Is TP53 p.Thr211= (c.633T>C) pathogenic?

TP53 p.Thr211= (c.633T>C) is classified Benign in TP53 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-03). Very rare (popmax 8.47e-05%, nfe); Associated with Li-Fraumeni syndrome 1.

What condition is associated with TP53 p.Thr211= (c.633T>C)?

TP53 p.Thr211= (c.633T>C) is associated with Li-Fraumeni syndrome 1 (ClinVar).

How common is TP53 p.Thr211= (c.633T>C) in the general population?

TP53 p.Thr211= (c.633T>C) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

TP53 p.Thr211=

c.633T>C · VCV4071446

Benign Single submitter

Classification

Benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

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 0.96	GERP -3.8, phastCons 0.99
Overall
CADD	9.661	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,016 alleles

Overall 6.84e-05% 1/1,461,892 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: TP53
Protein: p.Thr211=
Coding: c.633T>C
MANE Select: NM_000546
Type: single nucleotide variant
Location: chr17:7674898 (GRCh38)
Gene constraint: LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 75.83 · 321 PDB
Residue 211: a DNA-binding region; the 'interaction with axin1' region; a turn; 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 a sporadic cancer; somatic mutation); the 'required for interaction with znf385a' region; the 'required for interaction with fbxo42' region

Full TP53 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Li-Fraumeni syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

TP53 p.Thr211fs Pathogenic ★★ same residue
TP53 p.Thr211Ala Uncertain significance ★★ ⚠ same residue
TP53 p.Thr211Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Thr211Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
TP53 p.Thr211Ser Uncertain significance ★ ⚠ same residue
TP53 p.Met237Ile Pathogenic ★★★ ⚠ same condition
TP53 p.Val272Met Pathogenic ★★★ same condition
TP53 p.Arg156His Uncertain significance ★★★ ⚠ 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-thr211 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown