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NM_000546.6:c.574C>T
p.Gln192Ter · TP53
0%
complete
Final classification
Likely Pathogenic
PVS1PM2
TP53
c.574C>T
p.Gln192Ter
nonsense · exon 6

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 relevant to Li-Fraumeni syndrome, an autosomal-dominant cancer-predisposition condition caused by loss of p53 tumor-suppressor function.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.574C>T
GRCh38
chr17:7674957 G>A
GRCh37
chr17:7578275 G>A
Likely Pathogenic: PVS1 (very strong) plus PM2 (supporting) total 9 points under the ClinGen TP53 Expert Panel's Version 2.4 framework.
Classification rationale
PVS1PM2 Likely Pathogenic
TP53 c.574C>T nonsense · exon 6

PVS1 very strong: TP53 p.Gln192Ter creates a premature stop upstream of p.Lys351, meeting the VCEP nonsense-mediated-decay rule. PM2 supporting: the variant is absent from gnomAD v2.1 and v4.1, satisfying the TP53 VCEP rarity threshold.

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 · 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 · 2
Strength Supporting Moderate Strong Very strong
PVS1 very strong Pathogenic
Met, very strong: TP53 p.Gln192Ter creates a premature stop at codon 192, upstream of p.Lys351, meeting the VCEP NMD PVS1 rule.
The case normalization identifies NM_000546.6:c.574C>T as NP_000537.3:p.(Gln192Ter)/p.(Q192*), a nonsense variant in exon 6.The TP53 VCEP PVS1 flowchart states that nonsense variants upstream of p.Lys351 predicted to undergo NMD receive PVS1.The predicted protein ends at amino acid 192 instead of the normal 394 amino acids, consistent with a premature truncation well upstream of the TP53 C-terminal threshold.
PM2 supporting Pathogenic
Met at supporting: the variant is absent from gnomAD v2.1 and v4.1, corresponding to observed frequency 0 versus the TP53 VCEP PM2 threshold <0.00003.
The TP53 VCEP specifies PM2 at supporting strength for allele frequency <0.00003 (0.003%) and, when multiple alleles are present in an ancestry group, frequency <0.00004 (0.004%); founder-effect ancestry groups are excluded.The variant is reported as absent from gnomAD v2.1 and gnomAD v4.1, giving an observed frequency of 0 in both queried population datasets and satisfying the VCEP PM2 threshold.
Assessed · not applied · 2 not met · 8 not assessed
Pathogenic
PS2 Not assessed: no verified de novo observation, parental testing, or PS2 phenotype points are documented for this variant.
PS3 Not assessed: TP53's functional worksheet has no p.Gln192Ter entry, and no reviewed publication reports a validated functional assay for this exact nonsense variant.
PS4 Not assessed: the PS4 point total is unavailable, so the VCEP thresholds of 1-1.5, 2-3.5, 4-7.5, or >=8 points cannot be applied.
PP1 Not assessed: no affected-relative genotypes or verified cosegregating meioses are documented for this variant.
PP4 Not assessed: no qualifying TP53 VAF observation is documented, so the VCEP thresholds of 5-25% or 5-35% cannot be applied.
Benign
BA1 Not met: gnomAD v2.1 and v4.1 report absence, not a TP53 VCEP BA1 filtering allele frequency >=0.001 in one eligible ancestry group.
BS1 Not met: gnomAD v2.1 and v4.1 report absence, not a TP53 VCEP BS1 filtering allele frequency from 0.0003 to below 0.001.
BS2 Not assessed: no single-source count of at least two unrelated unaffected females aged 60 or older is available for the TP53 VCEP BS2 rule.
BS3 Not assessed: no exact p.Gln192Ter functional result was found in the governing TP53 worksheet or reviewed literature to demonstrate retained function.
BS4 Not assessed: no affected family members with verified non-segregation or genotype results are documented.
N/A · 16 PS1 · PM1 · PM3 · PM4 · PM5 · PM6 · PP2 · PP3 · PP5 · 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 (6 clinical laboratories) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 406579)
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. 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 Hotspot
COSMIC
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52660737, n = 267 times).
Hotspots
This variant lies 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 · 9 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
15604628 ↗ Genetic cancer risk assessment and counseling: recommendations of the national society of genetic counselors. CLINVAR
17392385 ↗ American Cancer Society guidelines for breast screening with MRI as an adjunct to mammography. CLINVAR
23619274 ↗ American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. CLINVAR