Starting
Initialising…
0%
TP53
Final classification
Likely Pathogenic
TP53 c.833C>G · p.Pro278Arg
TP53

NM_000546.5:c.833C>G (p.Pro278Arg) is a missense variant in TP53 exon 8, absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (AF=6.2e-7, 1/1,614,022 alleles).

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.833C>G
Consequence
N/A
GRCh38
chr17:7673787 G>C
GRCh37
chr17:7577105 G>C
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 moderate (+2) = 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 moderate (+2) = 9 points, which maps to Likely Pathogenic.
Classification rationale
PS3PM1PM2PP3 Likely Pathogenic
TP53 c.833C>G

NM_000546.5:c.833C>G (p.Pro278Arg) is a missense variant in TP53 exon 8, absent from gnomAD v2.1 and present at extremely low frequency in gnomAD v4.1 (AF=6.2e-7, 1/1,614,022 alleles).1 PS3 (Strong) is met: the variant is Non-functional in the Kato et al. functional assay AND demonstrates loss of function by the majority of other eligible assays (Giacomelli: LOF, Kotler: LOF, Funk: noLOF), per the TP53 VCEP Functional-worksheet.xlsx (Supplementary Table S3).2 PM1 (Moderate) is met: codon 278 is a statistically significant hotspot residue in cancerhotspots.org, and the Pro278Arg change has 82 somatic occurrences in COSMIC, far exceeding the VCEP threshold of >=10 for PM1_Moderate.3 PM2 (Supporting) is met: the variant allele frequency in gnomAD v4.1 (6.2e-7) is well below the VCEP PM2_Supporting threshold of 0.00003, with no genetic ancestry group exceeding 0.00004.4 PP3 (Moderate) is met per the TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2): aGVGD class C65 with BayesDel score 0.607821 (>=0.16), and SpliceAI predicts no splicing impact (max delta 0.00).5 Multiple criteria remain unassessed due to absent data: PS1 (requires VCEP classification of alternate nucleotide change c.833C>A for same amino acid P278R), PS2 (no de novo report with confirmed parentage), PS4 (germline proband counts unavailable), PM5 (formal VCEP classifications for codon 278 comparators needed), PP1 (no cosegregation data), PP4 (no VAF data), BS2 (no data on elderly unaffected carriers), and BS4 (no lack-of-segregation reports).6 Applying the TP53 VCEP v2.4.0 Tavtigian point system: PS3=4 + PM1=1 + PM2_Supporting=0.5 + PP3_Moderate=1 = 6.5 points, which falls in the Likely Pathogenic range (6-9 points).7 This variant has been reported in ClinVar with conflicting classifications: Uncertain significance (3 clinical laboratories), Likely pathogenic (1), and Pathogenic (1). (ClinVar Variation ID: 376644)8

PS3 + PM1 + PM2 + PP3 Likely Pathogenic
2 vcep_functional_worksheetcspec ↗
5 vcep_pp3_bp4_codesbayesdelspliceai ↗cspec ↗
7 cspec ↗final_classification_framework
Gene diagram · NM_000546.5 · variants mapped to exon structure
TP53 NM_000546.5
Fetching transcript structure from UCSC…
Applied criteria · 4 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= 6.1957e-07; MAF= 0.00006%, 1/1614022 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47448e-07; MAF= 0.00008%, 1/1180014 alleles, homozygotes = 0).
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      This variant is absent from gnomAD-Canada.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      6.2e-05% · 1 / 1,614,022
      0 hom
      European (non-Finnish)
      1 / 1,180,014
      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
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (3 clinical laboratories) and as Likely pathogenic (1 clinical laboratory) and as Pathogenic (1 clinical laboratory). (ClinVarID = 376644)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.951. BayesDel score = 0.607821.
      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; COSV52661225, n = 82 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      1papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 9 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.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      Sources & reference links
      8Sources
      CSpec VCEP
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      21760996 ↗ Mutations in TP53 and CTNNB1 in Relation to Hepatitis B and C Infections in Hepatocellular Carcinomas from Thailand. ONCOKB
      15138567 ↗ Spectrum of p53 mutations in biopsies from breast cancer patients selected for preoperative chemotherapy analysed by the functional yeast assay to predict therapeutic response. CLINVAR
      18555592 ↗ Presence of dominant negative mutation of TP53 is a risk of early recurrence in oral cancer. CLINVAR
      20195489 ↗ Activation of p73 and induction of Noxa by DNA damage requires NF-kappa B. CLINVAR
      21760960 ↗ High-level expression of wild-type p53 in melanoma cells is frequently associated with inactivity in p53 reporter gene assays. CLINVAR
      23124483 ↗ Correlation of telomere length shortening with TP53 somatic mutations, polymorphisms and allelic loss in breast tumors and esophageal cancer. CLINVAR
      19042984 ↗ National Academy of Clinical Biochemistry laboratory medicine practice guidelines for use of tumor markers in testicular, prostate, colorectal, breast, and ovarian cancers. CLINVAR
      22964825 ↗ Screening for ovarian cancer: U.S. Preventive Services Task Force reaffirmation recommendation statement. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR