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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 the most frequently mutated gene in human cancers, and inherited variants cause Li-Fraumeni syndrome with markedly elevated early-onset cancer risk. The VUS classification reflects strong functional evidence that p.(Gly266Val) abolishes p53 transactivation, tempered by the absence of clinical observations (de novo status, segregation, or phenotype) needed to confirm pathogenicity. Definitive interpretation will require additional clinical or functional evidence.
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.797G>T
GRCh38
chr17:7673823 C>A
GRCh37
chr17:7577141 C>A
BasisUncertain Significance (VUS): 5 total points under the TP53 VCEP Bayesian framework — PS3 Strong (+4) and PM2 Supporting (+1) — within the VUS range of -1 to 5.▾
Uncertain Significance (VUS): 5 total points under the TP53 VCEP Bayesian framework — PS3 Strong (+4) and PM2 Supporting (+1) — within the VUS range of -1 to 5.
Classification rationale
PS3PM2VUS
TP53 c.797G>Tmissense · exon 8
PS3 (Strong): p.(Gly266Val) is Non-functional on Kato et al. transactivation data with concordant loss of function across other eligible systematic assays. PM2 (Supporting): absent from gnomAD v4.1 and gnomAD-Canada, with gnomAD v2.1 allele frequency 0 (0/248,882 alleles). Classification: VUS — 5 points from PS3 Strong (+4) and PM2 Supporting (+1) fall within the VCEP's Uncertain Significance range (-1 to 5).
PS3 + PM2→VUS
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 · 16 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
✓
PS3strongPathogenic
Met (Strong): p.(Gly266Val) is Non-functional on Kato et al. transactivation data, with concordant loss of function across the other eligible systematic assays.
VCEP Functional-worksheet.xlsx (Supplementary Table S3) exact match row for G266V: Kato = Non-functional, other assay columns = LOF/LOF/LOF, worksheet-assigned code = PS3.TP53 VCEP PS3 rule (cspec v2.4): 'Non-functional on Kato et al. data AND loss of function (LOF) by the majority of other eligible assays' = PS3 Strong.TP53 VCEP eligible functional assays per Flowchart-for-application-of-functional-rule-codes.pdf: Kato (PMID:12826609), Funk (PMID:39774325), Giacomelli (PMID:30224644), Kotler (PMID:29979965), Kawaguchi (PMID:16007150).
Met (Supporting): absent from gnomAD v4.1 and gnomAD-Canada, with gnomAD v2.1 allele frequency 0 (0/248,882 alleles) below the 0.00003 threshold.
The governing ClinGen TP53 VCEP specification, version 2.4, requires PM2_supporting for AF <0.00003 in gnomAD or another large sequenced population; if multiple alleles occur in an ancestry group, that group must have AF <0.00004, and founder-effect groups are ignored.gnomAD v2.1 reports 0 variant alleles among 248,882 tested alleles, total AF 0, and 0 homozygotes; every listed ancestry group has 0 observed variant alleles.The variant is absent from gnomAD v4.1 and gnomAD-Canada v1.0.
This variant is present in gnomAD v2.1 (AF= 0; MAF= 0.00000%, 0/248882 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/16110 alleles, homozygotes = 0).
🇨🇦 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 / 248,882
0 hom
Not observed in any ancestry group.
+ 8 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Pathogenic (1 clinical laboratory). (ClinVarID = 233303)
This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52666760, n = 110 times).
Hotspots
This variant lies in a statistically significant hotspot.
Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 2 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.
29979965 ↗A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.
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 · 2 PMIDs not cited in assessment
16143127 ↗Gene-expression profiling predicts recurrence in Dukes' C colorectal cancer.ONCOKB
27328919 ↗TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and GeONCOKB