NM_000314.8(PTEN):c.658_659dup (p.Leu220_Lys221insTer) AND PTEN hamartoma tumor syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 21, 2020
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:
RCV002273001.3

Allele description [Variation Report for NM_000314.8(PTEN):c.658_659dup (p.Leu220_Lys221insTer)]

NM_000314.8(PTEN):c.658_659dup (p.Leu220_Lys221insTer)

Gene:
PTEN:phosphatase and tensin homolog [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
10q23.31
Genomic location:
Preferred name:
NM_000314.8(PTEN):c.658_659dup (p.Leu220_Lys221insTer)
HGVS:
  • NC_000010.11:g.87957876_87957877dup
  • NG_007466.2:g.99438_99439dup
  • NM_000314.8:c.658_659dupMANE SELECT
  • NM_001304717.5:c.1177_1178dup
  • NM_001304718.2:c.67_68dup
  • NP_000305.3:p.Leu220_Lys221insTer
  • NP_001291646.4:p.Leu393_Lys394insTer
  • NP_001291647.1:p.Leu23_Lys24insTer
  • LRG_311t1:c.658_659dup
  • LRG_311:g.99438_99439dup
  • NC_000010.10:g.89717633_89717634dup
  • NM_000314.4:c.658_659dupCT
Links:
dbSNP: rs2132276566
NCBI 1000 Genomes Browser:
rs2132276566
Molecular consequence:
  • NM_000314.8:c.658_659dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001304717.5:c.1177_1178dup - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001304718.2:c.67_68dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV002557533Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(May 21, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Neurobehavioral phenotype of autism spectrum disorder associated with germline heterozygous mutations in PTEN.

Busch RM, Srivastava S, Hogue O, Frazier TW, Klaas P, Hardan A, Martinez-Agosto JA, Sahin M, Eng C; Developmental Synaptopathies Consortium..

Transl Psychiatry. 2019 Oct 8;9(1):253. doi: 10.1038/s41398-019-0588-1.

PubMed [citation]
PMID:
31594918
PMCID:
PMC6783427

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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002557533.2

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

Description

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (exon 7 of 9). (P) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0701 - Comparable variants have very strong previous evidence for pathogenicity (Decipher, ClinVar, Busch, R. M. et al. (2019)) (P) 0807 - Variant has not previously been reported in a clinical context. (N) 0905 - No segregation evidence has been identified for this variant. (N) 1007 - No published functional evidence has been identified for this variant. (N) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

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

Last Updated: Jul 23, 2024