Starting
Initialising…
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TP53
Final classification
Likely Pathogenic
TP53 c.422G>A · p.Cys141Tyr
TP53

NM_000546.5:c.422G>A (p.Cys141Tyr) is a missense variant in exon 5 of TP53.

Gene
TP53
Transcript
NM_000546.5
HGVS · transcript:coding
NM_000546.5:c.422G>A
Consequence
N/A
GRCh38
chr17:7675190 C>T
GRCh37
chr17:7578508 C>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 moderate (+2) = 7 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 moderate (+2) = 7 points, which maps to Likely Pathogenic.
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
2 vcep_functional_worksheetPMID:12826609 ↗
3 vcep_pp3_bp4_codesbayesdelrevel
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 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      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.
      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
      0.00019% · 3 / 1,614,148
      0 hom · FAF 6.8e-05%
      European (non-Finnish)
      3 / 1,180,016
      0.00025%
      + 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 Pathogenic (5 clinical laboratories) and as Likely pathogenic (2 clinical laboratories). (ClinVarID = 140801)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.897. BayesDel score = 0.568676.
      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; COSV52664953, n = 182 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. 10 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
      VCEP Functional-worksheet.xlsx assigns PS3 for C141Y Kato assay (PMID:12826609): Non-functional Funk assay: LOF Giacomelli assay (PMID:30224644): LOF Kotler assay (PMID:29979965): LOF Majority of eligible assays (3/3 non-Kato) show LOF
      Applied to
      PS3 supports · met
      PMID 29979965
      Found
      VCEP Functional-worksheet.xlsx assigns PS3 for C141Y Kato assay (PMID:12826609): Non-functional Funk assay: LOF Giacomelli assay (PMID:30224644): LOF Kotler assay (PMID:29979965): LOF Majority of eligible assays (3/3 non-Kato) show LOF
      Applied to
      PS3 supports · met
      PMID 30224644
      Found
      VCEP Functional-worksheet.xlsx assigns PS3 for C141Y Kato assay (PMID:12826609): Non-functional Funk assay: LOF Giacomelli assay (PMID:30224644): LOF Kotler assay (PMID:29979965): LOF Majority of eligible assays (3/3 non-Kato) show LOF
      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 · 10 PMIDs not cited in assessment
      15037740 ↗ A global suppressor motif for p53 cancer mutants. ONCOKB
      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. CLINVAR
      20128691 ↗ Analysis of the DNA-binding activity of p53 mutants using functional protein microarrays and its relationship to transcriptional activation. CLINVAR
      21232794 ↗ A comprehensive study of TP53 mutations in chronic lymphocytic leukemia: Analysis of 1287 diagnostic and 1148 follow-up CLL samples. CLINVAR
      21343334 ↗ Dominant-negative features of mutant TP53 in germline carriers have limited impact on cancer outcomes. CLINVAR
      24256616 ↗ Identification of new p53 target microRNAs by bioinformatics and functional analysis. CLINVAR
      25741868 ↗ 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. 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