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NM_000546.5:c.202G>T
p.Glu68Ter · TP53
0%
complete
Final classification
Likely Pathogenic
PVS1
TP53
c.202G>T
p.Glu68Ter
nonsense · exon 4

TP53 encodes the p53 tumor suppressor protein, a transcription factor that responds to cellular stress such as DNA damage by switching on genes that trigger cell cycle arrest, DNA repair, senescence, or programmed cell death. In healthy cells, p53 is kept at low levels by constant degradation, but stress signals stabilize and activate it to protect against damaged cells surviving and dividing. Inherited mutations in TP53 cause Li-Fraumeni syndrome, a condition marked by a high risk of developing multiple cancers at a young age. TP53 is the most commonly mutated gene across human cancers, and loss of its normal function promotes tumor growth, spread, drug resistance, and genomic instability.

This variant

This TP53 truncating variant is relevant to Li-Fraumeni syndrome because inherited TP53 loss of function impairs the p53 tumor-suppressor response to cellular stress and increases risk for multiple early-onset cancers.

Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.202G>T
GRCh38
chr17:7676167 C>A
GRCh37
chr17:7579485 C>A
Likely Pathogenic: TP53 VCEP PVS1 at very strong strength for the exon 4 nonsense variant yields 8 points, which falls within the VCEP's Likely Pathogenic range.
Classification rationale
PVS1 Likely Pathogenic
TP53 c.202G>T nonsense · exon 4

PVS1 very strong: the exon 4 nonsense variant truncates TP53 at codon 68, upstream of p.Lys351, with predicted nonsense-mediated decay.

PVS1 Likely Pathogenic
LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
Fetching transcript structure from UCSC…
Applied criteria · 1 applied · 10 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 · 1
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
Met: TP53 VCEP full-strength PVS1 applies because the exon 4 stop at codon 68 is upstream of p.Lys351 and predicted to undergo NMD.
The TP53 VCEP Version 2.4 specifies that PVS1 applies to nonsense variants predicted to undergo NMD when the premature stop is upstream of p.Lys351.The TP53 PVS1 flowchart states that nonsense variants upstream of p.Lys351, with a premature termination codon not in exon 11 or the 3'-most 50 nucleotides of exon 10, are predicted to undergo NMD and receive PVS1.Variant normalization and validation identify NM_000546.5:c.202G>T as NP_000537.3:p.(Glu68Ter)/p.(E68*), located in exon 4; the selected transcript has a newer NM_000546.6 version, which is the transcript named by the VCEP flowchart and preserves the same consequence context.
Assessed · not applied · 0 not met · 10 not assessed
Pathogenic
PS2 Not assessed: no documented de novo observation, parental testing, or eligible proband cancer-point total is available to assign the TP53 PS2 threshold.
PS4 Not assessed: no documented proband phenotype or PS4 points, and PM2_Supporting is not established.
PM2 Not assessed: gnomAD frequency and ancestry-specific allele counts needed for the TP53 PM2 thresholds of <0.00003 and <0.00004 are unavailable.
PP1 Not assessed: no affected relatives with matching genotypes or countable informative meioses are documented for comparison with the 3-meiosis PP1 Supporting threshold.
PP4 Not assessed: no variant allele fraction observations are reported for comparison with the VCEP's 5-25% or 5-35% thresholds.
Benign
BA1 Not assessed: no qualifying ancestry-specific filtering allele frequency is available to compare with the TP53 VCEP BA1 threshold of 0.001.
BS1 Not assessed: no qualifying ancestry-specific filtering allele frequency is available to compare with the TP53 VCEP BS1 range of 0.0003 to <0.001.
BS2 Not assessed: no single-source series of unrelated female carriers aged at least 60 years without cancer is documented for the TP53 BS2 rule.
BS4 Not assessed: no affected family members with LFS-associated cancer and documented variant testing are available to demonstrate lack of segregation.
BP2 Not assessed: no affected-proband observations, comparator TP53 variants, or phase data establish the VCEP's trans or three-observation BP2 rule.
N/A · 17 PS1 · PS3 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · BS3 · BP1 · BP3 · BP4 · BP5 · BP6 · BP7
Research & evidence
Population frequency · supports pathogenic
v4.1
This variant is absent from gnomAD v4.1.
v2.1
This variant is absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant has been reported in ClinVar as Pathogenic (5 clinical laboratories) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 224551)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.18). BayesDel score = 0.66.
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; COSV52692559, n = 29 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 · 8 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
25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
26845104 ↗ Improving performance of multigene panels for genomic analysis of cancer predisposition. CLINVAR
30224644 ↗ Mutational processes shape the landscape of TP53 mutations in human cancer. CLINVAR