TAF4 p.Pro390=
c.1170G>A · rs2516038223 · VCV2652464
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00378%, sas)
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 -0.93 | GERP -1.1, phastCons 0.23 |
| Overall | ||
| CADD | 7.899 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00378%
South Asian · 2/52,888 alleles
Filtering AF
0.000627%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000235%
Overall
0.000301%
4/1,331,002 alleles · very rare
exomes 4/1,181,752 · genomes 0/149,250 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00378% | 26,444 |
| Remaining individualsnot grpmax-eligible | 0.00201% | 49,810 |
| European (non-Finnish) | 9.54e-05% | 1,047,924 |
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.Pro390=
- Coding
- c.1170G>A
- MANE Select
- NM_003185
- dbSNP
- rs2516038223
- Type
- single nucleotide variant
- Location
- chr20:62064641 (GRCh38)
- Gene constraint
- LOEUF 0.205 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.71 · 32 PDB
- Residue 390
- the 'disordered' region
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-pro390 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown