rs786203847
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PS4_ModeratePVS1_StrongPM2_Supporting
This summary comes from the ClinGen Evidence Repository: NM_000314.8(PTEN):c.165-1G>A meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.1.0). Please see a summary of the rules and criteria codes in the “PTEN ACMG Specifications Summary” document (assertion method column).PVS1_Strong: in-frame but truncated/altered region is critical to protein function. PM2_P: Absent in large sequenced populations in the gnomAD cohort. (PMID 27535533).PS4_P: Probands with phenotype specificity score of 1-1.5. (PMID:21659347). LINK:https://erepo.genome.network/evrepo/ui/classification/CA000129/MONDO:0017623/003
Frequency
Consequence
NM_000314.8 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTEN | NM_000314.8 | c.165-1G>A | splice_acceptor_variant | ENST00000371953.8 | |||
PTEN | NM_001304717.5 | c.684-1G>A | splice_acceptor_variant | ||||
PTEN | NM_001304718.2 | c.-540-5534G>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTEN | ENST00000371953.8 | c.165-1G>A | splice_acceptor_variant | 1 | NM_000314.8 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Apr 22, 2021 | Canonical splice site variant expected to result in aberrant splicing, although in the absence of functional evidence the actual effect of this sequence change is unknown.; Not observed in large population cohorts (Lek 2016); Observed in individuals with features of PTEN hamaratoma tumor syndrome (Pilarski 2011, Tan 2011); This variant is associated with the following publications: (PMID: 21194675, 26681312, 21659347, 30311380) - |
Pathogenic, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Jun 30, 2022 | PP5, PM2, PVS1 - |
Cowden syndrome 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | MGZ Medical Genetics Center | Oct 25, 2021 | - - |
PTEN hamartoma tumor syndrome Pathogenic:1
Likely pathogenic, reviewed by expert panel | curation | Clingen PTEN Variant Curation Expert Panel, Clingen | Apr 05, 2024 | NM_000314.8(PTEN):c.165-1G>A meets criteria to be classified as likely pathogenic for PTEN Hamartoma Tumor syndrome in an autosomal dominant manner using modified ACMG criteria (ACMG Classification Rules Specified for PTEN Variant Curation version 3.1.0). Please see a summary of the rules and criteria codes in the "PTEN ACMG Specifications Summary" document (assertion method column). PVS1_Strong: in-frame but truncated/altered region is critical to protein function. PM2_P: Absent in large sequenced populations in the gnomAD cohort. (PMID 27535533). PS4_P: Probands with phenotype specificity score of 1-1.5. (PMID: 21659347). - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 08, 2022 | The c.165-1G>A intronic pathogenic mutation results from a G to A substitution one nucleotide upstream from coding exon 3 of the PTEN gene. Alterations that disrupt the canonical splice site are expected to result in aberrant splicing. In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. The resulting transcript is predicted to be in-frame and is not expected to trigger nonsense-mediated mRNAdecay; however, direct evidence is unavailable. The exact functional effect of the altered amino acid sequence is unknown; however, the impacted region is critical for protein function based on internal structural analysis and is anticipated to result in a significant decrease in structural stability (Ambry internal data; Lee et al. Angew. Chem. Int. Ed. Engl. 2015 Nov;54(46):13796-800). RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This alteration has previously been reported in one individual satisfying relaxed Cowden syndrome clinical criteria (Tan M et al. Am. J. Hum. Genet. 2011 Jan; 88(1):42-56). It was also identified in 1/10030 consecutive patients referred for evaluation by an NGS hereditary cancer panel (Susswein LR et al. Genet. Med. 2016 Aug;18(8):823-32). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at