TFAP2B p.Arg39=
c.117G>A · rs367843046 · VCV3037790
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00507%, amr)
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 4.9 | GERP -0.6, phastCons 1 |
| Overall | ||
| CADD | 12.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00507%
Admixed American · 3/59,194 alleles
Filtering AF
0.00135%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000673%
Overall
0.000436%
7/1,606,600 alleles · very rare
exomes 7/1,454,778 · genomes 0/151,822 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00507% | 19,731 |
| Remaining individualsnot grpmax-eligible | 0.00322% | 31,074 |
| African / African-American | 0.00134% | 74,652 |
| European (non-Finnish) | 8.5e-05% | 1,176,854 |
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
- TFAP2B
- Protein
- p.Arg39=
- Coding
- c.117G>A
- MANE Select
- NM_003221
- dbSNP
- rs367843046
- Type
- single nucleotide variant
- Location
- chr6:50823442 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.95 · 1 PDB
- Residue 39
- the 'disordered' region
Similar variants
- TFAP2B p.Arg39Leu Uncertain significance ★ ⚠ same residue
- TFAP2B p.Arg39Pro Uncertain significance ★ ⚠ same residue
- TFAP2B p.Arg236His Likely pathogenic ★★ same type
- TFAP2B p.Arg285Gln Pathogenic/Likely pathogenic ★★ same type
- TFAP2B p.Ala54Gly Uncertain significance ★★ same type
- TFAP2B p.Asp31Gly Uncertain significance ★★ ⚠ same type
- TFAP2B p.Asp346Glu Uncertain significance ★★ same type
- TFAP2B p.Pro205Ser 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/tfap2b-p-arg39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown