Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.33%, eas)
Conditions
1
Woodhouse-Sakati syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.062 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.63, phastCons 1 |
| Overall | ||
| CADD | 8.996 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.33%
East Asian · 1,495/44,864 alleles
Filtering AF
3.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.14%
Overall
0.125%
2,024/1,613,878 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 3.33% | 30 |
| Remaining individualsnot grpmax-eligible | 0.536% | 187 |
| South Asian | 0.117% | 851 |
| Admixed American | 0.0483% | 2,068 |
| African / African-American | 0.0386% | 2,588 |
| Middle Eastern | 0.033% | 3,027 |
| European (non-Finnish) | 0.00229% | 43,697 |
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
- DCAF17
- Protein
- p.Ala440=
- Coding
- c.1320T>C
- MANE Select
- NM_025000
- dbSNP
- rs3731980
- Type
- single nucleotide variant
- Location
- chr2:171480091 (GRCh38)
- Gene constraint
- LOEUF 0.855 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.38
Disease context
Woodhouse-Sakati syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Woodhouse-Sakati syndrome (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Childhood
Similar variants
- DCAF17 p.Ala440Thr Uncertain significance ★★ ⚠ same residue
- DCAF17 c.127-1G>C Pathogenic/Likely pathogenic ★★ same condition
- DCAF17 p.Arg194Ter Pathogenic/Likely pathogenic ★★ same condition
- DCAF17 p.Met1Val Pathogenic/Likely pathogenic ★★ same condition
- DCAF17 p.Trp129Ter Pathogenic ★★ same condition
- DCAF17 p.Trp302Ter Pathogenic ★★ same condition
- DCAF17 c.1266+4T>C Uncertain significance ★★ same condition
- DCAF17 c.*126A>T Uncertain significance ★★ same condition
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/dcaf17-p-ala440 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown