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

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Interpretation:
Pathogenic​

Review status:
criteria provided, single submitter
Submissions:
3 (Most recent: Nov 19, 2021)
Last evaluated:
May 18, 2019
Accession:
VCV000635377.5
Variation ID:
635377
Description:
single nucleotide variant
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NM_000314.8(PTEN):c.1026+1G>T

Allele ID
623200
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
10q23.31
Genomic location
10: 87961119 (GRCh38) GRCh38 UCSC
10: 89720876 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_311:g.102681G>T
LRG_311t1:c.1026+1G>T
NC_000010.11:g.87961119G>T
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000010.11:87961118:G:T
Functional consequence
sequence_variant_affecting_splicing [Sequence Ontology SO:1000071]
Intron inclusion between exons 8 & 9, and loss of exon 9 expression, based on review of RNA-seq in U-118 MG cancer cell line which has PTEN NM_000314.6:c.1026+1G>T variant. [submitted by MutSpliceDB: a database of splice sites variants effects on splicing,NIH]
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs786201041
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic 1 criteria provided, single submitter May 18, 2019 RCV001220442.2
Pathogenic 2 no assertion criteria provided Mar 10, 2020 RCV000786804.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PTEN Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh38
GRCh37
2003 2245

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(May 18, 2019)
criteria provided, single submitter
Method: clinical testing
PTEN hamartoma tumor syndrome
Allele origin: germline
Invitae
Accession: SCV001392431.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (5)
Comment:
This sequence change affects a donor splice site in the last intron (intron 8) of the PTEN gene. While this is not anticipated to result … (more)
Pathogenic
(Mar 10, 2020)
no assertion criteria provided
Method: clinical testing
not provided
Allele origin: germline
PerkinElmer Genomics
Accession: SCV002019541.1
Submitted: (Nov 19, 2021)
Evidence details
not provided
(-)
no assertion provided
Method: in vitro
not provided
Allele origin: not applicable
MutSpliceDB: a database of splice sites variants effects on splicing,NIH
Accession: SCV000925696.2
Submitted: (Nov 07, 2019)
Evidence details

Functional evidence

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Functional consequence Method Result Submitter Supporting information
sequence_variant_affecting_splicing
  1. Based on review of RNA-seq data in sample with variant.
  1. Intron inclusion between exons 8 & 9, and loss of exon 9 expression
MutSpliceDB: a database of splice sites variants effects on splicing,NIH
Accession: SCV000925696.2
Submitted: (Nov 07, 2019)
Evidence details
Comment:
Intron inclusion between exons 8 & 9, and loss of exon 9 expression, based on review of RNA-seq in U-118 MG cancer cell line which … (more)

Citations for this variant

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Title Author Journal Year Link
Characterization of cryptic splicing in germline PTEN intronic variants in Cowden syndrome. Chen HJ Human mutation 2017 PMID: 28677221
Mutations in Epigenetic Regulation Genes Are a Major Cause of Overgrowth with Intellectual Disability. Tatton-Brown K American journal of human genetics 2017 PMID: 28475857
A clinical scoring system for selection of patients for PTEN mutation testing is proposed on the basis of a prospective study of 3042 probands. Tan MH American journal of human genetics 2011 PMID: 21194675
Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization. Buratti E Nucleic acids research 2007 PMID: 17576681
Statistical features of human exons and their flanking regions. Zhang MQ Human molecular genetics 1998 PMID: 9536098
https://brb.nci.nih.gov/cgi-bin/splicing/splicing_evidence.cgi?caid=CA377486187 - - - -

Text-mined citations for rs786201041...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Nov 28, 2021