PS3 (strong): p.Lys132Met is non-functional in the Kato et al. yeast transactivation assay and shows loss of function by the majority of other eligible functional assays (Giacomelli, Kotler, Kawaguchi), meeting the TP53 VCEP PS3 criteria at strong strength.1 PM2_Supporting: The variant is absent from all gnomAD population databases (v2.1, v4.1, Canada), with an allele frequency of 0, satisfying the VCEP PM2_Supporting threshold of <0.00003.2 PP3_Moderate: Per the VCEP PP3-BP4-codes spreadsheet, c.395A>T is pre-assigned PP3_moderate. The variant has aGVGD Class C65, BayesDel score 0.18419 (≥0.16), REVEL 0.924, and SpliceAI max delta 0.00.3 Tavtigian point sum: PS3 (+4) + PM2_Supporting (+1) + PP3_Moderate (+2) = 7 points. Per TP53 VCEP v2.4 point-based rules, 6-9 points = Likely Pathogenic.4
Final classification
Likely Pathogenic
PS3PM2PP3
TP53
c.395A>T
p.Lys132Met
This variant
PS3 (strong): p.Lys132Met is non-functional in the Kato et al. yeast transactivation assay and shows loss of function by the majority of other eligible functional assays (Giacomelli, Kotler, Kawaguchi), meeting the TP53 VCEP PS3 criteria at strong strength.
ClinGen TP53 Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for TP53 Version 2.4 v2.4 point-based framework: PS3 strong (+4) + PM2 supporting (+1) + PP3 moderate (+2) = 7 points, which maps to Likely Pathogenic.
Classification rationale
PS3PM2PP3
Likely Pathogenic
TP53 c.395A>T
PS3 + PM2 + PP3
→
Likely Pathogenic
1
vcep_functional_worksheetPMID:12826609 ↗PMID:30224644 ↗PMID:29979965 ↗
3
vcep_pp3_bp4_codesbayesdelrevelspliceai ↗
4
final_classification_framework
Gene diagram
· NM_000546.6 · variants mapped to exon structure
TP53
NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 12 assessed
MetEvidence satisfies this criterion.
Not metEvaluated against available evidence; threshold not reached.
Not assessedApplies in principle, but no evidence was found to evaluate it.
N/ADoesn't apply to this variant type.
Applied · 3
Strength
Supporting
Moderate
Strong
Very strong
PS3
strong
Pathogenic
Per the TP53 VCEP Functional Worksheet (Supplementary Table S3), p.Lys132Met (K132M) is non-functional in the Kato et al. yeast-based transactivation assay and demonstrates loss of function (LOF) by the majority of other eligible functional assays (Giacomelli LOF, Kotler LOF, Kawaguchi LOF). This satisfies the VCEP PS3 rule: non-functional on Kato et al. data AND LOF by the majority of other eligible assays → PS3 at strong strength.
VCEP Functional Worksheet: K132M = Non-functional (Kato)LOF (Giacomelli)LOF (Kotler)
PM2
supporting
Pathogenic
The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency = 0). This satisfies the TP53 VCEP PM2_Supporting requirement: allele frequency <0.00003 (0.003%).
gnomAD v2.1: absent (AC=0AF=0)gnomAD v4.1: absent (AC=0
PP3
moderate
Pathogenic
Per the TP53 VCEP PP3-BP4-codes spreadsheet (Supplementary Table S2), c.395A>T (p.Lys132Met) is pre-assigned PP3_moderate. The variant meets VCEP PP3 moderate criteria: aGVGD Class C65 and BayesDel score 0.18419 ≥0.16, with SpliceAI max delta 0.00 (no predicted splicing impact). REVEL score 0.924 further supports a deleterious computational prediction.
VCEP PP3-BP4-codes: c.395A>T pre-assigned PP3_moderateaGVGD Class C65 (pathogenic class)BayesDel score 0.18419 ≥ 0.16 threshold
Assessed · not applied
· 12 not met · 0 not assessed
Pathogenic
PS2
No de novo observation data are available for this variant in the case materials.
PS4
No proband-level phenotype data with Li-Fraumeni syndrome cancer point scoring are available.
PM1
Codon 132 is not among the VCEP-specified hotspot codons (175, 245, 248, 249, 273, 282).
PM5
Multiple missense variants at codon 132 are recorded in the VCEP Functional Worksheet (K132E, K132N, K132Q, K132R, K132T all assigned PS3), but none have a confirmed VCEP-classified pathogenic or likely pathogenic determination.
PP1
No cosegregation data are available for this variant.
PP4
No variant allele fraction (VAF) data from patient samples are available.
Benign
BA1
The variant is absent from gnomAD v2.1 and v4.1.
BS1
The variant is absent from gnomAD v2.1 and v4.1.
BS2
No data are available on cancer-free females aged ≥60 carrying this variant.
BS3
K132M is non-functional on Kato et al.
BS4
No segregation data are available showing lack of segregation in affected family members with LFS-associated cancers.
BP4
The variant is classified as aGVGD Class C65 (pathogenic) with BayesDel score 0.18419.
N/A · 11
PVS1 · PS1 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency · supports pathogenic
gnomAD v4.1
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
ClinVar
This variant has been reported in ClinVar as Pathogenic (1 clinical laboratory) and as Uncertain significance (1 clinical laboratory). (ClinVarID = 376629)
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.924. BayesDel score = 0.295714.
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.
COSMIC
Cancer hotspots
Somatic evidence
Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52701687, n = 25 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
3papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 3 further PMIDs triaged but not cited — see Sources & references.
Rule & framework references · cited for criterion definitions, not variant evidence
12826609 ↗
Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.
29979965 ↗
A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.
30224644 ↗
Mutational processes shape the landscape of TP53 mutations in human cancer.
Sources & reference links
9Sources
Triaged references · 3 PMIDs not cited in assessment
27328919 ↗
TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data.
ONCOKB
23619274 ↗
American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders.
CLINVAR