TP53 p.Phe113del
c.336CTT[1] · rs764486868 · VCV811715
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
3
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 · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.032 | GERP 0.079, phastCons 0.59 |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- TP53
- Protein
- p.Phe113del
- Coding
- c.336CTT[1]
- MANE Select
- NM_000546
- dbSNP
- rs764486868
- Type
- Microsatellite
- Location
- chr17:7676028 (GRCh38)
- Gene constraint
- LOEUF 0.449 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.83 · 321 PDB
- Residue 113
- a DNA-binding region; the 'interaction with ccar2' region; a UniProt-annotated variant site (in sporadic cancers; somatic mutation); a UniProt-annotated variant site (in a sporadic cancer; somatic mutation; requires 2 nucleotide substitutions); a UniProt-annotated variant site (in a sporadic cancer; somatic mutation); the 'interaction with hipk1' region; the 'required for interaction with znf385a' region; the 'required for interaction with fbxo42' region
Similar variants
- TP53 p.Phe113Ile Likely pathogenic ★★★ same residue
- TP53 p.Phe113Val Likely pathogenic ★★★ same residue
- TP53 p.Phe113Ser Pathogenic/Likely pathogenic ★★ same residue
- TP53 p.Phe113_Gly117del Pathogenic ★ same residue
- TP53 p.Phe113Cys Pathogenic ★ same residue
- TP53 p.Phe113Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- TP53 p.Asn30del Likely benign ★★★ same condition
- TP53 p.Gln317fs 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-phe113del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown