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TP53
Final classification
VUS
PS3PM2
TP53
c.797G>T
p.Gly266Val
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 is the most frequently mutated gene in human cancers, and inherited variants cause Li-Fraumeni syndrome with markedly elevated early-onset cancer risk. The VUS classification reflects strong functional evidence that p.(Gly266Val) abolishes p53 transactivation, tempered by the absence of clinical observations (de novo status, segregation, or phenotype) needed to confirm pathogenicity. Definitive interpretation will require additional clinical or functional evidence.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.797G>T
GRCh38
chr17:7673823 C>A
GRCh37
chr17:7577141 C>A
Basis Uncertain Significance (VUS): 5 total points under the TP53 VCEP Bayesian framework — PS3 Strong (+4) and PM2 Supporting (+1) — within the VUS range of -1 to 5.
Uncertain Significance (VUS): 5 total points under the TP53 VCEP Bayesian framework — PS3 Strong (+4) and PM2 Supporting (+1) — within the VUS range of -1 to 5.
Classification rationale
PS3PM2 VUS
TP53 c.797G>T missense · exon 8

PS3 (Strong): p.(Gly266Val) is Non-functional on Kato et al. transactivation data with concordant loss of function across other eligible systematic assays. PM2 (Supporting): absent from gnomAD v4.1 and gnomAD-Canada, with gnomAD v2.1 allele frequency 0 (0/248,882 alleles). Classification: VUS — 5 points from PS3 Strong (+4) and PM2 Supporting (+1) fall within the VCEP's Uncertain Significance range (-1 to 5).

PS3 + PM2 VUS
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 16 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 · 2
Strength Supporting Moderate Strong Very strong
PS3 strong Pathogenic
Met (Strong): p.(Gly266Val) is Non-functional on Kato et al. transactivation data, with concordant loss of function across the other eligible systematic assays.
VCEP Functional-worksheet.xlsx (Supplementary Table S3) exact match row for G266V: Kato = Non-functional, other assay columns = LOF/LOF/LOF, worksheet-assigned code = PS3.TP53 VCEP PS3 rule (cspec v2.4): 'Non-functional on Kato et al. data AND loss of function (LOF) by the majority of other eligible assays' = PS3 Strong.TP53 VCEP eligible functional assays per Flowchart-for-application-of-functional-rule-codes.pdf: Kato (PMID:12826609), Funk (PMID:39774325), Giacomelli (PMID:30224644), Kotler (PMID:29979965), Kawaguchi (PMID:16007150).
PM2 supporting Pathogenic
Met (Supporting): absent from gnomAD v4.1 and gnomAD-Canada, with gnomAD v2.1 allele frequency 0 (0/248,882 alleles) below the 0.00003 threshold.
The governing ClinGen TP53 VCEP specification, version 2.4, requires PM2_supporting for AF <0.00003 in gnomAD or another large sequenced population; if multiple alleles occur in an ancestry group, that group must have AF <0.00004, and founder-effect groups are ignored.gnomAD v2.1 reports 0 variant alleles among 248,882 tested alleles, total AF 0, and 0 homozygotes; every listed ancestry group has 0 observed variant alleles.The variant is absent from gnomAD v4.1 and gnomAD-Canada v1.0.
Assessed · not applied · 4 not met · 12 not assessed
Pathogenic
PS1 Not assessed: no alternate nucleotide change producing the same p.(Gly266Val) with an established VCEP pathogenic classification was available.
PS2 Not assessed: no de novo observation, parental testing results, or maternity/paternity confirmation was available.
PS4 Not assessed: no eligible germline proband observations with Li-Fraumeni-associated cancer were available for PS4 point assignment.
PM1 Not assessed: codon 266 is not among the six VCEP hotspot codons (175, 245, 248, 249, 273, 282) required for PM1.
PM5 Not assessed: no different missense variant at codon 266 with an established pathogenic classification was available as a PM5 comparator.
PP1 Not assessed: no family pedigree, carrier results, or countable meioses were available.
PP3 Not assessed: BayesDel score 0.599 exceeds the 0.16 floor, but the required paired aGVGD class was unavailable.
PP4 Not assessed: no eligible observations with variant allele fraction (VAF) data were available.
PP5 Not assessed: ClinVar holds no expert-panel pathogenic assertion for this variant, only a single-laboratory submission.
Benign
BA1 Not met: allele frequency is 0 (0/248,882 gnomAD v2.1 alleles), below the FAF >=0.001 stand-alone benign threshold.
BS1 Not met: no variant alleles observed in gnomAD, below the FAF >=0.0003 to <0.001 BS1 threshold.
BS2 Not assessed: no carrier-level age, sex, cancer status, or variant allele fraction data were available.
BS3 Not met: functional data show loss of function (Kato Non-functional), the opposite of the BS3 'functional on Kato' requirement.
BS4 Not assessed: no affected relatives tested negative for the variant, so no non-segregation evidence was available.
BP4 Not met: BayesDel score 0.599 is far above the <=-0.008 (Moderate) and <0.16 (Supporting) benign thresholds.
BP6 Not assessed: ClinVar holds no expert-panel benign or likely benign assertion for this variant.
N/A · 10 PVS1 · PM3 · PM4 · PM6 · PP2 · BP1 · BP2 · BP3 · BP5 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/248882 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/16110 alleles, homozygotes = 0).
🇨🇦 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 / 248,882
0 hom
Not observed in any ancestry group.
+ 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Pathogenic (1 clinical laboratory). (ClinVarID = 233303)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.17). REVEL score = 0.974. BayesDel score = 0.599005.
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; COSV52666760, n = 110 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. 2 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
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 2 PMIDs not cited in assessment
16143127 ↗ Gene-expression profiling predicts recurrence in Dukes' C colorectal cancer. ONCOKB
27328919 ↗ TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Ge ONCOKB