TP63 p.Gln11=
c.33A>G · rs779762640 · VCV502432
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00341%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 8 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 19.09 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00341%
South Asian · 3/87,856 alleles
Filtering AF
0.000907%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000452%
Overall
0.000438%
7/1,597,396 alleles · very rare
exomes 7/1,445,332 · genomes 0/152,064 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00341% | 29,285 |
| Admixed American | 0.00172% | 58,032 |
| Remaining individualsnot grpmax-eligible | 0.00162% | 61,872 |
| African / African-American | 0.00135% | 74,102 |
| European (non-Finnish) | 8.53e-05% | 1,171,840 |
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
- TP63
- Protein
- p.Gln11=
- Coding
- c.33A>G
- MANE Select
- NM_003722 · reported on NM_001114980
- dbSNP
- rs779762640
- Type
- single nucleotide variant
- Location
- chr3:189789833 (GRCh38)
- Gene constraint
- LOEUF 0.296 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.70 · 26 PDB
- Residue 11
- the 'transcription activation' region
Similar variants
- TP63 p.Ala354Glu Likely pathogenic ★★ same type
- TP63 p.Arg243Gln Pathogenic/Likely pathogenic ★★ same type
- TP63 p.Arg243Trp Pathogenic ★★ same type
- TP63 p.Arg266Gln Pathogenic/Likely pathogenic ★★ same type
- TP63 p.Arg318Cys Pathogenic ★★ same type
- TP63 p.Arg318His Pathogenic/Likely pathogenic ★★ same type
- TP63 p.Arg319Cys Pathogenic/Likely pathogenic ★★ same type
- TP63 p.Arg319His Pathogenic ★★ same type
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-gln11 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown