not provided	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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV000541584.5

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

Description

In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a PTEN-related disease. This sequence change replaces arginine with serine at codon 173 of the PTEN protein (p.Arg173Ser). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and serine.

#	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: Mar 5, 2024

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