TFAP2A p.Pro61=
c.183C>T · rs1270082486 · VCV2703813
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000117%, nfe)
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 7.3 | GERP -3.8, phastCons 1 |
| Overall | ||
| CADD | 16.13 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000117%
European (non-Finnish) · 1/857,376 alleles
Overall
8.47e-05%
1/1,180,570 alleles · very rare
exomes 0/1,041,884 · genomes 1/138,686 · joint denominator
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
- TFAP2A
- Protein
- p.Pro61=
- Coding
- c.183C>T
- MANE Select
- NM_001372066
- dbSNP
- rs1270082486
- Type
- single nucleotide variant
- Location
- chr6:10410204 (GRCh38)
- Gene constraint
- LOEUF 0.334 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 67.76 · 3 PDB
- Residue 61
- the 'disordered' region
Similar variants
- TFAP2A p.Ala258Val Pathogenic/Likely pathogenic ★★ same type
- TFAP2A p.Arg239Gln Pathogenic/Likely pathogenic ★★ same type
- TFAP2A p.Arg325Ter Pathogenic ★★ same type
- TFAP2A p.Gln32Ter Likely pathogenic ★★ same type
- TFAP2A p.Glu235Lys Likely pathogenic ★★ same type
- TFAP2A p.His386Tyr Likely pathogenic ★★ same type
- TFAP2A p.Ala342Pro Uncertain significance ★★ ⚠ same type
- TFAP2A p.Asn287Ser Uncertain significance ★★ ⚠ 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/tfap2a-p-pro61 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown