TAF1 p.Asp99=
c.297T>C · rs144106353 · VCV696740
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0604%, 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 0.14 | GERP 0.87, phastCons 0.99 |
| Overall | ||
| CADD | 7.928 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0604%
European (non-Finnish) · 541/895,401 alleles
Filtering AF
0.0562%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0545%
Overall
0.0473%
573/1,210,631 alleles · ultra-rare
exomes 534/1,098,229 · genomes 39/112,402 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0604% | 1,655 |
| Remaining individualsnot grpmax-eligible | 0.0252% | 3,969 |
| Middle Eastern | 0.023% | 4,356 |
| South Asian | 0.0158% | 6,324 |
| Admixed American | 0.0153% | 6,540 |
| African / African-American | 0.00523% | 19,129 |
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
- TAF1
- Protein
- p.Asp99=
- Coding
- c.297T>C
- MANE Select
- NM_004606
- dbSNP
- rs144106353
- Type
- single nucleotide variant
- Location
- chrX:71368115 (GRCh38)
- Structure
- AlphaFold pLDDT 62.62 · 65 PDB
- Residue 99
- the protein kinase 1 domain
Similar variants
- TAF1 p.Arg1062Cys Likely pathogenic ★★ ⚠ same type
- TAF1 p.Arg1234Gln Pathogenic/Likely pathogenic ★★ same type
- TAF1 p.Arg1432His Pathogenic ★★ same type
- TAF1 p.Arg870Cys Pathogenic/Likely pathogenic ★★ same type
- TAF1 p.Asn1497His Pathogenic/Likely pathogenic ★★ same type
- TAF1 p.Ile1317Thr Pathogenic ★★ same type
- TAF1 p.Phe403Val Pathogenic/Likely pathogenic ★★ same type
- TAF1 c.1774-3T>C 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/taf1-p-asp99 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown