TFAP2B p.Asp159=
c.477C>T · rs1179960017 · VCV1981598
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00405%, afr)
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 -0.19 | GERP -0.94, phastCons 0.26 |
| Overall | ||
| CADD | 6.675 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00405%
African / African-American · 3/74,102 alleles
Filtering AF
0.00108%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000498%
Overall
0.000317%
5/1,579,136 alleles · very rare
exomes 2/1,426,942 · genomes 3/152,194 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00405% | 24,701 |
| European (non-Finnish) | 0.000172% | 581,335 |
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.Asp159=
- Coding
- c.477C>T
- MANE Select
- NM_003221
- dbSNP
- rs1179960017
- Type
- single nucleotide variant
- Location
- chr6:50823802 (GRCh38)
- Gene constraint
- LOEUF 0.353 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.95 · 1 PDB
Similar variants
- 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
- TFAP2B p.Ser277Trp Uncertain significance ★★ ⚠ same type
- TFAP2B p.Thr306Met 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-asp159 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown