DCAF4 p.Ser32=
c.96T>C · VCV3499885
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0184%, amr)
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 -4 | GERP -5.2 |
| Overall | ||
| CADD | 0.35 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0184%
Admixed American · 11/59,644 alleles
Filtering AF
0.0103%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.008%
Overall
0.00217%
35/1,611,064 alleles · ultra-rare
exomes 29/1,458,858 · genomes 6/152,206 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0184% | 5,422 |
| Remaining individualsnot grpmax-eligible | 0.00641% | 15,589 |
| European (non-Finnish) | 0.00161% | 62,037 |
| African / African-American | 0.00134% | 74,852 |
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
- DCAF4
- Protein
- p.Ser32=
- Coding
- c.96T>C
- MANE Select
- NM_015604
- Type
- single nucleotide variant
- Location
- chr14:72939805 (GRCh38)
- Gene constraint
- LOEUF 0.787 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.34 · 1 PDB
- Residue 32
- the 'disordered' region
Similar variants
- DCAF4 p.Ser28= Benign ★★ same type
- DCAF4 p.Ser325Gly Likely benign ★★ same type
- DCAF4 p.Ala125Val Uncertain significance ★ ⚠ same type
- DCAF4 p.Ala168Gly Uncertain significance ★ ⚠ same type
- DCAF4 p.Ala179Thr Uncertain significance ★ ⚠ same type
- DCAF4 p.Ala233Val Uncertain significance ★ ⚠ same type
- DCAF4 p.Ala285Ser Uncertain significance ★ ⚠ same type
- DCAF4 p.Ala461Thr 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/dcaf4-p-ser32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown