Is DCAF10 p.Pro22Leu (c.65C>T) pathogenic?

DCAF10 p.Pro22Leu (c.65C>T) is classified Uncertain significance in DCAF10 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-15). AlphaMissense: likely benign (0.0881); Very rare (popmax 8.86e-05%, nfe).

How common is DCAF10 p.Pro22Leu (c.65C>T) in the general population?

DCAF10 p.Pro22Leu (c.65C>T) is very rare (popmax 8.86e-05%, nfe) (gnomAD).

What do computational predictors say about DCAF10 p.Pro22Leu (c.65C>T)?

AlphaMissense predicts likely benign (score 0.0881) — an in-silico prediction, not a clinical call.

DCAF10 p.Pro22Leu

c.65C>T · rs2489926515 · VCV2618752

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0881 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.86e-05%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0881	likely benign
REVEL	0.143	moderately benign-leaning
SaProt	LLR -7.49	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 0.09	GERP 0.16, phastCons 0.001
Regional constraint	o/e 1.10	unconstrained · MANE · 447 bp · p 0.13 · regional, not allelic
Overall
CADD	10.19	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 8.86e-05% European (non-Finnish) · 1/1,129,272 alleles

Overall 7.45e-05% 1/1,341,480 alleles · very rare

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: DCAF10
Protein: p.Pro22Leu
Coding: c.65C>T
MANE Select: NM_024345
dbSNP: rs2489926515
Type: single nucleotide variant
Location: chr9:37800931 (GRCh38)
Gene constraint: LOEUF 0.664 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 70.93
Residue 22: the 'disordered' region

Full DCAF10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCAF10 p.Ala114Val Uncertain significance ★ ⚠ same type
DCAF10 p.Ala44Val Uncertain significance ★ ⚠ same type
DCAF10 p.Arg130Cys Uncertain significance ★ ⚠ same type
DCAF10 p.Arg146His Uncertain significance ★ ⚠ same type
DCAF10 p.Arg223Gln Uncertain significance ★ ⚠ same type
DCAF10 p.Arg383Pro Uncertain significance ★ ⚠ same type
DCAF10 p.Arg522Cys Uncertain significance ★ ⚠ same type
DCAF10 p.Arg52Gln 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/dcaf10-p-pro22leu (accessed [today's date]).

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