Is DCAF17 p.Arg30= (c.90G>A) pathogenic?

DCAF17 p.Arg30= (c.90G>A) is classified Likely benign in DCAF17 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-08). Ultra-rare (popmax 0.0197%, mid); Associated with Woodhouse-Sakati syndrome.

What condition is associated with DCAF17 p.Arg30= (c.90G>A)?

DCAF17 p.Arg30= (c.90G>A) is associated with Woodhouse-Sakati syndrome (ClinVar).

How common is DCAF17 p.Arg30= (c.90G>A) in the general population?

DCAF17 p.Arg30= (c.90G>A) is ultra-rare (popmax 0.0197%, mid) (gnomAD).

How is Woodhouse-Sakati syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DCAF17 p.Arg30=

c.90G>A · rs1693695297 · VCV2918775

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0197%, mid)

Conditions

Woodhouse-Sakati syndrome

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 7.6	GERP 1.9, phastCons 1
Overall
CADD	16.29	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0197% Middle Eastern · 1/5,068 alleles

Filtering AF 0.00056% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000442%

Overall 0.00105% 16/1,521,406 alleles · ultra-rare exomes 16/1,369,154 · genomes 0/152,252 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.0197%	5,068
Remaining individualsnot grpmax-eligible	0.00508%	19,669
European (non-Finnish)	0.00105%	95,289

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.Arg30=
Coding: c.90G>A
MANE Select: NM_025000
dbSNP: rs1693695297
Type: single nucleotide variant
Location: chr2:171434667 (GRCh38)
Gene constraint: LOEUF 0.855 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 87.38

Full DCAF17 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Woodhouse-Sakati syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Woodhouse-Sakati syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Childhood

Similar variants

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
DCAF17 p.Ala242Thr 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-arg30 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown