Genetic Information

Gene & Transcript Details

Gene
TP53
Transcript
NM_000546.6 MANE Select
Total Exons
—
Reference Sequence
NC_000017.10
Alternative Transcripts
IDStatusDetails
NM_000546.3 Alternative 2640 nt | 252–1433
NM_000546.5 RefSeq Select 2591 nt | 203–1384
NM_000546.6 MANE Select 2512 nt | 143–1324
NM_000546.4 Alternative 2586 nt | 198–1379
NM_000546.2 Alternative 2629 nt | 252–1433

Variant Details

HGVS Notation
NM_000546.6:c.796G>A
Protein Change
G266R
Location
Exon 8 (Exon 8 of )
8
5'Exon Structure3'
Functional Consequence
Loss of Function
Alternate Identifiers
—

Clinical & Population Data

Population Frequency

gnomAD
Global Frequency
0.0 in 100,000
Extremely Rare
ACMG Criteria Applied PM2
This variant is absent or extremely rare in population databases (PM2 criteria applies).

ClinVar

Open
Classification
Pathogenic
1 publications
Publications List
PMID: 27523101

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 266 of the TP53 protein (p.Gly266Arg). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with clinical features of Li-Fraumeni syndrome (PMID: 27523101; externalcommunication). ClinVar contains an entry for this variant (Variation ID: 458566). Advanced modeling performed at Invitae incorporating data from internal and/or published experimental studies (PMID: 12826609, 29979965, 30224644) indicates that this missense variant is expected to disrupt TP53 function with a positive predictive value of 97.5%. Experimental studies have shown that this missense change affects TP53 function (PMID: 12826609, 16827139, 20407015, 29979965, 30224644). For these reasons, this variant has been classified as Pathogenic.

Clinical Statement

"This variant has been reported in ClinVar as Pathogenic (6 clinical laboratories)."

COSMIC Somatic Evidence

Open
COSMIC ID
COSM10794
Recurrence
125 occurrences
PM1 Criteria
Applied
COSMIC Database Preview
COSMIC Preview
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Functional Impact & Domains

Functional Domain

Hotspot Status
Not a hotspot
Domain Summary
This variant is not located in a mutational hotspot or critical domain.
Related Variants in This Domain
No evidence of other pathogenic variants at this position in gene TP53.

Functional Studies & Therapeutic Relevance

Functional Summary

Error in OpenAI Consolidation. OncoKB: TP53G266RTP53G266RSomaticNCBI Gene:7157|Show additional gene information Variant OverviewTP53, a tumor suppressor in the DNA damage pathway, is the most frequently mutated gene in cancer.The TP53 G266R mutation is likely oncogenic.Hide mutation effect description The TP53 G266R mutation occurs in the protein's DNA binding domain. Expression of this mutation in TP53-null cell lines resulted in decreased TP53-induced transactivation, as evidenced by luciferase assays (PMID: 16827139). JAX-CKB: TP53 G266R lies within the DNA-binding domain of the Tp53 protein (PMID: 22713868). G266R is predicted to confer a loss of function to the Tp53 protein, as demonstrated by decreased transactivation activity in cell culture (PMID: 16827139).

Database Previews
OncoKB
OncoKB Preview
JAX-CKB
JAX-CKB Preview

Click on previews to view full database entries. External databases may require institutional access.

Computational Analysis

Pathogenicity Predictions

SpliceAI
Predictor Consensus
Mixed/VUS
PP3 Applied
No
REVEL Score
0.0
Threshold: ≥0.75 = PP3 applied

SpliceAI Scores

Window: ±500bp
Effect Type Score Position
- Acceptor Loss (AL) 0.04 -11 bp
- Donor Loss (DL) 0.0 67 bp
+ Acceptor Gain (AG) 0.0 -2 bp
+ Donor Gain (DG) 0.0 -17 bp
High impact (≥0.5) Medium impact (0.2-0.49) Low impact (<0.2)

VCEP Guidelines

Applied ACMG/AMP Criteria (VCEP Specific)

Filter Criteria:
PS3

PS3 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PM2

PM2 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

PP5

PP5 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)

BP4

BP4 (Unknown (Pre-LLM))

From pre-LLM assessment (LLM Failed)