TAF4 p.Pro662=
c.1986C>T · VCV3777827
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0829%, nfe)
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 -1.9 | GERP -3.5 |
| Overall | ||
| CADD | 9.161 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0829%
European (non-Finnish) · 934/1,127,062 alleles
Filtering AF
0.0784%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0766%
Overall
0.0677%
1,032/1,523,610 alleles · ultra-rare
exomes 945/1,371,264 · genomes 87/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0829% | 1,207 |
| Remaining individualsnot grpmax-eligible | 0.0465% | 2,152 |
| African / African-American | 0.0391% | 2,554 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0352% | 2,841 |
| South Asian | 0.0333% | 2,999 |
| Middle Eastern | 0.0177% | 5,638 |
| Admixed American | 0.00595% | 16,819 |
| Finnishnot grpmax-eligible | 0.00486% | 20,590 |
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
- TAF4
- Protein
- p.Pro662=
- Coding
- c.1986C>T
- MANE Select
- NM_003185
- Type
- single nucleotide variant
- Location
- chr20:62006747 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.71 · 32 PDB
- Residue 662
- the tafh domain; a UniProt-annotated variant site (in mrd73; likely pathogenic); an α-helix
Similar variants
- TAF4 p.Ala153Val Uncertain significance ★★ ⚠ same type
- TAF4 p.Ala251Thr Uncertain significance ★★ ⚠ same type
- TAF4 p.Arg774Gln Uncertain significance ★★ ⚠ same type
- TAF4 p.Gly171Cys Uncertain significance ★★ ⚠ same type
- TAF4 p.Gly306Glu Uncertain significance ★★ ⚠ same type
- TAF4 p.Leu58Val Uncertain significance ★★ ⚠ same type
- TAF4 p.Pro241Leu Uncertain significance ★★ ⚠ same type
- TAF4 p.Asn220Ser Likely benign ★★ 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/taf4-p-pro662 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown