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LYFE SCIENCES
Project: HERA
NM_000314.8:c.70G>A
p.Asp24Asn  ·  PTEN
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Classification rationale
1

The PTEN c.70G>A (p.Asp24Asn) variant has been observed in somatic cancers in COSMIC (COSV64295411; 8 occurrences) and has been reported in ClinVar, where it is classified as pathogenic by three clinical laboratory submissions.

2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, supporting rarity in population databases.

3

Functional testing in the PTEN saturation mutagenesis phosphatase assay showed a high-confidence damaging result for D24N (Cum_score -1.549791026), which supports a deleterious effect on PTEN function.

PMID:29706350 ↗
4

Computational evidence supports a deleterious effect for this missense variant based on a REVEL score of 0.753, while SpliceAI predicts no significant splice impact (maximum delta score 0.02).

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
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Gaps remaining
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Rule
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Publications
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Research and evidence
ClinVar evidence
02
ClinVar
This variant has been reported in ClinVar as Pathogenic (3 clinical laboratories).
ClinVar ↗
Functional evidence
03
Functional
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 = 0.02).
SpliceAI ↗
COSMIC evidence
05
COSMIC
This variant has previously been reported in somatic cancers (COSMIC; COSV64295411, n = 8 times).
Cancer hotspots evidence
06
Cancer hotspots
No cancer hotspot summary recorded.