TP63 p.Ser580fs
c.1739_1740del · VCV4965462
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
TP63-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a LoF-intolerant gene |
|---|---|---|
| NMD | escapes | premature termination codon within the last 50 nt of the penultimate exon (13 of 14, 7 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 5.1 | GERP 2.9, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- TP63
- Protein
- p.Ser580fs
- Coding
- c.1739_1740del
- MANE Select
- NM_003722
- Type
- Deletion
- Location
- chr3:189890875 (GRCh38)
- Gene constraint
- LOEUF 0.296 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.70 · 26 PDB
- Residue 580
- the sam domain; a UniProt-annotated variant site (in rhs)
Similar variants
- TP63 p.Gln9fs Pathogenic ★★ same condition
- TP63 p.Ile324del Likely pathogenic ★★ same condition
- TP63 p.Ala234fs Likely pathogenic ★ same condition
- TP63 p.Ser580Pro Pathogenic same residue
- TP63 p.Arg243Gln Pathogenic/Likely pathogenic ★★ same condition
- TP63 p.Arg243Trp Pathogenic ★★ same condition
- TP63 p.Arg266Gln Pathogenic/Likely pathogenic ★★ same condition
- TP63 p.Arg318Cys 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/tp63-p-ser580fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown