Starting
Initialising…
0%
PTEN
Final classification
Likely Pathogenic
PTEN c.525del · p.Tyr176IlefsTer7
PTEN

The PTEN c.525del (p.Tyr176IlefsTer7; p.Y176Ifs*7) variant has not been observed in COSMIC, has been reported in ClinVar as Pathogenic by one clinical laboratory, and is listed in OncoKB as Likely Oncogenic with a likely loss-of-function effect.

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.525del
Consequence
N/A
GRCh38
chr10:87952149 TG>T
GRCh37
chr10:89711906 TG>T
Basis Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule20 (1 Pathogenic.Very Strong + 1 Pathogenic.Supporting) with applied criteria: PVS1 very strong, PM2 supporting; maps to Likely Pathogenic.
Richards et.al., 2015 - Combining rules v3.2.0 criteria-combination framework: matched Rule20 (1 Pathogenic.Very Strong + 1 Pathogenic.Supporting) with applied criteria: PVS1 very strong, PM2 supporting; maps to Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
PTEN c.525del

The PTEN c.525del (p.Tyr176IlefsTer7; p.Y176Ifs*7) variant has not been observed in COSMIC, has been reported in ClinVar as Pathogenic by one clinical laboratory, and is listed in OncoKB as Likely Oncogenic with a likely loss-of-function effect.1 This variant is absent from gnomAD v2.1 and gnomAD v4.1, which is below the PTEN PM2 threshold of 0.00001 (0.001%) and supports PM2 at supporting strength.2 This deletion causes a frameshift with premature termination at codon 176 and falls 5' of the PTEN-specific p.D375 (c.1121) PVS1 threshold in transcript NM_000314.8, supporting PVS1 as a loss-of-function variant in a gene where loss of function is an established disease mechanism.3 SpliceAI predicts no significant splice effect for this variant, with a maximum delta score of 0.02, so no separate computational splice criterion is added.4

PVS1 + PM2 Likely Pathogenic
3 cspec ↗vcep_pvs1_decisiontree_ptenpvs1_gene_contextpvs1_variant_assessment
Gene diagram · NM_000314.8 · variants mapped to exon structure
PTEN NM_000314.8
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency · supports pathogenic
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory).
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02).
      Functional / OncoKB screenshot
      Functional Likely Oncogenic
      OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots