Is DCAF17 p.Pro3= (c.9G>T) pathogenic?

DCAF17 p.Pro3= (c.9G>T) is classified Likely benign in DCAF17 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-03-14). Very rare (popmax 0.0012%, sas); Associated with Woodhouse-Sakati syndrome.

What condition is associated with DCAF17 p.Pro3= (c.9G>T)?

DCAF17 p.Pro3= (c.9G>T) is associated with Woodhouse-Sakati syndrome (ClinVar).

How common is DCAF17 p.Pro3= (c.9G>T) in the general population?

DCAF17 p.Pro3= (c.9G>T) is very rare (popmax 0.0012%, sas) (gnomAD).

How is Woodhouse-Sakati syndrome inherited?

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

DCAF17 p.Pro3=

c.9G>T · rs886104338 · VCV2086006

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.0012%, sas)

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
Pangolin	Δ0.39	gain · loss 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 0.55	GERP -2.6, phastCons 0.033
Overall
CADD	12.24	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0012% South Asian · 1/83,500 alleles

Overall 0.000145% 2/1,375,280 alleles · very rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0012%	83,500
European (non-Finnish)	8.74e-05%	1,143,696

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.Pro3=
Coding: c.9G>T
MANE Select: NM_025000
dbSNP: rs886104338
Type: single nucleotide variant
Location: chr2:171434586 (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-pro3 (accessed [today's date]).

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