rs587782360
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_000314.8(PTEN):c.403A>G(p.Ile135Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I135M) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000314.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTEN | NM_000314.8 | c.403A>G | p.Ile135Val | missense_variant | 5/9 | ENST00000371953.8 | |
PTEN | NM_001304717.5 | c.922A>G | p.Ile308Val | missense_variant | 6/10 | ||
PTEN | NM_001304718.2 | c.-348A>G | 5_prime_UTR_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTEN | ENST00000371953.8 | c.403A>G | p.Ile135Val | missense_variant | 5/9 | 1 | NM_000314.8 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Neoplasm of ovary Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne | Dec 01, 2018 | - - |
Cowden syndrome 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Oct 20, 2023 | This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 17392703, 23335809, 32378608, 37090027]. - |
PTEN hamartoma tumor syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Nov 21, 2023 | This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 135 of the PTEN protein (p.Ile135Val). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with PTEN hamartoma tumor syndrome and Bannayan-Riley-Ruvalcaba syndrome (PMID: 10400993, 17392703, 23335809). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 142287). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (Invitae) indicates that this missense variant is not expected to disrupt PTEN function with a negative predictive value of 95%. RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). This variant disrupts the p.Ile135 amino acid residue in PTEN. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 16894538). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jul 17, 2023 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports a deleterious effect on splicing; Although published functional studies demonstrate no impact on protein function for the p.I135V missense variant, a potential splice impact has not, to our knowledge, been interrogated (Mighell et al., 2018; Post et al., 2020; Chao et al., 2020); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 24609522, 28152038, 23161105, 16894538, 11849740, 11234884, 28188106, 23335809, 21194675, 25527629, 32366478, 32378608, 10400993, 30787465, 34355460, 32350270, 19457929, 24475377, 29706350, 17392703) - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2014 | The p.I135V pathogenic mutation (also known as c.403A>G), located in coding exon 5 of the PTEN gene, results from an A to G substitution at nucleotide position 403. The isoleucine at codon 135 is replaced by valine, an amino acid with highly similar properties.<span style="background-color: initial;">This alteration has been reported in a case of familial Bannayan-Riley-Ruvalcaba syndrome (BRRS) (Marsh DJ et al. Hum. Mol. Genet. 1999 Aug;8(8):1461-72).<span style="background-color: initial;">This alteration is in the phosphatase domain and approximately 38% of PTEN mutations are in the phosphatase core motif (Eng C et al. Hum Mutat. 2003 Sep;22(3):183-98).<span style="background-color: initial;">Several other mutation have been reported at this amnio acid position in both patients with BRRS and Cowden syndrome (CS) (Tan MH et al.Am J Hum Genet. 2011 Jan 7;88(1):42-56; Boccone L et al. Am. J. Med. Genet. A 2006 Sep;140(18):1965-9).<span style="background-color: initial;">This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6,503 samples (13,006 alleles) with coverage at this position. B<span style="background-color: initial;">ased on the available evidence, p.I135V is classified as a pathogenic mutation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at