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NM_000314.8(PTEN):c.1169A>G (p.Glu390Gly) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 15, 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:
RCV003289516.2

Allele description [Variation Report for NM_000314.8(PTEN):c.1169A>G (p.Glu390Gly)]

NM_000314.8(PTEN):c.1169A>G (p.Glu390Gly)

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.1169A>G (p.Glu390Gly)
HGVS:
  • NC_000010.11:g.87965429A>G
  • NG_007466.2:g.106991A>G
  • NM_000314.8:c.1169A>GMANE SELECT
  • NM_001304717.5:c.1688A>G
  • NM_001304718.2:c.578A>G
  • NP_000305.3:p.Glu390Gly
  • NP_000305.3:p.Glu390Gly
  • NP_001291646.4:p.Glu563Gly
  • NP_001291647.1:p.Glu193Gly
  • LRG_311t1:c.1169A>G
  • LRG_311:g.106991A>G
  • LRG_311p1:p.Glu390Gly
  • NC_000010.10:g.89725186A>G
  • NM_000314.4:c.1169A>G
Protein change:
E193G
Molecular consequence:
  • NM_000314.8:c.1169A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304717.5:c.1688A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304718.2:c.578A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004009206Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Uncertain significance
(May 15, 2023) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

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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

Details of each submission

From Ambry Genetics, SCV004009206.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

The p.E390G variant (also known as c.1169A>G), located in coding exon 9 of the PTEN gene, results from an A to G substitution at nucleotide position 1169. The glutamic acid at codon 390 is replaced by glycine, an amino acid with similar properties. In a massively parallel functional assay using a humanized yeast model, lipid phosphatase activity for this variant was wildtype-like (Mighell TL et al. Am J Hum Genet, 2018 May;102:943-955). This variant demonstrated wildtype-like intracellular protein abundance on one multiplex functional assay (Matreyek KA et al. Nat Genet, 2018 Jun;50:874-882). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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

Last Updated: May 1, 2024