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NM_000314.8(PTEN):c.1026+1G>C AND PTEN hamartoma tumor syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 16, 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:
RCV002516536.2

Allele description

NM_000314.8(PTEN):c.1026+1G>C

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.1026+1G>C
HGVS:
  • NC_000010.11:g.87961119G>C
  • NG_007466.2:g.102681G>C
  • NM_000314.8:c.1026+1G>CMANE SELECT
  • NM_001304717.5:c.1546+1G>C
  • NM_001304718.2:c.435+1G>C
  • LRG_311t1:c.1026+1G>C
  • LRG_311:g.102681G>C
  • NC_000010.10:g.89720876G>C
  • NM_000314.4:c.1026+1G>C
  • NM_000314.6:c.1026+1G>C
Links:
dbSNP: rs786201041
NCBI 1000 Genomes Browser:
rs786201041
Molecular consequence:
  • NM_000314.8:c.1026+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001304717.5:c.1546+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001304718.2:c.435+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
Functional consequence:
sequence_variant_affecting_splicing [Sequence Ontology: SO:1000071] - Comment(s)

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
SCV003441538Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 16, 2022) 		germlineclinical testing

PubMed (7)
[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

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (7)

Details of each submission

From Invitae, SCV003441538.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that disruption of this splice site is associated with altered splicing resulting in unknown protein product impact (PMID: 28677221; Invitae). ClinVar contains an entry for this variant (Variation ID: 189511). Disruption of this splice site has been observed in individuals with Cowden or Cowden-like syndrome, intellectual disability, and/or overgrowth (PMID: 21194675, 28475857, 28677221, 31664961). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 8 of the PTEN gene. While this variant is not anticipated to result in nonsense mediated decay, it likely alters RNA splicing and results in a disrupted protein product.

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

Last Updated: Sep 16, 2024