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
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).
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
PS3 + PM1 + PM2 + PP3
→
Likely Pathogenic
Gene diagram
· NM_000546.5 · variants mapped to exon structure
TP53
NM_000546.5
Fetching transcript structure from UCSC…
Applied criteria · 4 applied · 12 assessed
Applied · 4
Strength
Supporting
Moderate
Strong
Very strong
✓
PS3
strong
Pathogenic
PS3 (Strong) is met per the TP53 VCEP Functional-worksheet.xlsx (Supplementary Table S3). The p.Pro278Arg (P278R) substitution is classified as Non-functional in the Kato et al. (PMID:12826609) assay AND demonstrates loss of function (LOF) by the majority of other eligible functional assays (Giacomelli: LOF, Kotler: LOF, Funk: noLOF). Two of three non-Kato assays show LOF, satisfying the VCEP rule for PS3: 'Non-functional on Kato et al. data AND loss of function by the majority of other eligible assays.'
VCEP Functional-worksheet.xlsx pre-assigned code PS3 for P278R: Kato=Non-functionalGiacomelli=LOFKotler=LOF
✓
PM1
moderate
Pathogenic
PM1 (Moderate) is met per the TP53 VCEP specifications. Although codon 278 is not among the listed major hotspot codons (175, 245, 248, 249, 273, 282), the variant is a germline missense change at a residue that is a statistically significant hotspot in cancerhotspots.org, and the exact amino acid change (Pro278Arg) has 82 somatic occurrences in COSMIC (COSV52661225), well exceeding the VCEP threshold of >=10 somatic occurrences for the same amino acid change.
Codon 278 residue is a statistically significant hotspotCOSMIC reports 82 somatic occurrences of the exact variant (COSV52661225)>=10 threshold for PM1_Moderate is exceeded.
✓
PM2
supporting
Pathogenic
PM2_Supporting is met per the TP53 VCEP population frequency rules. The variant is absent from gnomAD v2.1 and has an allele frequency of 6.2e-7 (1/1,614,022 alleles) in gnomAD v4.1, with the highest subpopulation frequency of 8.5e-7 in European (non-Finnish) (1/1,180,014 alleles). Both the total allele frequency (<0.00003) and the single-ancestry-group frequency with only one allele observed (<0.00004) satisfy the PM2_Supporting threshold.
gnomAD v2.1: absentgnomAD v4.1: AF=6.2e-7 (1/1614
✓
PP3
moderate
Pathogenic
PP3_Moderate is met per the TP53 VCEP PP3-BP4-codes.xlsx (Supplementary Table S2), which pre-assigns PP3_moderate to c.833C>G (p.Pro278Arg). The variant has an aGVGD class of C65 and a BayesDel score of 0.607821 (>=0.16), satisfying the VCEP rule for PP3_Moderate. SpliceAI predicts no splicing impact (max delta = 0.00), so no splicing adjustment is needed.
PP3-BP4-codes.xlsx: c.833C>G assigned PP3_moderateaGVGD Class C65BayesDel 0.607821 >= 0.16
Assessed · not applied
Pathogenic
PS1
PS1 requires a different nucleotide change at the same codon that results in the same amino acid change (Pro278Arg) and has been previously classified as Pathogenic or Likely Pathogenic per the TP53 VCEP specifications.
PS2
PS2 requires documented de novo occurrence with confirmed parentage in a proband with Li-Fraumeni syndrome (LFS)-associated cancers.
PS4
PS4 under the TP53 VCEP requires counting independent probands with LFS-spectrum cancers using the PS4 points table (strongly associated cancers = 4 points, moderately associated = 2 points).
PM5
PM5 (same residue, different missense change previously established as pathogenic per VCEP) could potentially be applied because multiple different missense variants at codon 278 (P278A, P278H, P278L, P278S, P278T) receive PS3 (pathogenic functional evidence) in the VCEP Functional-worksheet, suggesting they would classify as Pathogenic under the VCEP framework.
PP1
PP1 requires cosegregation data with specific meiotic counts across families (>=3-4 meioses for Supporting, 5-6 for Moderate, >=7 across >1 family for Strong).
PP4
PP4 requires observation of the variant at variant allele fraction (VAF) 5-35% in blood, consistent with constitutional (non-somatic) origin.
Benign
BA1
BA1 requires a filtering allele frequency (FAF) >= 0.001 (0.1%) in gnomAD continental subpopulations.
BS1
BS1 requires a filtering allele frequency (FAF) >= 0.0003 but < 0.001 in gnomAD continental subpopulations.
BS2
BS2 requires >=2 unrelated females who have reached at least 60 years of age without cancer (from a single source).
BS3
BS3 requires functional evidence of no damaging effect (Functional on Kato data AND no LOF by majority of eligible assays).
BS4
BS4 requires lack of segregation in affected family members (i.e., family members diagnosed with LFS-associated cancers who do not carry the variant, or unaffected carriers).
BP4
BP4 (benign in silico evidence) is not met.
N/A · 12
PVS1 · PM3 · PM4 · PM6 · PP2 · PP5 · BP1 · BP2 · BP3 · BP5 · BP6 · BP7
Research & evidence
Population frequency · supports pathogenic
gnomAD v4.1
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
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
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent
· 0 / ?
0 hom
0 hom
Not observed in any ancestry group.
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)
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
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.
COSMIC
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
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
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