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TP53
Final classification
Likely Pathogenic
PS3PM2PP3
TP53
c.840A>C
p.Arg280Ser
missense · exon 8

TP53 encodes the p53 protein, a critical tumor suppressor that acts as a transcription factor to protect cells from damage. When activated by cellular stress such as DNA damage, p53 triggers responses including DNA repair, cell cycle arrest, and programmed cell death (apoptosis) to prevent the propagation of damaged cells. TP53 is the most frequently mutated gene in human cancers, and loss of its function contributes to tumor development, invasion, drug resistance, and genomic instability. Inherited mutations in TP53 cause Li-Fraumeni syndrome, a rare hereditary condition that greatly increases the risk of developing multiple types of cancer at a young age.

This variant

TP53 encodes the p53 tumor suppressor, and inherited loss-of-function mutations cause Li-Fraumeni syndrome with markedly elevated, early-onset cancer risk. This variant is classified Likely Pathogenic: it is non-functional in transactivation assays and absent from population databases, indicating impaired p53 tumor-suppressor activity consistent with TP53-associated cancer susceptibility.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.840A>C
GRCh38
chr17:7673780 T>G
GRCh37
chr17:7577098 T>G
Basis Likely Pathogenic: PS3 strong (+4) + PM2 supporting (+1) + PP3 moderate (+2) = 7 points under the ClinGen TP53 VCEP v2.4 point-based framework.
Likely Pathogenic: PS3 strong (+4) + PM2 supporting (+1) + PP3 moderate (+2) = 7 points under the ClinGen TP53 VCEP v2.4 point-based framework.
Classification rationale
PS3PM2PP3 Likely Pathogenic
TP53 c.840A>C missense · exon 8

PS3 (Strong): R280S is non-functional in the primary Kato transactivation assay and shows loss of function in the majority of other eligible assays, per the VCEP functional worksheet. PM2 (Supporting): the exact variant is absent from gnomAD v4.1, v2.1, and gnomAD-Canada, below the 0.003% threshold. PP3 (Moderate): the VCEP lookup assigns PP3_moderate for c.840A>C with aGVGD class C65 and BayesDel 0.471465. Combined: PS3 strong (+4) + PM2 supporting (+1) + PP3 moderate (+2) = 7 points maps to Likely Pathogenic under the TP53 VCEP v2.4 point-based framework.

PS3 + PM2 + PP3 Likely Pathogenic
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 14 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
Met (Strong): the VCEP functional worksheet assigns R280S non-functional on Kato data and loss of function in the majority of other eligible assays.
The TP53 VCEP Version 2.4 rule states that PS3_Strong requires a variant to be non-functional on Kato et al. data and to show loss of function by the majority of other eligible assays.The exact VCEP Functional-worksheet.xlsx row for R280S is: Kato category NA; Kato functional result Non-functional; other eligible assay results LOF, LOF, LOF; assigned code PS3.Kato et al. (PMID:12826609) used a systematic yeast-based p53 transactivation assay across 2,314 TP53 missense mutants and multiple sequence-specific promoter elements; the supplied extract does not name R280S, so it is used here for assay context and not as an independent allele-level quote.
PM2 supporting Pathogenic
Met (Supporting): the exact variant is absent from gnomAD v4.1, v2.1, and gnomAD-Canada, below the 0.003% PM2 threshold.
The TP53 VCEP v2.4 requires PM2 to be applied at Supporting strength when the allele frequency is <0.00003 (0.003%) in gnomAD or another large sequenced population; if multiple alleles occur in an ancestry group, that group frequency must be <0.00004 (0.004%). Founder-effect groups are ignored.The case bundle reports the exact variant NM_000546.6:c.840A>C (p.Arg280Ser) as absent from gnomAD v4.1, gnomAD v2.1, and gnomAD-Canada v1.0, supporting zero observed alleles and thus an allele frequency below the PM2 threshold in each queried dataset.
PP3 moderate Pathogenic
Met (Moderate): the VCEP lookup assigns PP3_moderate for c.840A>C with aGVGD C65 and BayesDel 0.471465; SpliceAI max delta 0.00.
TP53 VCEP v2.4 specifies PP3_Moderate for a missense variant with aGVGD Class C65 and BayesDel score at least 0.16.The TP53 VCEP Supplementary Table S2 exact entry for c.840A>C / p.Arg280Ser records Class C65, BayesDel 0.471465, and PP3_moderate.SpliceAI reports a maximum delta score of 0.00, below the VCEP threshold for predicted splice impact; therefore no separate splice-based PP3 is counted.
Assessed · not applied · 7 not met · 7 not assessed
Pathogenic
PVS1 Not met: missense substitution creates no premature stop codon or splice disruption, and SpliceAI max delta 0.00 predicts no splice impact.
PS1 Not met: no alternate-nucleotide p.Arg280Ser variant with a VCEP-qualified pathogenic assertion was found.
PS2 Not assessed: no proband phenotype, parental testing, or de novo observation was available.
PS4 Not assessed: no germline proband-level phenotype or PS4 point total was available; the two reported Arg280Ser tumors are somatic.
PM1 Not assessed: codon 280 is not in the VCEP-approved PM1 codon list (175, 245, 248, 249, 273, 282).
PM5 Not met: no different missense variant at Arg280 with a VCEP-qualified pathogenic classification was found.
PP1 Not assessed: no affected-family-member genotypes, pedigree, or meiosis count was available.
PP4 Not assessed: no observation with a reported 5-35% VAF, which the VCEP mosaic-variant rule requires, was available.
Benign
BA1 Not met: the variant is absent from gnomAD v4.1, v2.1, and gnomAD-Canada, so no FAF reaches the >=0.001 threshold.
BS1 Not met: the variant is absent from population databases, so no FAF falls in the BS1 interval (>=0.0003 to <0.001).
BS2 Not assessed: no carrier-level observations, ages, or cancer histories were available.
BS3 Not met: the variant's assays show non-functional/loss of function, the opposite of the functional results BS3 requires.
BS4 Not assessed: no pedigree or non-segregation observations in affected family members were available.
BP4 Not met: the VCEP assigns PP3_moderate for this exact variant, and BayesDel 0.471465 is outside the BP4 score ranges.
N/A · 11 PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency · supports pathogenic
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
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
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Likely pathogenic (1 clinical laboratory) and as Pathogenic (1 clinical laboratory). (ClinVarID = 634747)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.878. BayesDel score = 0.471465.
Functional / OncoKB screenshot
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.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52782181, n = 13 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. 4 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
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
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 4 PMIDs not cited in assessment
10761706 ↗ Mutations in zinc-binding domains of p53 as a prognostic marker of esophageal-ca ONCOKB
27328919 ↗ TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Ge ONCOKB
19042984 ↗ National Academy of Clinical Biochemistry laboratory medicine practice guidelines for use of tumor markers in testicular, prostate, colorectal, breast, and ovarian cancers. CLINVAR
23188549 ↗ NSGC practice guideline: risk assessment and genetic counseling for hereditary breast and ovarian cancer. CLINVAR