Is DCAF17 p.Ile305Val (c.913A>G) pathogenic?

DCAF17 p.Ile305Val (c.913A>G) is classified Uncertain significance in DCAF17 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2022-08-16). AlphaMissense: likely benign (0.2038); Ultra-rare (popmax 0.0694%, nfe); Associated with Inborn genetic diseases.

What condition is associated with DCAF17 p.Ile305Val (c.913A>G)?

DCAF17 p.Ile305Val (c.913A>G) is associated with Inborn genetic diseases, Woodhouse-Sakati syndrome (ClinVar).

How common is DCAF17 p.Ile305Val (c.913A>G) in the general population?

DCAF17 p.Ile305Val (c.913A>G) is ultra-rare (popmax 0.0694%, nfe) (gnomAD).

What do computational predictors say about DCAF17 p.Ile305Val (c.913A>G)?

AlphaMissense predicts likely benign (score 0.2038) — an in-silico prediction, not a clinical call.

DCAF17 p.Ile305Val

c.913A>G · rs114419034 · VCV332268

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.2038 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0694%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.2038	likely benign
REVEL	0.245	benign-leaning
SaProt	LLR -6.34	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 11	GERP 1.7, phastCons 1
Regional constraint	o/e 0.36	unconstrained · MANE · 89 bp · p 0.00015 · regional, not allelic
Overall
CADD	23.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0694% European (non-Finnish) · 819/1,179,998 alleles

Filtering AF 0.0654% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0639%

Overall 0.053% 855/1,614,150 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0694%	1,441
Remaining individualsnot grpmax-eligible	0.0272%	3,677
Finnishnot grpmax-eligible	0.0109%	9,149
African / African-American	0.00933%	10,721
Admixed American	0.00833%	12,005

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.Ile305Val
Coding: c.913A>G
MANE Select: NM_025000
dbSNP: rs114419034
Type: single nucleotide variant
Location: chr2:171468962 (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.Ile305= Likely benign ★ 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-ile305val (accessed [today's date]).

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