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TP53
Final classification
VUS
PS3PM2
TP53
c.1001G>T
p.Gly334Val
missense · exon 10

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 critical tumor suppressor, and inherited variants cause Li-Fraumeni syndrome, a hereditary condition of greatly elevated, early-onset cancer risk. This missense change at codon 334 shows partial loss of function in laboratory assays, yet evidence is still insufficient to confirm or exclude pathogenicity, so it remains a variant of uncertain significance pending further clinical and family data.

Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.1001G>T
GRCh38
chr17:7670708 C>A
GRCh37
chr17:7574026 C>A
Basis VUS: 3 total points (PS3 moderate +2, PM2 supporting +1) fall within the Rule3 range of -1 to 5, yielding uncertain significance.
VUS: 3 total points (PS3 moderate +2, PM2 supporting +1) fall within the Rule3 range of -1 to 5, yielding uncertain significance.
Classification rationale
PS3PM2 VUS
TP53 c.1001G>T missense · exon 10

PS3 (Moderate): p.Gly334Val is partially functional in Kato transactivation but shows loss of function in two other assays (Giacomelli growth suppression, Kawaguchi oligomerization). PM2 (Supporting): the variant is absent from gnomAD v4.1, gnomAD v2.1, and gnomAD-Canada. VUS: the TP53 VCEP Tavtigian framework totals 3 points (PS3 +2, PM2 +1), within the Rule3 range of -1 to 5, so the variant is classified as a variant of uncertain significance.

PS3 + PM2 VUS
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 2 applied · 14 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
PS3 moderate Pathogenic
Met (Moderate): p.Gly334Val is partially functional in Kato transactivation but shows loss of function in two other assays (Giacomelli, Kawaguchi).
Functional-worksheet.xlsx (Supplementary Table S3) row for G334V: Kato class = Partially functional; Funk class = NA; Giacomelli class = LOF; Kotler class = NA; Kawaguchi class = Monomer; Preliminary functional code = PS3_Moderate.TP53 VCEP cspec PS3 rule (v2.4): 'Partially functional on Kato et al. data AND loss of function (LOF) by the majority of other available assays' = PS3_Moderate.TP53 VCEP instructionsToUse for PS3 defines assay classification thresholds: Kato non-functional <=20% activity, partially-functional >20-75%, functional >75%; Giacomelli LOF = Etoposide Z-score <= -0.21; Kawaguchi abnormal = Monomer/dimer, normal = Tetramer.
PM2 supporting Pathogenic
Met (Supporting): the variant is absent from gnomAD v4.1, gnomAD v2.1, and gnomAD-Canada population databases.
The TP53 VCEP version 2.4 requires PM2 to be applied at supporting strength when allele frequency is <0.00003 in gnomAD or another large sequenced population; if multiple alleles occur in an ancestry group, that group's frequency must be <0.00004, and founder-effect groups are ignored.The variant NM_000546.6:c.1001G>T (p.Gly334Val) is absent from gnomAD v4.1, gnomAD v2.1, and gnomAD-Canada v1.0, providing population evidence compatible with PM2 supporting.
Assessed · not applied · 7 not met · 7 not assessed
Pathogenic
PS1 Not met: no other DNA change producing the same p.Gly334Val amino acid has been classified pathogenic or likely pathogenic.
PS2 Not assessed: no de novo observation or parental testing data was available for this variant.
PS4 Not assessed: no germline Li-Fraumeni cancer point totals from unrelated probands were available.
PM1 Not assessed: codon 334 is not on the TP53 VCEP PM1 codon list, and no verified hotspot occurrence count was available.
PM5 Not met: no other substitution at codon 334 carries a formal pathogenic or likely pathogenic TP53 VCEP classification.
PP1 Not assessed: no family segregation or meiosis count data was available.
PP3 Not met: Align-GVGD Class C15 falls below the C25-C65 range PP3 requires, despite BayesDel 0.56885.
PP4 Not assessed: no variant allele fraction or independent observation count was available to assess clonal hematopoiesis.
Benign
BA1 Not met: absent from gnomAD, so no allele frequency reaches the >=0.001 BA1 threshold.
BS1 Not met: absent from gnomAD, so no allele frequency reaches the >=0.0003 BS1 threshold.
BS2 Not assessed: no qualifying observations in unaffected women aged 60 or older, or in homozygotes, were available.
BS3 Not met: functional assays show loss of function, not the benign profile BS3 requires.
BS4 Not assessed: no family segregation data was available to test for non-segregation.
BP4 Not met: BayesDel 0.56885 is far above the <0.16 threshold BP4 requires.
N/A · 12 PVS1 · PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency
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 but submission details could not be extracted. (ClinVarID = 3764945)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.951. BayesDel score = 0.56885.
Functional / OncoKB screenshot
Functional Likely Oncogenic
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. TP53, a tumor suppressor in the DNA damage pathway, is the most frequently mutated gene in cancer.
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; COSV52759537, n = 27 times).
Hotspots
This variant lies in a statistically significant hotspot.
Literature · how each cited paper was used
2papers cited
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 5 further PMIDs triaged but not cited — see Sources & references.
Rule & framework references · cited for criterion definitions, not variant evidence
12826609 ↗ Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.
30224644 ↗ Mutational processes shape the landscape of TP53 mutations in human cancer.
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
25584008 ↗ Prevalence and functional consequence of TP53 mutations in pediatric adrenocorti ONCOKB
32675277 ↗ A Rare TP53 Mutation Predominant in Ashkenazi Jews Confers Risk of Multiple Canc ONCOKB
22918138 ↗ Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. CLINVAR
23619274 ↗ American College of Medical Genetics and Genomics technical standards and guidelines: microarray analysis for chromosome abnormalities in neoplastic disorders. CLINVAR
35101336 ↗ Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity): Joint recommendations of Clinical Genome Resource (ClinGen), Cancer Genomics Consortium (CGC), and Variant Interpretation for Cancer Consortium (VICC). CLINVAR