Analysis in progress
Initialising…
0%
complete
This report is still being assembled — sections appear as each stage finishes. It isn't final yet.
PTEN
Final classification
Likely Pathogenic
PTEN c.871_875del · p.Glu291TrpfsTer5
PTEN

NM_000314.8:c.871_875del is a 5 bp frameshift deletion in PTEN exon 8 that produces a premature termination codon at p.(Glu291TrpfsTer5), located 5' of the NMD boundary at p.D375, and is predicted to undergo nonsense-mediated decay, satisfying PVS1 at very strong strength per the PTEN VCEP v3.2.0 decision tree.

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.871_875del
Consequence
N/A
GRCh38
chr10:87960961 TAGAAA>T
GRCh37
chr10:89720718 TAGAAA>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.871_875del

NM_000314.8:c.871_875del is a 5 bp frameshift deletion in PTEN exon 8 that produces a premature termination codon at p.(Glu291TrpfsTer5), located 5' of the NMD boundary at p.D375, and is predicted to undergo nonsense-mediated decay, satisfying PVS1 at very strong strength per the PTEN VCEP v3.2.0 decision tree.1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada v1.0 (0 alleles across all populations), meeting the PTEN VCEP PM2_Supporting criterion (allele frequency <0.00001).2 The variant is absent from ClinVar and has not been reported in the published literature as a germline observation; no proband counts (PS4), de novo events (PS2/PM6), segregation data (PP1/BS4), or functional assay results (PS3/BS3) are available.3 OncoKB curates this variant as Likely Oncogenic with a Likely Loss-of-function biological effect, consistent with the predicted frameshift mechanism, though this somatic cancer annotation does not directly constitute germline ACMG/AMP evidence.4 SpliceAI predicts no cryptic splice impact (max delta score 0.03); the variant is not located in a PTEN catalytic motif (PM1 not met: residue 291 is outside motifs at 90-94, 123-130, 166-168).5 Of the 27 criteria assessed, two are met: PVS1 (very_strong) and PM2_Supporting. Under the PTEN VCEP v3.2.0 combination rules, PVS1 alone does not directly satisfy any single-rule Pathogenic or Likely Pathogenic inference without at least one additional Moderate or Strong criterion, or two Supporting criteria. The combination of 1 Very Strong + 1 Supporting does not match any VCEP rule. Per the adjudication framework, when the VCEP rules do not produce a classification, the generic ACMG/AMP 2015 framework (PMID:25741868) is applied as fallback: a null variant (frameshift) in a gene where loss of function is a well-established disease mechanism meets PVS1 at very strong strength, which alone is sufficient for a Pathogenic classification under generic rules.6

PVS1 + PM2 Likely Pathogenic
1 vcep_pvs1_decisiontree_ptencspec ↗pvs1_generic_framework ↗
6 cspec ↗generic_acmg_combination_rules
Gene diagram · NM_000314.8 · variants mapped to exon structure
PTEN NM_000314.8
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 13 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
NM_000314.8:c.871_875del is a 5 bp frameshift deletion in exon 8 that produces a premature termination codon at NP_000305.3:p.(Glu291TrpfsTer5), well 5' of the PTEN NMD cutoff at p.D375 (c.1121). Under the PTEN VCEP PVS1 decision tree, frameshift variants with a stop codon at or 5' to p.D375 in the biologically-relevant transcript NM_000314.8 that are predicted to undergo NMD are assigned PVS1 at very strong strength.
Frameshift deletion c.871_875del creates premature stop at codon 295Stop codon is 5' to p.D375 (c.1121) NMD boundaryPredicted to undergo nonsense-mediated decay
PM2 supporting Pathogenic
NM_000314.8:c.871_875del is absent from gnomAD v2.1, gnomAD v4.1, and gnomAD-Canada v1.0, meeting the PTEN VCEP PM2_Supporting threshold of allele frequency <0.00001 (0.001%).
Absent from gnomAD v2.1 (0 alleles)Absent from gnomAD v4.1 (0 alleles)Absent from gnomAD-Canada v1.0 (0 alleles)
Assessed · not applied
Pathogenic
PS2 No de novo observations of NM_000314.8:c.871_875del have been identified in ClinVar, the published literature, or any other source reviewed.
PS3 No well-established functional data are available for this frameshift variant.
PS4 No proband observations with PHTS phenotype and this variant have been identified.
PM1 The variant alters codon 291 (p.Glu291).
PM6 No assumed de novo observations of NM_000314.8:c.871_875del have been identified.
PP1 No co-segregation data are available for NM_000314.8:c.871_875del.
Benign
BA1 BA1 requires a gnomAD filtering allele frequency >0.00056 (0.056%) per the PTEN VCEP.
BS1 BS1 requires a gnomAD filtering allele frequency between 0.0000043 (0.00043%) and 0.00056 (0.056%) per the PTEN VCEP.
BS2 BS2 requires observation in a homozygous state in a healthy or PHTS-unaffected individual.
BS3 No functional studies demonstrating a benign effect have been reported for this variant.
BS4 No segregation data are available to assess lack of segregation in affected family members.
BP2 No observations of NM_000314.8:c.871_875del in trans with a pathogenic or likely pathogenic PTEN variant have been reported, nor are there three or more observations in cis or unknown phase with different pathogenic PTEN variants.
BP5 BP5 requires the variant to be found in a case with an alternate molecular basis for disease.
N/A · 12 PS1 · PM4 · PM5 · PP2 · PP3 · PP4 · PP5 · BP1 · BP3 · BP4 · BP6 · BP7
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.
🇨🇦 CA
This variant is absent from gnomAD-Canada.
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.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03).
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Likely Loss-of-function; curated oncogenicity label: Likely Oncogenic.
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
Triaged references · 2 PMIDs not cited in assessment
11237521 ↗ PTEN: life as a tumor suppressor. ONCOKB
17218262 ↗ Essential role for nuclear PTEN in maintaining chromosomal integrity. ONCOKB