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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 inherited loss-of-function mutations cause Li-Fraumeni syndrome, a hereditary condition marked by early-onset cancer. This frameshift is predicted to eliminate p53 function through nonsense-mediated decay, and it is absent from large population databases. The Likely Pathogenic classification therefore points to a probable loss-of-function mutation with clinical implications for cancer-risk surveillance.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.266_267del
GRCh38
chr17:7676101 AGG>A
GRCh37
chr17:7579419 AGG>A
Basis Score basis: PVS1 (Very Strong, +8) plus PM2 (Supporting, +1) totals 9 points, mapping to Rule 2 (6-9 points), which yields Likely Pathogenic.
Score basis: PVS1 (Very Strong, +8) plus PM2 (Supporting, +1) totals 9 points, mapping to Rule 2 (6-9 points), which yields Likely Pathogenic.
Classification rationale
PVS1PM2 Likely Pathogenic
TP53 c.266_267del frameshift · exon 4

PVS1 (Very Strong): 2-bp frameshift deletion introducing a premature stop codon upstream of p.Lys351, predicted to trigger nonsense-mediated decay. PM2 (Supporting): variant is absent from gnomAD v4.1, v2.1, and gnomAD-Canada v1.0 (allele frequency below 0.00003). Together these score 9 points under ClinGen TP53 VCEP Rule 2 (6-9 points), giving a final classification of Likely Pathogenic.

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 codon upstream of p.Lys351, predicting nonsense-mediated decay.
TP53 VCEP PVS1-Flowchart.pdf (Figure 1): 'Nonsense upstream of p.Lys351 / Frameshift induced premature termination codon (PTC) upstream of p.Lys351' with predicted NMD (PTC not in exon 11 or in the 3'-most 50nt of exon 10) is assigned PVS1 (Very Strong).Mutalyzer/VariantValidator normalization: NM_000546.6:c.266_267del is a 2-bp deletion in exon 4 (CDS c.1-1182), predicted protein NP_000537.3:p.(Pro89LeufsTer59), position_first=88 (i.e. change begins at residue 89), predicted termination at residue ~148 of the 393-residue wild-type protein — well upstream of p.Lys351.cspec TP53 VCEP 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.'
PM2 supporting Pathogenic
Met (Supporting): variant is absent from gnomAD v4.1, v2.1, and gnomAD-Canada v1.0, consistent with an allele frequency below 0.00003.
The TP53 VCEP Version 2.4 requires PM2 at supporting strength for allele frequency <0.00003 in gnomAD or another large sequenced population; if multiple alleles occur in an ancestry group, that group frequency must be <0.00004, excluding founder-effect groups.The exact variant NM_000546.6:c.266_267del was reported as absent from gnomAD v4.1, gnomAD v2.1, and gnomAD-Canada v1.0.The TP53 VCEP framework notes that population data for indels may be poorly called by next-generation sequencing, so the absence result is interpreted with moderate rather than high confidence.
Assessed · not applied · 2 not met · 6 not assessed
Pathogenic
PS2 Not assessed: no proband phenotype, parental testing, or family-history information was available to evaluate de novo occurrence.
PS4 Not assessed: no phenotype, cancer-type, case-count, or control data was available to score population enrichment.
PP1 Not assessed: no relatives, carrier status, phase, or meiosis information was available to evaluate cosegregation.
PP4 Not assessed: no variant allele fraction (VAF 5-35%) or tumor observations were available for this variant.
Benign
BA1 Not met: variant is absent from population databases, so no allele frequency reaches the >=0.001 benign threshold.
BS1 Not met: variant is absent from population databases, so no allele frequency falls in the 0.0003-0.001 BS1 range.
BS2 Not assessed: no healthy-adult carrier or homozygote observations were available for this variant.
BS4 Not assessed: no family segregation data was available; absence of data is not evidence against segregation.
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