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NM_000314.8(PTEN):c.653G>A (p.Cys218Tyr) AND PTEN hamartoma tumor syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 23, 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:
RCV001215947.8

Allele description [Variation Report for NM_000314.8(PTEN):c.653G>A (p.Cys218Tyr)]

NM_000314.8(PTEN):c.653G>A (p.Cys218Tyr)

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.653G>A (p.Cys218Tyr)
HGVS:
  • NC_000010.11:g.87957871G>A
  • NG_007466.2:g.99433G>A
  • NM_000314.8:c.653G>AMANE SELECT
  • NM_001304717.5:c.1172G>A
  • NM_001304718.2:c.62G>A
  • NP_000305.3:p.Cys218Tyr
  • NP_001291646.4:p.Cys391Tyr
  • NP_001291647.1:p.Cys21Tyr
  • LRG_311t1:c.653G>A
  • LRG_311:g.99433G>A
  • NC_000010.10:g.89717628G>A
  • NM_000314.4:c.653G>A
Protein change:
C218Y
Links:
dbSNP: rs1860540059
NCBI 1000 Genomes Browser:
rs1860540059
Molecular consequence:
  • NM_000314.8:c.653G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304717.5:c.1172G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304718.2:c.62G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

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

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001387716Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Uncertain significance
(Feb 23, 2022)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

A Saturation Mutagenesis Approach to Understanding PTEN Lipid Phosphatase Activity and Genotype-Phenotype Relationships.

Mighell TL, Evans-Dutson S, O'Roak BJ.

Am J Hum Genet. 2018 May 3;102(5):943-955. doi: 10.1016/j.ajhg.2018.03.018. Epub 2018 Apr 26.

PubMed [citation]
PMID:
29706350
PMCID:
PMC5986715

Multiplex assessment of protein variant abundance by massively parallel sequencing.

Matreyek KA, Starita LM, Stephany JJ, Martin B, Chiasson MA, Gray VE, Kircher M, Khechaduri A, Dines JN, Hause RJ, Bhatia S, Evans WE, Relling MV, Yang W, Shendure J, Fowler DM.

Nat Genet. 2018 Jun;50(6):874-882. doi: 10.1038/s41588-018-0122-z. Epub 2018 May 21.

PubMed [citation]
PMID:
29785012
PMCID:
PMC5980760
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001387716.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

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. Experimental studies have shown that this missense change does not substantially affect PTEN function (PMID: 29706350, 29785012). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available"). ClinVar contains an entry for this variant (Variation ID: 945328). This variant has not been reported in the literature in individuals affected with PTEN-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 218 of the PTEN protein (p.Cys218Tyr).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024