Is DCAF16 p.Asp9Val (c.26A>T) pathogenic?

DCAF16 p.Asp9Val (c.26A>T) is classified Uncertain significance in DCAF16 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-03). AlphaMissense: likely benign (0.2498); Ultra-rare (popmax 0.0245%, eas).

How common is DCAF16 p.Asp9Val (c.26A>T) in the general population?

DCAF16 p.Asp9Val (c.26A>T) is ultra-rare (popmax 0.0245%, eas) (gnomAD).

What do computational predictors say about DCAF16 p.Asp9Val (c.26A>T)?

AlphaMissense predicts likely benign (score 0.2498) — an in-silico prediction, not a clinical call.

DCAF16 p.Asp9Val

c.26A>T · rs774129412 · VCV3080277

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2498 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0245%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2498	likely benign
REVEL	0.212	benign-leaning
SaProt	LLR -5.15	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 0.81	GERP 0.79, phastCons 0.12
Regional constraint	o/e 1.01	unconstrained · MANE · 647 bp · p 0.93 · regional, not allelic
Overall
CADD	20.0	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 0.0245% East Asian · 11/44,872 alleles

Filtering AF 0.0137% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0106%

Overall 0.000744% 12/1,613,884 alleles · ultra-rare exomes 12/1,461,666 · genomes 0/152,218 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0245%	4,079
Remaining individualsnot grpmax-eligible	0.0016%	62,488

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: DCAF16
Protein: p.Asp9Val
Coding: c.26A>T
MANE Select: NM_017741
dbSNP: rs774129412
Type: single nucleotide variant
Location: chr4:17804116 (GRCh38)
Gene constraint: LOEUF 0.985 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 38.26 · 3 PDB
Residue 9: the 'disordered' region

Full DCAF16 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCAF16 p.Ala144Thr Uncertain significance ★ ⚠ same type
DCAF16 p.Ala78Thr Uncertain significance ★ ⚠ same type
DCAF16 p.Arg191His Uncertain significance ★ ⚠ same type
DCAF16 p.Arg91Gln Uncertain significance ★ ⚠ same type
DCAF16 p.Arg96Ser Uncertain significance ★ ⚠ same type
DCAF16 p.Asn171Ser Uncertain significance ★ ⚠ same type
DCAF16 p.Asp137Glu Uncertain significance ★ ⚠ same type
DCAF16 p.Glu27Asp Uncertain significance ★ ⚠ same type

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/dcaf16-p-asp9val (accessed [today's date]).

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