DCAF4 p.Ser54=
c.162G>A · VCV4658617
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.267%, afr)
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 -4.7 |
| Overall | ||
| CADD | 4.608 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.267%
African / African-American · 200/74,970 alleles
Filtering AF
0.236%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.225%
Overall
0.014%
225/1,611,488 alleles · rare
exomes 111/1,459,140 · genomes 114/152,348 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.267% | 375 |
| Middle Eastern | 0.033% | 3,029 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,238 |
| Admixed American | 0.0134% | 7,476 |
| European (non-Finnish) | 0.000424% | 235,782 |
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.Ser54=
- Coding
- c.162G>A
- MANE Select
- NM_015604
- Type
- single nucleotide variant
- Location
- chr14:72939871 (GRCh38)
- Gene constraint
- LOEUF 0.787 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.34 · 1 PDB
- Residue 54
- the 'disordered' region
Similar variants
- DCAF4 p.Ser54Ala Uncertain significance ★ ⚠ same residue
- 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
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-ser54 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown