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LYFE SCIENCES
Project: HERA
NM_000314.8:c.898dup
p.Ile300AsnfsTer3  ·  PTEN
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Classification rationale
1

The PTEN c.898dup (p.Ile300AsnfsTer3; p.I300Nfs*3) variant has not been observed in COSMIC and has not been reported in ClinVar; OncoKB classifies it as likely oncogenic with a likely loss-of-function effect.

clinvar ↗ oncokb ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, which is below the PTEN PM2_Supporting threshold of 0.001% and is consistent with rarity in the general population.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

This frameshift introduces a premature stop codon upstream of the PTEN-specific p.D375 (c.1121) threshold in NM_000314.8, which is consistent with predicted nonsense-mediated decay and supports PVS1 at very strong strength under the PTEN-specific decision tree.

cspec ↗
4

SpliceAI predicts no significant splice impact for this variant, with a maximum delta score of 0.01, indicating that the primary predicted effect is protein truncation rather than altered splicing.

spliceai ↗
Applied criteria
Met
Not met
Not assessed
N/A
Very strong
Strong
Moderate
Supporting
Pathogenic evidence
PVS
PVS1
PS
PS1
PS2
PS3
PS4
PM
PM1
PM2
PM3
PM4
PM5
PM6
PP
PP1
PP2
PP3
PP4
PP5
Benign evidence
BA
BA1
BS
BS1
BS2
BS3
BS4
BP
BP1
BP2
BP3
BP4
BP5
BP6
BP7
PVS1
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Rationale
Select a criterion to inspect its explanation.
Evidence used
  • —
Gaps remaining
  • —
Rule
—
Publications
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Research and evidence
ClinVar evidence
02
ClinVar
This variant is absent from ClinVar.
ClinVar ↗
Functional evidence
03
Functional
OncoKB: Likely Oncogenic
OncoKB classifies this variant as Likely Oncogenic; biological effect: Likely Loss-of-function.
OncoKB ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
COSMIC ↗
Cancer hotspots evidence
06
Cancer hotspots Not found
This variant does not lie in a statistically significant hotspot.
ResidueI300
Hotspots ↗