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PTEN
Final classification
VUS
PTEN c.1211G>T · p.Ter404LeuextTer8
PTEN

NM_000314.8:c.1211G>T (p.Ter404LeuextTer8) is a stop-loss variant in PTEN that removes the native stop codon and extends the protein by 8 amino acids. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting under the PTEN VCEP v3.2.

Gene
PTEN
Transcript
NM_000314.8
HGVS · transcript:coding
NM_000314.8:c.1211G>T
Consequence
N/A
GRCh38
chr10:87965471 G>T
GRCh37
chr10:89725228 G>T
Basis ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2 v3.2 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
ClinGen PTEN Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTEN Version 3.2 v3.2 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2 VUS
PTEN c.1211G>T

NM_000314.8:c.1211G>T (p.Ter404LeuextTer8) is a stop-loss variant in PTEN that removes the native stop codon and extends the protein by 8 amino acids. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, meeting PM2_Supporting under the PTEN VCEP v3.2.1 The variant is absent from ClinVar. It has been reported in COSMIC (COSV64296267) in two somatic cancer samples, but no germline disease associations have been established.2 No functional data is available for this stop-loss variant. The PTEN VCEP PVS1 decision tree does not cover stop-loss variants (limited to nonsense, frameshift, splice site, and exon deletions). The Mighell et al. 2018 phosphatase saturation mutagenesis assay evaluates missense substitutions only and does not include stop-loss variants.3 No de novo observations, segregation data, or case-control studies are available. No publications were identified that mention this specific variant.4 With only PM2_Supporting met (absent from population databases) and all other criteria either not met or not applicable, this variant does not reach any classification threshold under the PTEN VCEP v3.2 combination rules and remains a Variant of Uncertain Significance (VUS). Notably, PM4 (protein extension from stop-loss) is flagged for human review — the VCEP PM4 rule explicitly covers stop-loss variants causing protein extension, and if applied at Moderate strength, the combination of PM4 + PM2_Supporting could support Likely Pathogenic under certain rule configurations.5

PM2 VUS
Gene diagram · NM_000314.8 · variants mapped to exon structure
PTEN NM_000314.8
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 12 assessed
Applied · 1
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000314.8:c.1211G>T 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%) in large sequenced populations.
Absent from gnomAD v2.1 (exomes).Absent from gnomAD v4.1 (exomes).Absent from gnomAD-Canada v1.0 (genomes).
Assessed · not applied
Pathogenic
PS1 No same amino acid change previously established as pathogenic has been identified at this position.
PS2 No de novo observations have been reported for this variant.
PS4 No proband counts or phenotype specificity scores are available.
PM1 The PTEN VCEP defines PM1 for residues in three catalytic motifs: WPD loop (residues 90-94), P-loop (residues 123-130), and TI-loop (residues 166-168) per NP_000305.3.
PM6 No de novo observations (assumed or confirmed) have been reported for this variant.
PP1 No co-segregation data is available.
Benign
BA1 The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency = 0).
BS1 The variant is absent from gnomAD (allele frequency = 0).
BS2 No homozygous observations of this variant have been reported in healthy or PHTS-unaffected individuals.
BS4 No segregation data is available to assess lack of segregation in affected family members.
BP2 No observations of this variant in trans with a pathogenic or likely pathogenic PTEN variant, nor in cis/unknown phase with different pathogenic PTEN variants, have been reported.
BP5 No cases have been identified where this variant was found in an individual with an alternate molecular basis for disease.
N/A · 15 PVS1 · PS3 · PM3 · PM4 · PM5 · PP2 · PP3 · PP4 · PP5 · BS3 · BP1 · BP3 · BP4 · BP6 · BP7
Research & evidence
Population frequency
v4.1
This variant is absent from gnomAD v4.1.
v2.1
This variant is absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
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 = 0.01). BayesDel score = -0.375297.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PTEN, a lipid and protein phosphatase, is one of the most frequently mutated genes in cancer.
OncoKB ↗
COSMIC screenshot
COSMIC
Somatic evidence
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV64296267, n = 2 times).
Hotspots
This variant does not lie in a statistically significant cancer hotspot.
COSMIC ↗
Sources & reference links
8Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC