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NM_000546.6:c.997_1006del
p.Arg333SerfsTer9 · TP53
0%
complete
Final classification
Likely Pathogenic
PVS1PM2
TP53
c.997_1006del
p.Arg333SerfsTer9
frameshift · exon 10

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 truncating TP53 variant is consistent with loss of the p53 tumor-suppressor function that underlies the inherited cancer susceptibility of Li-Fraumeni syndrome.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.997_1006del
GRCh38
chr17:7670702 TCACGCCCACG>T
GRCh37
chr17:7574020 TCACGCCCACG>T
Likely Pathogenic: PVS1 very strong (+8) plus PM2 supporting (+1) total 9 points under the ClinGen TP53 Expert Panel Version 2.4 framework.
Classification rationale
PVS1PM2 Likely Pathogenic
TP53 c.997_1006del frameshift · exon 10

PVS1 very strong: the exon 10 frameshift creates a premature termination codon at p.341, upstream of p.Lys351 and outside the exon 10 NMD-escape region. PM2 supporting: the variant is absent from gnomAD v4.1 and v2.1, with an observed allele frequency of 0.

PVS1 + PM2 → 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_000546.6 · 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: the exon 10 frameshift creates a PTC at p.341, upstream of p.Lys351 and outside the exon 10 NMD-escape region.
The normalized consequence is NM_000546.6:c.997_1006del, a frameshift producing NP_000537.3:p.(Arg333SerfsTer9), with predicted protein position_last_predicted 341 and original terminal residue 394.Variant Validator places the deletion entirely in exon 10 of the biologically relevant NM_000546.6 transcript.The TP53 VCEP PVS1 flowchart assigns PVS1 to a frameshift-induced PTC upstream of p.Lys351 when the PTC is not in exon 11 or the 3'-most 50 nucleotides of exon 10; this variant meets that branch.
PM2 supporting Pathogenic
Met at supporting strength: the variant is absent from gnomAD v4.1 and v2.1, with observed frequency 0, below the TP53 PM2 threshold of <0.00003.
The TP53 VCEP Version 2.4 PM2 rule is supporting only and requires allele frequency <0.00003 in gnomAD; if multiple alleles are present in an ancestry group, that group must have frequency <0.00004.The queried frameshift variant NM_000546.6:c.997_1006del is reported absent from gnomAD v4.1 and gnomAD v2.1, corresponding to observed allele count 0 and allele frequency 0 in the reported datasets.
Assessed · not applied · 2 not met · 6 not assessed
Pathogenic
PS2 Not assessed: no proband cancer, parental testing, or confirmed parentage data are available to calculate the TP53 VCEP PS2 point total.
PS4 Not assessed: no proband phenotype or PS4 point total is available to compare with the VCEP thresholds of 1-1.5, 2-3.5, 4-7.5, or >=8 points.
PP1 Not assessed: no affected variant-positive relatives, obligate carriers, family structure, or documented meioses are available for PP1 assignment.
PP4 Not assessed: VAF and multigene-panel context are unavailable for comparison with the VCEP PP4 ranges of 5-25% or 5-35%.
Benign
BA1 Not met: the variant is absent from gnomAD v4.1 and v2.1, rather than reaching the TP53 BA1 threshold of FAF >=0.001.
BS1 Not met: the variant is absent from gnomAD v4.1 and v2.1, rather than having TP53 BS1 FAF >=0.0003 and <0.001.
BS2 Not assessed: no qualifying healthy female carrier count, age, cancer status, single-source provenance, or VAF data is available for the TP53 BS2 thresholds.
BS4 Not assessed: no affected relatives with relevant LFS-associated cancers and documented absence of the variant are available to establish non-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 is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI returned NO scores for this variant, so no SpliceAI-based splice prediction is available. This is missing data, NOT evidence of absent splice impact: it must not be used to support BP4 or to argue against PP3/PVS1. Pangolin scores may be present but are not calibrated for PP3/BP4 here.
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 not previously been reported in somatic cancers (COSMIC).
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 · 5 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