Other Resources

TP53 Sequences

Reference sequences used to annotate TP53 gene variations

Graphical view of the Genomic sequence (hg38) with exon-intron boundaries for the main p53 isoform.
Coding and protein sequence with residue numbers, amino-acids, highlighted CpG sites and exon-intron boundaries.
NCBI link to cDNA sequence corresponding to the NM_000546 isoform.

Sequences in other species

3D Sequence Structures

Variant Nomenclatures

The genomic reference sequence used for annotating TP53 variants is NC_000017.11 (hg38 build) from GenBank.

Variants are reported according to HGVS nomenclature recommendations.

We recommend to use Mutalyzer, to help you format your variant data according to HGVS guidelines and to convert positions between different genome build or isoforms.

Protocols and Tools

Protocols

To assess TP53 variant status it is recommended to perform gene sequencing of all exons, including the splice junctions and completed with MLPA to detect large deletion/duplications. Immuno-histochemical analysis is not a good method for assessing TP53 variant status, as it cannot distinguish between the various types of variants, does not detect truncating variants (false-negative results), and gives false-positive results (over-expressed WT protein).

Some Example of Sequencing Protocols:

Direct Sequencing by Sanger: TP53_SangerSequencing_NIH.pdf
TP53 sequencing by a next generation sequencing technology (NGS). The detailed list of primers can be downloaded here: NGS_TP53_Primers.txt
MLPA
Some caution regarding TP53 variants detected by multigene panel testing by NGS: a study by Weitzel et al.
Sequencing and Haplotyping: TP53_SNP_sequencing.pdf

Recent developments on p53 antibodies

Other tools

Mutalyzer, a package to support checks of sequence variant nomenclature according to the guidelines of the Human Genome Variation Society
Resources for the systematic analysis of p53 interactions with DNA and other transcription factors.
p53retriever, for the detection and display of p53 putative response elements (REs) on DNA sequences
TargetGeneReg, for displaying gene of interest in the p53 and cell cycle gene regulatory networks
TP53 RNA expression data from TCGA at GEPIA
Datamed, a search engine for TP53 datasets
Align-AGVGD, for the prediction of the functional impact of missense variants
SIFT, for the prediction of the functional impact of missense variants
Scorecons, for scoring residue conservation
The Cancer Genome Interpreter, to identify driver variants in tumor samples
LFSPRO, a tool for estimating TP53 Variant Carrier Probability
Famdenovo, an algorithm that calculates the probability of a germline variant to be de novo based on family history data
Amino-acid letter codes and properties
Genetic code
LOVD, a software to build variant databases

3D Structures Analysis

3D Viewer

Use mouse or control buttons (located on the right) to explore.

Structural Impacts of Variants

Analysis by A.C. Martin: Publication
Analysis by Mathe (2006). See details here: Structure-Function Predictions Based on Scores Derived from Delaunay Tessellations
UniProt information
Stability and oligomeric structure of p53 tetramerization domain mutants by Kamada et al. (2011)
Solved crystal structures:

by Joerger AC et al. (2005)

by Joerger AC et al. (2006)

Thermodynamic Stability Data

Definitions and Functions

p53 in the Clinic

Li-Fraumeni syndrome at GeneReviews
Videocast of the Li-Fraumeni Syndrome Workshop 2010
p53 in clinical trials at ClinicalTrials.gov
"p53 in the clinics" book, 2012
LFSPRO, a tool for estimating TP53 Variant Carrier Probability
Famdenovo, an algorithm that calculates the probability of a germline variant to be de novo, taking TP53 as an example application

Other Databases

TP53 databases

There are several links to different TP53 databases available on the web. Several resources are not updated anymore and may contain obsolete data. It is recommended to use up-to-date resources.

The TP53 Database (last updated in July 2019)
The p53 database by Thierry Soussi (last updated in 2017)
LOVD TP53, a database system for direct data submission
The database of germline TP53 mutations in Prague (not updated anymore)
p53 Knowledgebase at Singapore (obsolete)
Human p53 database and software, N. Cariello (1997) (obsolete)

Related Databases

Books

p53 in the Clinics

With over 60,000 referenced publications, p53 has emerged as one of the most important factors in human cancer. Research on p53 has led to a complete overhaul of our understanding of the molecular basis of human cancer.

25 Years of p53 Research

The discovery of p53 in 1979 marks the beginning of a most fascinating era of modern cancer research and molecular biology, an era that is still in full swing and does not show any signs of ending in the foreseeable future.