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NM_000314.8(PTEN):c.190C>T (p.His64Tyr) AND PTEN hamartoma tumor syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 19, 2021
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:
RCV001857439.5

Allele description [Variation Report for NM_000314.8(PTEN):c.190C>T (p.His64Tyr)]

NM_000314.8(PTEN):c.190C>T (p.His64Tyr)

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.190C>T (p.His64Tyr)
HGVS:
  • NC_000010.11:g.87925538C>T
  • NG_007466.2:g.67100C>T
  • NM_000314.8:c.190C>TMANE SELECT
  • NM_001304717.5:c.709C>T
  • NM_001304718.2:c.-541-5508C>T
  • NP_000305.3:p.His64Tyr
  • NP_001291646.4:p.His237Tyr
  • LRG_311t1:c.190C>T
  • LRG_311:g.67100C>T
  • NC_000010.10:g.89685295C>T
  • NM_000314.4:c.190C>T
  • p.H64Y
Protein change:
H237Y
Links:
dbSNP: rs587781535
NCBI 1000 Genomes Browser:
rs587781535
Molecular consequence:
  • NM_001304718.2:c.-541-5508C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000314.8:c.190C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001304717.5:c.709C>T - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002302137Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Feb 19, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002302137.2

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

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. 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: "Possibly Damaging"; Align-GVGD: "Not Available"). This variant has not been reported in the literature in individuals with PTEN-related conditions. ClinVar contains an entry for this variant (Variation ID: 141154). This variant is not present in population databases (ExAC no frequency). This sequence change replaces histidine with tyrosine at codon 64 of the PTEN protein (p.His64Tyr). The histidine residue is highly conserved and there is a moderate physicochemical difference between histidine and tyrosine.

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

Last Updated: Sep 29, 2024