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LYFE SCIENCES
Project: HERA
NM_024675.3:c.7G>T
p.Glu3Ter  ·  PALB2
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Classification rationale
1

The PALB2 c.7G>T (p.Glu3Ter, p.E3*) variant has not been observed in somatic cancers in COSMIC and has been reported in ClinVar as pathogenic, including review by the ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer expert panel.

clinvar ↗
2

This variant is absent from gnomAD v2.1 and gnomAD v4.1, placing it below the PALB2 PM2_Supporting population threshold of 0.000333%.

gnomad_v2 ↗ gnomad_v4 ↗ cspec ↗
3

This variant introduces a premature stop codon at amino acid 3, and the active PALB2 expert specification supports loss of function as an established disease mechanism, consistent with application of PVS1 and the PALB2 truncation-based PM5 rule.

cspec ↗
4

SpliceAI predicts a limited splice effect with a maximum delta score of 0.15, which is below the PALB2 PP3 threshold of 0.2 and above the BP4 threshold of 0.1, so computational splice evidence is indeterminate; a BayesDel score of 0.63 is available but is not the governing PP3/BP4 rule in this gene-specific framework.

spliceai ↗ cspec ↗
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 has been reported in ClinVar as Pathogenic (8 clinical laboratories) and as Pathogenic by ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 241571)
ClinVar ↗
Functional evidence
03
Functional
OncoKB: 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 ↗
In silico evidence
04
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.15). BayesDel score = 0.63.
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.
ResidueE3
Hotspots ↗