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TP53
Final classification
Likely Pathogenic
TP53 c.700T>A · p.Tyr234Asn
TP53

Functional studies demonstrate that p.Tyr234Asn is non-functional in the Kato et al. transactivation assay with loss of function across all other eligible assays (Giacomelli, Kotler, Funk), meeting PS3 at strong strength per the TP53 VCEP v2.4.0 Functional-worksheet.

Gene
TP53
Transcript
NM_000546.6
HGVS · transcript:coding
NM_000546.6:c.700T>A
Consequence
N/A
GRCh38
chr17:7674263 A>T
GRCh37
chr17:7577581 A>T
Basis Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework: PS3 strong (+4) + PM2 supporting (+1) + PP3 supporting (+1) = 6 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) + PM2 supporting (+1) + PP3 supporting (+1) = 6 points, which maps to Likely Pathogenic.
Classification rationale
PS3PM2PP3 Likely Pathogenic
TP53 c.700T>A

Functional studies demonstrate that p.Tyr234Asn is non-functional in the Kato et al. transactivation assay with loss of function across all other eligible assays (Giacomelli, Kotler, Funk), meeting PS3 at strong strength per the TP53 VCEP v2.4.0 Functional-worksheet.1 This variant is absent from gnomAD v2.1 and v4.1 population databases (allele count = 0), meeting PM2_Supporting per the TP53 VCEP threshold of allele frequency <0.003%.2 Computational evidence supports a deleterious effect: aGVGD Class C35, BayesDel score 0.489, REVEL score 0.941, with no predicted splicing impact (SpliceAI max delta 0.00). The TP53 VCEP PP3-BP4-codes spreadsheet assigns PP3 at supporting level.3 This variant has been reported in ClinVar as Pathogenic by two clinical laboratories and Likely pathogenic by one laboratory (ClinVar Variation ID 376692), and has been observed in somatic cancers (COSMIC, n=35).4 Applying the TP53 VCEP v2.4.0 Tavtigian point system: PS3_Strong (+5) + PM2_Supporting (+1) + PP3_Supporting (+0.5) = 6.5 total points, which falls within the Likely Pathogenic range (6-9 points).5

PS3 + PM2 + PP3 Likely Pathogenic
1 vcep_functional_worksheet
3 vcep_pp3_bp4_codesrevelbayesdelspliceai ↗
Gene diagram · NM_000546.6 · variants mapped to exon structure
TP53 NM_000546.6
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 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      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
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      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 Pathogenic (2 clinical laboratories) and as Likely pathogenic (1 clinical laboratory). (ClinVarID = 376692)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.941. BayesDel score = 0.489361.
      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; COSV52730114, n = 35 times).
      Hotspots
      This variant lies in a statistically significant hotspot.
      Literature · how each cited paper was used
      3papers cited
      Each card is an audit: what was searched, what was found, whether it names the variant, which criteria it fed, and why. 3 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
      A Systematic p53 Mutation Library Links Differential Functional Impact to Cancer Mutation Pattern and Evolutionary Conservation.
      Found
      Structured finding pending for this record — see source link.
      Applied to
      PS3 supports · met
      Mutational processes shape the landscape of TP53 mutations in human cancer.
      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 · 3 PMIDs not cited in assessment
      27328919 ↗ TP53 Variations in Human Cancers: New Lessons from the IARC TP53 Database and Genomics Data. ONCOKB
      9824113 ↗ p53 gene mutations in osteosarcomas of low-grade malignancy. ONCOKB
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR