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TP53
Final classification
Pathogenic
TP53 c.473G>T · p.Arg158Leu
TP53

PS3 (Strong): R158L is non-functional on Kato et al. transactivation assay and demonstrates loss of function across all eligible functional assays (Funk, Giacomelli, Kotler), meeting the VCEP rule for PS3 at Strong strength.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.473G>T
Consequence
N/A
GRCh38
chr17:7675139 C>A
GRCh37
chr17:7578457 C>A
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) + PM5 strong (+4) + PP3 moderate (+2) + PP5 supporting (+1) = 14 points, which maps to 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) + PM5 strong (+4) + PP3 moderate (+2) + PP5 supporting (+1) = 14 points, which maps to Pathogenic.
Classification rationale
PS3PM1PM2PM5PP3PP5 Pathogenic
TP53 c.473G>T

PS3 (Strong): R158L is non-functional on Kato et al. transactivation assay and demonstrates loss of function across all eligible functional assays (Funk, Giacomelli, Kotler), meeting the VCEP rule for PS3 at Strong strength.1 PM5 (Strong): At least three different missense variants at codon 158 (R158G, R158H, R158P) carry PS3 assignments per the VCEP Functional-worksheet, meeting the VCEP rule for PM5 at Strong strength (≥2 different pathogenic missense variants at the same residue).2 PM1 (Moderate): The variant has 181 somatic occurrences in COSMIC, exceeding the VCEP threshold of ≥10 somatic occurrences for the same amino acid change, meeting PM1 at Moderate strength.3 PP3 (Moderate): Per VCEP PP3-BP4-codes.xlsx, c.473G>T is assigned PP3_moderate (aGVGD Class C65, BayesDel 0.576, REVEL 0.891).4 PM2 (Supporting): Variant is extremely rare in gnomAD (v2.1: 1/251,268; v4.1: 1/1,614,128), far below the VCEP PM2_Supporting threshold of <0.003%.5 PP5 (Supporting): The ClinGen TP53 VCEP has classified this variant as Pathogenic (ClinVar Variation ID 528248, expert panel reviewed).6 BA1, BS1, BS3, BP4 not met: Population frequencies are far below benign thresholds. Functional data demonstrate complete loss of function, contradicting BS3. In silico predictions are decisively pathogenic, contradicting BP4.7 PVS1, PS1, PS2, PS4, PS5, PM6, PP1, PP2, PP4, BS2, BS4, BP1, BP2, BP3, BP5, BP6, BP7 not applicable or not assessed due to variant type, VCEP rules, or absence of required evidence.8

PS3 + PM1 + PM2 + PM5 + PP3 + PP5 Pathogenic
1 PMID:12826609 ↗vcep_functional_worksheet
2 vcep_functional_worksheetcspec ↗
4 vcep_pp3_bp4_codesbayesdelrevel
7 gnomad_v2 ↗gnomad_v4 ↗vcep_functional_worksheetbayesdel
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
Fetching transcript structure from UCSC…
Applied criteria · 6 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
      v4.1
      This variant is present in gnomAD v4.1 (AF= 6.1953e-07; MAF= 0.00006%, 1/1614128 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47433e-07; MAF= 0.00008%, 1/1180034 alleles, homozygotes = 0).
      v2.1
      This variant is present in gnomAD v2.1 (AF= 3.97981e-06; MAF= 0.00040%, 1/251268 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 6.15991e-05; MAF= 0.00616%, 1/16234 alleles, homozygotes = 0).
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,614,128
      0 hom
      European (non-Finnish)
      1 / 1,180,034
      8.5e-05%
      + 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
      gnomAD v2.1
      0.0004% · 1 / 251,268
      0 hom
      African/African American
      1 / 16,234
      0.0062%
      + 7 not observed (Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Remaining individuals, South Asian)
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Pathogenic (7 clinical laboratories) and as Likely pathogenic (2 clinical laboratories) and as Pathogenic by ClinGen TP53 Variant Curation Expert Panel, ClinGen (expert panel). (ClinVarID = 528248)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.891. BayesDel score = 0.575563.
      Functional / OncoKB screenshot
      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 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; COSV52676395, n = 181 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      2papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 4 further PMIDs triaged but not cited — see Sources & References.
      Understanding the function-structure and function-mutation relationships of p53 tumor suppressor protein by high-resolution missense mutation analysis.
      Searched
      c.473G>Tp.Arg158LeuR158LR158
      Found
      Kato et al. performed high-resolution missense mutation analysis of p53 using a yeast-based transactivation assay across 2,314 p53 mutants representing all possible amino acid substitutions. The paper describes the functional assay system and structure-function relationships but does not list individual variant results in the main text. The VCEP Functional-worksheet.xlsx derives R158L functional data (Non-functional) from this paper's supplementary data.
      Variant
      ◇ Residue / gene-level — variant not named
      Applied to
      PS3 supports · met
      Why
      Variant-specific functional data (Non-functional) derived from this paper's dataset and codified in VCEP Functional-worksheet; referenced in PS3 assessment at Strong strength.
      Location Functional data for R158L in supplementary materials (not in main text body); VCEP Functional-worksheet.xlsx cites Kato et al. as the source of Non-functional classification.  ·  Context Yeast-based p53 transactivation assay; p53 mutants expressed in S. cerevisiae reporter strain, assessed across 8 p53 response elements  ·  full text
      A global suppressor motif for p53 cancer mutants.
      Searched
      c.473G>Tp.Arg158LeuR158LR158
      Found
      R158L was identified as one of the 30 most common p53 cancer mutants and functionally characterized. R158L showed no detectable transcriptional activity in both yeast and mammalian (H1299) reporter gene assays. The 235-239-240 global suppressor motif partially rescued R158L function: ~20% of WT activity on single p53 DNA-binding sites, ~50% on the p21 promoter, and 65-125% of WT p53 activity in apoptosis assays.
      Variant
      ✓ Names this variant — characterised directly
      Applied to
      PS3 supports · met
      Why
      Variant-specific functional data confirms complete loss of transcriptional activity for R158L alone; partial rescue by suppressor motif demonstrates the mutation is in the DNA-binding core domain. Referenced in PS3 assessment as corroborating functional evidence.
      Four mutants, R158L, V173M, Y205C, and Y220C, in combination with suppressor amino acids, showed only 20% of WT p53 activity.
      Location Abstract; Results (Table 2, entry 27-30); Figure 2 (mammalian reporter assay); Figure 3 (p21 promoter assay); Figure 4 (apoptosis assay)  ·  Context Luciferase reporter gene assays in H1299 (p53-null lung adenocarcinoma) cells; p21 promoter reporter; apoptosis assays in baby hamster kidney cells; yeast p53 functional assay in S. cerevisiae strain RBy377  ·  full text
      Sources & reference links
      9Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 4 PMIDs not cited in assessment
      16861262 ↗ 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. ONCOKB
      25584008 ↗ Prevalence and functional consequence of TP53 mutations in pediatric adrenocortical carcinoma: a children's oncology group study. ONCOKB
      10229196 ↗ Novel p53 mutants selected in BRCA-associated tumours which dissociate transformation suppression from other wild-type p53 functions. CLINVAR
      17308077 ↗ Younger age of cancer initiation is associated with shorter telomere length in Li-Fraumeni syndrome. CLINVAR