TAF1 p.Asp3=
c.9C>T · VCV4951473
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0238%, mid)
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 -1.6 | GERP -1.5 |
| Overall | ||
| CADD | 5.785 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0238%
Middle Eastern · 1/4,202 alleles
Filtering AF
0.00171%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00143%
Overall
0.00248%
30/1,210,978 alleles · ultra-rare
exomes 30/1,097,942 · genomes 0/113,036 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0238% | 4,202 |
| Finnishnot grpmax-eligible | 0.00855% | 11,699 |
| European (non-Finnish) | 0.00257% | 38,931 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,604 |
| South Asian | 0.00176% | 56,958 |
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.Asp3=
- Coding
- c.9C>T
- MANE Select
- NM_004606
- Type
- single nucleotide variant
- Location
- chrX:71366383 (GRCh38)
- Structure
- AlphaFold pLDDT 62.62 · 65 PDB
- Residue 3
- 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-asp3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown