Variant classification summary

NM_000546.6:c.473G>T

TP53 · NP_000537.3:p.(Arg158Leu) · NM_000546.6

GRCh37: chr17:7578457 C>A · GRCh38: chr17:7675139 C>A

Gene: TP53 Transcript: NM_000546.6

Final call

Pathogenic

PS3 strong PM1 moderate PM2 supporting PM5 strong PP3 moderate PP5 supporting

Variant details

Gene

TP53

Transcript

NM_000546.6

Protein

NP_000537.3:p.(Arg158Leu)

gnomAD AF

6.195295540378459e-07 (v4.1)

ClinVar

Pathogenic

OncoKB

Likely Oncogenic

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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).

3

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.

4

PP3 (Moderate): Per VCEP PP3-BP4-codes.xlsx, c.473G>T is assigned PP3_moderate (aGVGD Class C65, BayesDel 0.576, REVEL 0.891).

5

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%.

6

PP5 (Supporting): The ClinGen TP53 VCEP has classified this variant as Pathogenic (ClinVar Variation ID 528248, expert panel reviewed).

7

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.

8

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.

Final determination: Tavtigian et.al., 2020 - Bayesian adaptation of Richards et.al., 2015 v2.4.0 point-based framework yields a total score of 14, which maps to Pathogenic under the specified Tavtigian-style ranges.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 is not applicable to missense variants. The TP53 VCEP PVS1 decision tree (PVS1-Flowchart.pdf) applies only to null variants: nonsense, frameshift, canonical ±1,2 splice sites, initiation codon variants, CNVs, and single/multi-exon deletions. c.473G>T is a missense substitution (p.Arg158Leu) and does not fall into any PVS1-eligible variant bucket.	cspec vcep_pvs1_flowchart
PS1	Not assessed	PS1 requires a different nucleotide change producing the same p.Arg158Leu amino acid change that has been previously established as pathogenic. No such comparator variant was identified in the evidence reviewed. The variant c.473G>T is a single nucleotide substitution (G→T at position 473); no other nucleotide change producing p.Arg158Leu (e.g., at c.472 or c.474) was found with a confirmed VCEP pathogenic classification.
PS2	Not assessed	No de novo observation data for NM_000546.6:c.473G>T was identified in the evidence reviewed. PS2 requires confirmed de novo occurrence with maternity/paternity confirmation. The VCEP PS2 point system requires proband cancer phenotype scoring (LFS-associated cancers), but no proband-level clinical data were available.
PS3	Met	R158L is non-functional on Kato et al. (PMID:12826609) transactivation assay data AND demonstrates loss of function (LOF) across all other eligible functional assays (Funk, Giacomelli, Kotler), meeting the TP53 VCEP rule for PS3 (Strong): 'Non-functional on Kato et al. data AND loss of function by the majority of other eligible assays.' Functional assignment confirmed in VCEP Functional-worksheet.xlsx Supplementary Table S3. Additional functional evidence from Baroni et al. (PMID:15037740) demonstrates R158L has no detectable transcriptional activity in yeast and mammalian reporter gene assays, with partial rescue by the 235-239-240 intragenic suppressor motif.	PMID:12826609 PMID:15037740 vcep_functional_worksheet vcep_flowchart_for_application_of_functional_rule_codes
PS4	Not assessed	PS4 requires proband-level case data with Li-Fraumeni syndrome cancer phenotype scoring per the VCEP PS4-Points-Table. No individual proband phenotype data (cancer types, ages of onset, family history) were available in the evidence reviewed. Although the variant is well-established in ClinVar and somatic databases, case-control prevalence comparison data for germline PS4 assessment were not provided.
PS5	N/A	PS5 is not a recognized criterion in the ACMG/AMP 2015 framework (Richards et al., PMID:25741868) nor in the TP53 VCEP specifications v2.4.0. Standard pathogenic strong criteria are PS1-PS4. No PS5 criterion exists for adjudication.
PM1	Met	Codon 158 is not among the VCEP-listed hotspot codons (175, 245, 248, 249, 273, 282) for the codon-position PM1 rule. However, the variant has 181 somatic occurrences in COSMIC (COSV52676395), far exceeding the VCEP threshold of ≥10 somatic occurrences for the same amino acid change (R158L), meeting PM1 at Moderate strength per VCEP rule: 'This code weight can also be used for germline missense variants seen in cancerhotspots.org with ≥10 somatic occurrences for the same amino acid change.' The residue also lies in a statistically significant hotspot.	cspec
PM2	Met	Variant is extremely rare in population databases. gnomAD v2.1: AF = 3.98e-06 (1/251,268 alleles, 0 homozygotes). gnomAD v4.1: AF = 6.20e-07 (1/1,614,128 alleles, 0 homozygotes). Absent from gnomAD-Canada v1.0. Both frequencies are far below the VCEP PM2_Supporting threshold of <0.00003 (0.003%). Single-allele observations across populations with no genetic ancestry group exceeding the 0.00004 multi-allele threshold.	gnomad_v2 gnomad_v4 gnomad_canada cspec
PM5	Met	Although the automated PM5 pipeline misclassified this variant as non-missense, manual review confirms c.473G>T is a missense variant producing p.Arg158Leu. Per the VCEP Functional-worksheet.xlsx, at least three different missense variants at codon 158 carry PS3 (Strong) assignments: R158G (PS3), R158H (PS3), and R158P (PS3). These represent ≥2 different missense variants at the same amino acid residue previously determined to be pathogenic per VCEP specifications, meeting PM5 at Strong strength per VCEP rule: 'Missense variant at an amino acid residue where ≥2 different missense variants previously determined to be pathogenic according to the TP53 VCEP's specifications have been seen before.'	vcep_functional_worksheet cspec
PM6	N/A	PM6 is designated as Not Applicable by the TP53 VCEP specifications v2.4.0 and is not used for TP53 variant classification under this framework.	cspec
PP1	Not assessed	No cosegregation data were available in the evidence reviewed. PP1 requires observation of variant cosegregation with LFS-associated cancers across multiple meioses (VCEP thresholds: Supporting = 3-4 meioses, Moderate = 5-6 meioses, Strong = ≥7 meioses across >1 family).
PP2	N/A	PP2 is designated as Not Applicable by the TP53 VCEP specifications v2.4.0. The VCEP does not use PP2 (missense variant in a gene with low rate of benign missense variation) for TP53 classification.	cspec
PP3	Met	Per VCEP PP3-BP4-codes.xlsx Supplementary Table S2: c.473G>T is assigned PP3_moderate. The variant has aGVGD Class C65 and BayesDel score 0.575563 (≥0.16), meeting the VCEP rule for PP3_Moderate: 'aGVGD Class C65 and BayesDel score ≥0.16.' REVEL score is 0.891 (strongly pathogenic prediction). SpliceAI max delta is 0.00 (no predicted splicing impact).	vcep_pp3_bp4_codes bayesdel revel spliceai cspec
PP4	Not assessed	PP4 per VCEP requires variant allele fraction (VAF) data: Moderate = ≥2 independent observations with VAF 5-25%, Supporting = observation with VAF 5-35%. No VAF or patient phenotype data were available in the evidence reviewed. VCEP PP4 is specifically designed to address clonal hematopoiesis concerns in TP53 by requiring low VAF documentation.
PP5	Met	Expert panel ClinGen TP53 Variant Curation Expert Panel, ClinGen classified as Pathogenic.	clinvar cspec
BA1	Not met	gnomAD allele frequencies are far below the VCEP BA1 threshold of ≥0.001 (0.1%) FAF in any continental subpopulation. gnomAD v2.1 max subpopulation AF: 6.16e-05 (African/African American). gnomAD v4.1 max subpopulation AF: 8.47e-07 (European non-Finnish). Only single-allele observations in any population; no subpopulation exceeds the BA1 threshold.	gnomad_v2 gnomad_v4 cspec
BS1	Not met	gnomAD allele frequencies are far below the VCEP BS1 threshold of FAF ≥0.0003 (0.03%) in any continental subpopulation. No subpopulation has sufficient allele count or frequency to meet BS1. The single-allele observations in gnomAD are consistent with a rare pathogenic variant, not a benign polymorphism.	gnomad_v2 gnomad_v4 cspec
BS2	Not assessed	BS2 per VCEP requires observation in unrelated females who have reached ≥60 years of age without cancer. No such data were available in the evidence reviewed. VCEP thresholds: Strong = ≥8, Moderate = 4-7, Supporting = 2-3 unrelated females ≥60 years without cancer, all from a single source.
BS3	Not met	BS3 requires functional studies showing no damaging effect on protein function. This is contradicted by the VCEP Functional-worksheet.xlsx, which assigns PS3 (Strong) to R158L based on non-functional status in Kato et al. assay and LOF across all other eligible assays (Funk, Giacomelli, Kotler). BS3 is explicitly not met because functional evidence demonstrates complete loss of function.	vcep_functional_worksheet PMID:12826609 PMID:15037740
BS4	Not assessed	BS4 requires lack of segregation in affected family members with LFS-associated cancers. No segregation data were available in the evidence reviewed.
BP1	N/A	BP1 is designated as Not Applicable by the TP53 VCEP specifications v2.4.0.	cspec
BP2	N/A	BP2 is designated as Not Applicable by the TP53 VCEP specifications v2.4.0.	cspec
BP3	N/A	BP3 is designated as Not Applicable by the TP53 VCEP specifications v2.4.0.	cspec
BP4	Not met	BP4 requires BayesDel score ≤ -0.008 (BP4_Moderate) or < 0.16 and > -0.008 (BP4_Supporting) with no predicted splicing impact. The variant has BayesDel 0.575563 (≥0.16) and aGVGD Class C65, which triggers PP3_moderate per VCEP PP3-BP4-codes.xlsx. BP4 is contradicted by the in silico evidence. SpliceAI delta = 0.00 indicates no splicing impact, but the missense prediction scores are decisively pathogenic.	vcep_pp3_bp4_codes bayesdel spliceai
BP5	N/A	BP5 is designated as Not Applicable by the TP53 VCEP specifications v2.4.0.	cspec
BP6	N/A	BP6 is designated as Not Applicable by the TP53 VCEP specifications v2.4.0.	cspec
BP7	N/A	BP7 applies only to synonymous (silent) variants or intronic variants outside the core splice motif per VCEP. c.473G>T is a missense variant (p.Arg158Leu) and does not qualify for BP7 assessment.	cspec

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