TP63 p.Ser38=
c.114C>T · rs779485146 · VCV3032212
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00833%, amr)
Conditions
1
TP63-related disorder
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 -2.1 | GERP -0.6 |
| Overall | ||
| CADD | 7.386 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00833%
Admixed American · 5/59,994 alleles
Filtering AF
0.00323%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00207%
Overall
0.00266%
43/1,613,850 alleles · very rare
exomes 39/1,461,692 · genomes 4/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00833% | 11,999 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,619 |
| European (non-Finnish) | 0.00271% | 36,872 |
| African / African-American | 0.00267% | 37,453 |
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.Ser38=
- Coding
- c.114C>T
- MANE Select
- NM_003722
- dbSNP
- rs779485146
- Type
- single nucleotide variant
- Location
- chr3:189737791 (GRCh38)
- Gene constraint
- LOEUF 0.296 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 63.70 · 26 PDB
- Residue 38
- the 'transcription activation' region
Similar variants
- 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
- TP63 p.Arg319Cys Pathogenic/Likely pathogenic ★★ same condition
- TP63 p.Arg319His Pathogenic ★★ same condition
- TP63 p.Arg337Gln Pathogenic/Likely pathogenic ★★ same condition
- TP63 p.Arg337Ter Pathogenic/Likely 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-ser38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown