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
BasisLikely 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
PVS1PM2Likely Pathogenic
TP53 c.266_267delframeshift · 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
TP53NM_000546.6
Fetching transcript structure from UCSC…
Exons
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Transcript span
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Strand
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Variants mapped
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Source
UCSC ncbiRefSeqCurated
All variants in TP53—click a row to locate it on the plot · use the link column to open its page
Variant ↕
Protein
Location
Classification
Link
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
✓
PVS1very strongPathogenic
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.
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.
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.
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