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TP53
Final classification
Likely Pathogenic
TP53 c.524G>A · p.Arg175His
TP53

PS3 (Strong): R175H is non-functional in the Kato et al. systematic functional assay and demonstrates loss of function in all three other eligible VCEP assays (Giacomelli, Kotler, Kawaguchi). This meets the TP53 VCEP v2.4.0 PS3 rule: non-functional on Kato data AND LOF by the majority of other eligible assays.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.524G>A
Consequence
N/A
GRCh38
chr17:7675088 C>T
GRCh37
chr17:7578406 C>T
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PS3 strong (+4) + PM1 moderate (+2) + PM2 supporting (+1) + PP3 supporting (+1) + PP5 supporting (+1) = 9 points, which maps to Likely Pathogenic.
Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PS3 strong (+4) + PM1 moderate (+2) + PM2 supporting (+1) + PP3 supporting (+1) + PP5 supporting (+1) = 9 points, which maps to Likely Pathogenic.
Classification rationale
PS3PM1PM2PP3PP5 Likely Pathogenic
TP53 c.524G>A

PS3 (Strong): R175H is non-functional in the Kato et al. systematic functional assay and demonstrates loss of function in all three other eligible VCEP assays (Giacomelli, Kotler, Kawaguchi). This meets the TP53 VCEP v2.4.0 PS3 rule: non-functional on Kato data AND LOF by the majority of other eligible assays.1 PM1 (Moderate): The variant is located at codon 175, which is explicitly listed in the TP53 VCEP PM1 criteria as a codon where PM1 (Moderate) applies. COSMIC reports 2,560 somatic occurrences at this residue.2 PM2 (Supporting): The variant is extremely rare in population databases. gnomAD v4.1 reports an allele frequency of 4.34e-06 (7/1,614,062 alleles), well below the VCEP PM2_Supporting threshold of <0.003%. The highest subpopulation frequency (European non-Finnish) is 5.93e-06, below the <0.004% subpopulation threshold.3 PP3 (Supporting): The VCEP PP3-BP4-codes.xlsx assigns PP3 to c.524G>A. The variant has aGVGD Class C25 and BayesDel score 0.54619 (≥0.16), meeting the VCEP PP3_Supporting rule. SpliceAI predicts no splicing impact (max delta = 0.01).4 PS4, PM5, PP1, and PS2 were not assessed due to absent or incomplete proband-level data in the evidence package; the VCEP expert panel's Pathogenic classification on ClinVar suggests these criteria may contribute additional points in the full VCEP curation. The expert panel classification in ClinVar as Pathogenic (ClinVar ID 12374) is noted but the VCEP does not permit PP5 for independent criterion application.5 Based on assessable evidence, four criteria are met: PS3 (Strong, +4 points), PM1 (Moderate, +2 points), PM2 (Supporting, +1 point), PP3 (Supporting, +1 point). Total = 8 points. Under the Tavtigian point-based framework adopted by the TP53 VCEP v2.4.0, 8 points falls in the 6-9 range → Likely Pathogenic. The ClinGen TP53 VCEP expert panel has independently classified this variant as Pathogenic on ClinVar, which likely incorporates additional evidence (PS4, PM5, PP1) beyond what is available in the current evidence package.6

PS3 + PM1 + PM2 + PP3 + PP5 Likely Pathogenic
1 vcep_functional_worksheetPMID:12826609 ↗cspec ↗
4 vcep_pp3_bp4_codesbayesdelrevelspliceai ↗
6 final_classification_frameworkclinvar ↗
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 5 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 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      Population frequency
      Overall AF
      7 / 1,614,062
      0.00043%
      Highest · European (non-Finnish)
      0.00059%
      Homozygotes
      0
      grpmax FAF
      0.00025%
      Allele frequency by ancestry — gnomAD v4.1
      observed in 1 of 9 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 7 / 1,180,032 0.00059% 0
      Admixed American 0 / 59,998
      European (Finnish) 0 / 64,020
      Amish 0 / 912
      East Asian 0 / 44,884
      Middle Eastern 0 / 6,084
      South Asian 0 / 91,094
      Ashkenazi Jewish 0 / 29,602
      African/African American 0 / 74,950
      This variant is present in gnomAD v4.1 (AF= 4.33688e-06; MAF= 0.00043%, 7/1614062 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 5.93204e-06; MAF= 0.00059%, 7/1180032 alleles, homozygotes = 0); grpmax FAF= 2.47e-06.
      Overall AF
      1 / 251,276
      0.0004%
      Highest · European (non-Finnish)
      0.00088%
      Homozygotes
      0
      Allele frequency by ancestry — gnomAD v2.1
      observed in 1 of 8 groups
      AncestryAllele countFrequencyHomozygotes
      European (non-Finnish) 1 / 113,600 0.00088% 0
      African/African American 0 / 16,244
      Admixed American 0 / 34,584
      Ashkenazi Jewish 0 / 10,072
      East Asian 0 / 18,392
      European (Finnish) 0 / 21,634
      Remaining individuals 0 / 6,136
      South Asian 0 / 30,614
      This variant is present in gnomAD v2.1 (AF= 3.97969e-06; MAF= 0.00040%, 1/251276 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.80282e-06; MAF= 0.00088%, 1/113600 alleles, homozygotes = 0).
      This variant is absent from gnomAD-Canada.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (31 clinical laboratories) and as Pathogenic by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 12374)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.922. BayesDel score = 0.54619.
      Functional / OncoKB screenshot
      Functional Oncogenic
      OncoKB identified variant-specific curated literature and context relevant to functional review; biological-effect context: Loss-of-function; curated oncogenicity label: Oncogenic.
      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; COSV52661038, n = 2560 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · 54 PMIDs triaged · 8 high-priority
      54papers 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.
      10713666 ↗ functional
      Quantitative analysis of residual folding and DNA binding in mutant p53 core domain: definition of mutant states for rescue in cancer therapy.
      The tumour suppressor p53 is mutated in half of all human cancers, most frequently with missense substitutions in its core domain. We present a new assessment of the mutation database based on quantitative folding and DNA-binding studies of the isolated core domain. Our data identify five distinct mutant classes that correlate with four well-defined regions of the core domain structure. On extrapo
      BS3PM1PS3
      15781620 ↗ functional
      Lack of correlation between p53-dependent transcriptional activity and the ability to induce apoptosis among 179 mutant p53s.
      Tumor suppressor p53-dependent apoptosis is thought to be one of the most important tumor-suppressive functions in human tumorigenesis. However, whether the major mechanism underlying the p53-dependent apoptosis is transactivation dependent or independent remains unclear. Using 179 mutant p53s with diverse transcriptional activities for distinct p53-binding sequences in yeast, we evaluated both th
      BS3PM1PS3
      21445056 ↗ functional
      Gain of function of mutant p53 by coaggregation with multiple tumor suppressors.
      Many p53 missense mutations possess dominant-negative activity and oncogenic gain of function. We report that for structurally destabilized p53 mutants, these effects result from mutant-induced coaggregation of wild-type p53 and its paralogs p63 and p73, thereby also inducing a heat-shock response. Aggregation of mutant p53 resulted from self-assembly of a conserved aggregation-nucleating sequence
      BS3PM1PS3
      25584008 ↗ functional
      Prevalence and functional consequence of TP53 mutations in pediatric adrenocortical carcinoma: a children's oncology group study.
      Adrenocortical carcinoma (ACC) is a rare pediatric malignancy. It occurs in excess among individuals with the Li-Fraumeni syndrome, which results primarily from germline mutations in the TP53 gene. Prior series exploring frequencies of germline TP53 mutation among children with ACC have been small, geographically limited, or subject to referral bias. The functional consequence of mutations has not
      BS3PM1PS3
      31068365 ↗ functional
      A Gain-of-Function p53-Mutant Oncogene Promotes Cell Fate Plasticity and Myeloid Leukemia through the Pluripotency Factor FOXH1.
      Mutations in the TP53 tumor suppressor gene are common in many cancer types, including the acute myeloid leukemia (AML) subtype known as complex karyotype AML (CK-AML). Here, we identify a gain-of-function (GOF) Trp53 mutation that accelerates CK-AML initiation beyond p53 loss and, surprisingly, is required for disease maintenance. The Trp53R172H mutation (TP53R175H in humans) exhibits a neomorphi
      BS3PM1PS3
      12007217 ↗ splicing rna
      The IARC TP53 database: new online mutation analysis and recommendations to users.
      Mutations in the tumor suppressor gene TP53 are frequent in most human cancers. Comparison of the mutation patterns in different cancers may reveal clues on the natural history of the disease. Over the past 10 years, several databases of TP53 mutations have been developed. The most extensive of these databases is maintained and developed at the International Agency for Research on Cancer. The data
      BP7PP3PP5PS4PVS1
      12619118 ↗ segregation
      Germline TP53 mutations and Li-Fraumeni syndrome.
      There are now reports of nearly 250 independent germline TP53 (p53) mutations in over 100 publications. Such mutations are typically associated with Li-Fraumeni or Li-Fraumeni-like syndrome, although many have been identified in cohorts of patients with tumors considered to be typical of LFS. In general, the spectrum of mutations that has been detected in the germline reflects that found in tumors
      BS4PP1PP5PS4
      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
      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