Is DCAF17 p.Arg73Cys (c.217C>T) pathogenic?

DCAF17 p.Arg73Cys (c.217C>T) is classified Conflicting classifications of pathogenicity in DCAF17 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2022-09-05). AlphaMissense: likely benign (0.0463); Very rare (popmax 0.00223%, eas); Associated with Inborn genetic diseases.

What condition is associated with DCAF17 p.Arg73Cys (c.217C>T)?

DCAF17 p.Arg73Cys (c.217C>T) is associated with Inborn genetic diseases, Woodhouse-Sakati syndrome (ClinVar).

How common is DCAF17 p.Arg73Cys (c.217C>T) in the general population?

DCAF17 p.Arg73Cys (c.217C>T) is very rare (popmax 0.00223%, eas) (gnomAD).

What do computational predictors say about DCAF17 p.Arg73Cys (c.217C>T)?

AlphaMissense predicts likely benign (score 0.0463) — an in-silico prediction, not a clinical call.

DCAF17 p.Arg73Cys

c.217C>T · rs766629618 · VCV2085772

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0463 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00223%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0463	likely benign
REVEL	0.185	benign-leaning
SaProt	LLR -7.32	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 6	GERP 0.48, phastCons 1
Regional constraint	o/e 0.98	unconstrained · MANE · 34 kb · p 0.67 · regional, not allelic
Overall
CADD	21.7	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00223% East Asian · 1/44,856 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.000248% 4/1,612,418 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00223%	44,856
African / African-American	0.00134%	74,846
European (non-Finnish)	0.00017%	589,352

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.Arg73Cys
Coding: c.217C>T
MANE Select: NM_025000
dbSNP: rs766629618
Type: single nucleotide variant
Location: chr2:171435173 (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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Woodhouse-Sakati syndrome

Similar variants

DCAF17 p.Arg73Leu 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-arg73cys (accessed [today's date]).

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