Classification rationale

PS3PM2PP3 Likely Pathogenic

TP53 c.422G>A

NM_000546.5:c.422G>A (p.Cys141Tyr) is a missense variant in exon 5 of TP53. This variant is extremely rare in population databases: gnomAD v4.1 total allele frequency = 1.86e-6 (3/1,614,148 alleles), meeting PM2_Supporting (VCEP threshold <0.00003). It is absent from gnomAD v2.1 and gnomAD-Canada.¹ Functional studies demonstrate complete loss of function. The variant is non-functional in the Kato transactivation assay, and all additional eligible assays (Funk, Giacomelli, Kotler) show LOF, satisfying PS3 (strong) per TP53 VCEP specifications.² In silico predictions strongly support a deleterious effect: BayesDel score = 0.568676, aGVGD Class C65, REVEL = 0.897. The VCEP PP3-BP4-codes.xlsx assigns PP3_moderate for c.422G>A.³ SpliceAI predicts no splicing impact (max delta = 0.00), confirming this variant is assessed as a missense change without splicing aberration.⁴ The variant has been reported in ClinVar as Pathogenic by 5 clinical laboratories and Likely Pathogenic by 2, and has been observed 182 times in COSMIC somatic cancer database.⁵ Combined Tavtigian point score (TP53 VCEP v2.4.0): PS3 (strong) = +4, PP3_moderate = +2, PM2_Supporting = +1. Total = +7 points, which falls in the Likely Pathogenic range (6-9 points).⁶ Additional criteria (PS4, PS2, PP1) could not be assessed due to lack of proband-level cancer phenotype data, de novo observations, and cosegregation data in the available evidence. If PS4 evidence becomes available with ≥4 points (≥1 proband with strongly associated LFS cancer), the total would reach ≥10 points, reclassifying the variant as Pathogenic.

PS3 + PM2 + PP3 → Likely Pathogenic

1 gnomad_v4 ↗gnomad_v2 ↗

2 vcep_functional_worksheetPMID:12826609 ↗

3 vcep_pp3_bp4_codesbayesdelrevel

4 spliceai ↗

5 clinvar ↗

6 cspec ↗

Gene diagram · NM_000546.5 · variants mapped to exon structure

TP53 NM_000546.5

Fetching transcript structure from UCSC…

Applied criteria · 3 met · select any tile

Met

Not met

Not assessed

N/A

Strength very strong supporting

Pathogenic evidence

PVS

PS

PM

PP

Benign evidence

BA

BS

BP

—

Rationale

Select a criterion.

Sources

Evidence used

Gaps remaining

Rule

—

Research & evidence

Population frequency · supports pathogenic

gnomAD v4.1

gnomAD v2.1

Population frequency

Overall AF

3 / 1,614,148

0.00019%

Highest · European (non-Finnish)

0.00025%

Homozygotes

0

grpmax FAF

6.8e-05%

Allele frequency by ancestry — gnomAD v4.1

observed in 1 of 9 groups

Ancestry	Allele count	Frequency	Homozygotes
European (non-Finnish)	3 / 1,180,016	0.00025%	0
Admixed American	0 / 60,012	—	—
European (Finnish)	0 / 64,034	—	—
Amish	0 / 912	—	—
East Asian	0 / 44,882	—	—
Middle Eastern	0 / 6,062	—	—
South Asian	0 / 91,084	—	—
Ashkenazi Jewish	0 / 29,604	—	—
African/African American	0 / 75,034	—	—

“

This variant is present in gnomAD v4.1 (AF= 1.85857e-06; MAF= 0.00019%, 3/1614148 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54234e-06; MAF= 0.00025%, 3/1180016 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.

“

Absent from gnomAD v2.1.

“

This variant is absent from gnomAD-Canada.

gnomAD v4 ↗ gnomAD v2 ↗ gnomAD 🇨🇦 ↗

ClinVar

This variant has been reported in ClinVar as Pathogenic (5 clinical laboratories) and as Likely pathogenic (2 clinical laboratories). (ClinVarID = 140801)

ClinVar ↗

In silico

SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.897. BayesDel score = 0.568676.

SpliceAI ↗

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

Cancer hotspots

Somatic evidence Hotspot

COSMIC

This variant lies in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV52664953, n = 182 times).

Hotspots

This variant lies in a statistically significant hotspot.

COSMIC ↗ Hotspots ↗

Literature · 23 PMIDs triaged · 8 high-priority

23papers screened

Papers triaged by theme: functional/splicing/segregation/case_observation. high_priority_papers include abstract snippets. Use these to support PS3/BS3/PS4/PP1/PP3/PP5.

15037740 ↗ functional

A global suppressor motif for p53 cancer mutants.

The transcription factor and tumor suppressor protein p53 is frequently inactivated in human cancers. In many cases, p53 gene mutations result in high levels of inactive, full-length p53 protein with one amino acid change in the core domain that recognizes p53 DNA-binding sites. The ability to endow function to mutated p53 proteins would dramatically improve cancer therapy, because it would reacti

BS3PM1PS3

12826609 ↗ functional

Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.

Inactivation of the tumor suppressor p53 by missense mutations is the most frequent genetic alteration in human cancers. The common missense mutations in the TP53 gene disrupt the ability of p53 to bind to DNA and consequently to transactivate downstream genes. However, it is still not fully understood how a large number of the remaining mutations affect p53 structure and function. Here, we used a

BS3PP5PS3PS4

16861262 ↗ functional

Inactive full-length p53 mutants lacking dominant wild-type p53 inhibition highlight loss of heterozygosity as an important aspect of p53 status in human cancers.

Over 1000 different mutants of the tumor suppressor protein p53 with one amino acid change in the core domain have been reported in human cancers. In mouse knock-in models, two frequent mutants displayed loss of wild-type (wt) p53 function, inhibition of wt p53 and wt p53-independent gain of function. The remaining mutants have been systematically characterized for loss of wt p53 function, but not

BS3PP5PS3PS4

20128691 ↗ functional

Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation.

Sequence-specific DNA binding is the key function through which tumor suppressor p53 exerts transactivation of the downstream target genes, often being impaired in cancer cells by mutations in the TP53 gene. Functional protein microarray technology enables a high-throughput parallel analysis of protein properties within one experiment under the same conditions. Using an array approach, we analyzed

BS3PP5PS3PS4

21232794 ↗ functional

A comprehensive study of TP53 mutations in chronic lymphocytic leukemia: Analysis of 1287 diagnostic and 1148 follow-up CLL samples.

TP53 plays a pivotal role in the process of DNA repair and apoptosis. In 10-20% of patients with chronic lymphocytic leukemia (CLL), the TP53 pathway is affected. In this study, we analyzed the TP53 mutation status in 2435 consecutive CLL samples, including 1287 diagnostic samples and 1148 samples during follow-up, using FASAY (Functional Analysis of Separated Alleles in Yeast) and direct sequenci

BS3PP5PS3PS4

21343334 ↗ functional

Dominant-negative features of mutant TP53 in germline carriers have limited impact on cancer outcomes.

Germline TP53 mutations result in cancer proneness syndromes known as Li-Fraumeni, Li-Fraumeni-like, and nonsyndromic predisposition with or without family history. To explore genotype/phenotype associations, we previously adopted a functional classification of all germline TP53 mutant alleles based on transactivation. Severe deficiency (SD) alleles were associated with more severe cancer pronenes

BS3PP5PS3PS4

24256616 ↗ functional

Identification of new p53 target microRNAs by bioinformatics and functional analysis.

The tumor suppressor p53 is a sequence-specific transcription factor that regulates an extensive network of coding genes, long non-coding RNAs and microRNAs, that establish intricate gene regulatory circuits influencing many cellular responses beyond the prototypical control of cell cycle, apoptosis and DNA repair. Using bioinformatic approaches, we identified an additional group of candidate micr

BS3PP5PS3PS4

25741868 ↗ functional

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.

The American College of Medical Genetics and Genomics (ACMG) previously developed guidance for the interpretation of sequence variants.(1) In the past decade, sequencing technology has evolved rapidly with the advent of high-throughput next-generation sequencing. By adopting and leveraging next-generation sequencing, clinical laboratories are now performing an ever-increasing catalogue of genetic

BS3PS3PS4

19042984 ↗ background review

National Academy of Clinical Biochemistry laboratory medicine practice guidelines for use of tumor markers in testicular, prostate, colorectal, breast, and ovarian cancers.

PP5PS4

22964825 ↗ background review

Screening for ovarian cancer: U.S. Preventive Services Task Force reaffirmation recommendation statement.

PP5PS4

28492532 ↗ background review

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

PS3PS4

Sources & reference links

8Sources

CSpec VCEP

ClinVar

gnomAD v2.1

gnomAD v4.1

SpliceAI

OncoKB

COSMIC

Cancer hotspots