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TP53
Final classification
Likely Pathogenic
PVS1PM2
TP53
c.266_267del
p.Pro89LeufsTer59
frameshift · exon 4

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 a tumor suppressor whose loss of function causes Li-Fraumeni syndrome, a hereditary condition of markedly elevated, early-onset cancer risk. This frameshift is predicted to abolish p53 function through nonsense-mediated decay, matching the gene's established loss-of-function disease mechanism, and the likely pathogenic result supports clinical surveillance for variant carriers.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.266_267del
GRCh38
chr17:7676101 AGG>A
GRCh37
chr17:7579419 AGG>A
Basis Likely Pathogenic: 9 points (PVS1 very strong +8, PM2 supporting +1) under the TP53 VCEP v2.4 point framework, mapping to the >=6 to <=9 Likely Pathogenic range.
Likely Pathogenic: 9 points (PVS1 very strong +8, PM2 supporting +1) under the TP53 VCEP v2.4 point framework, mapping to the >=6 to <=9 Likely Pathogenic range.
Classification rationale
PVS1PM2 Likely Pathogenic
TP53 c.266_267del frameshift · exon 4

PVS1 (Very Strong): frameshift creates a premature stop at residue ~147, upstream of p.Lys351, predicted to trigger nonsense-mediated decay. PM2 (Supporting): variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, consistent with an allele frequency below the 0.00003 threshold. Synthesis: 9 points under the TP53 VCEP v2.4 point framework (PVS1 +8, PM2 +1) fall in the 6-9 range, giving Likely Pathogenic (Rule 2).

PVS1 + PM2 Likely Pathogenic
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 8 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
PVS1 very strong Pathogenic
Met (Very Strong): 2-bp frameshift deletion creates a premature stop at residue ~147, upstream of p.Lys351, predicted to trigger nonsense-mediated decay.
TP53 VCEP PVS1 flowchart (PVS1-Flowchart.pdf, Figure 1, transcript NM_000546.6): frameshift-induced PTC upstream of p.Lys351 predicted to undergo NMD = PVS1 (full/very strong).cspec v2.4 PVS1 rule text: 'PVS1 applies to variants predicted to result in nonsense-mediated decay (NMD) for nonsense variants upstream of p.Lys351 and for frameshift induced premature termination codon (PTC) upstream of p.Lys351.'Mutalyzer normalization (prefetch.json): protein prediction NP_000537.3:p.(Pro89LeufsTer59), predicted new stop at residue ~147 of a 393-aa wild-type protein, well upstream of p.Lys351 (codon 351), consistent with NMD-eligible PTC location.
PM2 supporting review Pathogenic
Met (Supporting): variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada, consistent with an allele frequency below the 0.00003 threshold.
The governing ClinGen TP53 VCEP specification, version 2.4, requires PM2 at Supporting strength for an allele frequency <0.00003; if multiple alleles are present in an ancestry group, the ancestry-specific frequency must be <0.00004, and founder-effect groups are ignored.gnomAD v2.1 reports the exact variant as absent.gnomAD v4.1 reports the exact variant as absent.
Assessed · not applied · 2 not met · 6 not assessed
Pathogenic
PS2 Not assessed: no proband phenotype or parental-testing data was available to establish a confirmed de novo occurrence.
PS4 Not assessed: no variant-specific germline proband phenotypes were available to assign Li-Fraumeni syndrome cancer points.
PP1 Not assessed: no affected relatives, variant-positive family members, or meiosis counts were available for cosegregation analysis.
PP4 Not assessed: no qualifying variant allele fraction observation was provided for this variant.
Benign
BA1 Not met: BA1 requires a gnomAD allele frequency of at least 0.001; the variant is absent from all queried gnomAD datasets.
BS1 Not met: BS1 requires a gnomAD allele frequency between 0.0003 and 0.001; the variant is absent from all queried gnomAD datasets.
BS2 Not assessed: no documented cancer-free TP53 carriers meeting the VCEP age thresholds were available.
BS4 Not assessed: no affected-family-member genotypes or documented non-segregation were available.
N/A · 18 PS1 · PS3 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · BS3 · BP1 · BP2 · BP3 · BP4 · 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 Pathogenic (1 clinical laboratory). (ClinVarID = 3328161)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.12).
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 Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV105874382, n = 1 times).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 6 PMIDs not cited in assessment
11753428 ↗ A novel mechanism of tumorigenesis involving pH-dependent destabilization of a mutant p53 tetramer. ONCOKB
11900253 ↗ Rescuing the function of mutant p53. ONCOKB
16007150 ↗ The relationship among p53 oligomer formation, structure and transcriptional activity using a comprehensive missense mutation library. ONCOKB
19336573 ↗ High incidence of protein-truncating TP53 mutations in BRCA1-related breast cancer. ONCOKB
21467160 ↗ Prognostic significance of truncating TP53 mutations in head and neck squamous cell carcinoma. ONCOKB
25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR