TP53 p.Arg213=
c.639A>C · VCV4071253
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Li-Fraumeni syndrome 1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.5 | GERP -2.1 |
| Overall | ||
| CADD | 8.178 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- TP53
- Protein
- p.Arg213=
- Coding
- c.639A>C
- MANE Select
- NM_000546
- Type
- single nucleotide variant
- Location
- chr17:7674892 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.83 · 321 PDB
- Residue 213
- a DNA-binding region; the 'interaction with axin1' region; the 'interaction with ccar2' region; the 'interaction with hipk1' region; a UniProt-annotated variant site (in sporadic cancers; somatic mutation); a UniProt-annotated variant site (in lfs; germline mutation and in sporadic cancers; somatic mutation); the 'required for interaction with znf385a' region; the 'required for interaction with fbxo42' region
Similar variants
- TP53 p.Arg213fs Pathogenic ★★★ same residue
- TP53 p.Arg213_Tyr220del Likely pathogenic ★ same residue
- TP53 p.Arg213Gln Pathogenic/Likely pathogenic ★★ same residue
- TP53 p.Arg213Pro Pathogenic/Likely pathogenic ★★ same residue
- TP53 p.Arg213Ter Pathogenic ★★ same residue
- TP53 p.Arg213Gly Conflicting classifications of pathogenicity ★ ⚠ same residue
- TP53 p.Arg213Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- TP53 p.Met237Ile Pathogenic ★★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/tp53-p-arg213 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown