TP73 p.Thr247=
c.741G>A · rs140541850 · VCV719698
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0946%, nfe)
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 -9.6 | GERP -4.4 |
| Overall | ||
| CADD | 2.042 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0946%
European (non-Finnish) · 1,116/1,179,292 alleles
Filtering AF
0.09%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0881%
Overall
0.0814%
1,312/1,611,680 alleles · ultra-rare
exomes 1,213/1,459,470 · genomes 99/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0946% | 1,057 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0881% | 1,135 |
| South Asian | 0.0813% | 1,230 |
| Admixed American | 0.0551% | 1,816 |
| Remaining individualsnot grpmax-eligible | 0.0545% | 1,836 |
| African / African-American | 0.0307% | 3,259 |
| Finnishnot grpmax-eligible | 0.00957% | 10,452 |
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
- TP73
- Protein
- p.Thr247=
- Coding
- c.741G>A
- MANE Select
- NM_005427
- dbSNP
- rs140541850
- Type
- single nucleotide variant
- Location
- chr1:3727123 (GRCh38)
- Gene constraint
- LOEUF 0.576 · pLI 0.29 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.25 · 28 PDB
- Residue 247
- a UniProt-annotated variant site (in cild47); the 'dna-binding' region
Similar variants
- TP73 p.Arg538Cys Uncertain significance ★★ ⚠ same type
- TP73 p.Gly451Arg Uncertain significance ★★ ⚠ same type
- TP73 c.65+9G>A Benign/Likely benign ★★ same type
- TP73 p.Ala325Thr Benign ★★ same type
- TP73 p.Gln391= Benign ★★ same type
- TP73 p.His418= Benign/Likely benign ★★ same type
- TP73 p.Ser563= Benign ★★ same type
- TP73 p.Thr136= Benign/Likely benign ★★ 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/tp73-p-thr247 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown