Is DCAF10 p.Ala114Val (c.341C>T) pathogenic?

DCAF10 p.Ala114Val (c.341C>T) is classified Uncertain significance in DCAF10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-31). AlphaMissense: likely benign (0.0881); Ultra-rare (popmax 0.0667%, sas).

How common is DCAF10 p.Ala114Val (c.341C>T) in the general population?

DCAF10 p.Ala114Val (c.341C>T) is ultra-rare (popmax 0.0667%, sas) (gnomAD).

What do computational predictors say about DCAF10 p.Ala114Val (c.341C>T)?

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

DCAF10 p.Ala114Val

c.341C>T · rs745311749 · VCV2363832

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

ultra-rare (popmax 0.0667%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0881	likely benign
REVEL	0.12	moderately benign-leaning
SaProt	LLR -7.48	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 0.29	GERP 0.14, phastCons 0.001
Regional constraint	o/e 1.10	unconstrained · MANE · 447 bp · p 0.13 · 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 0.0667% South Asian · 56/83,994 alleles

Filtering AF 0.0527% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0476%

Overall 0.00824% 128/1,553,430 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0667%	1,500
Middle Eastern	0.0518%	1,929
European (non-Finnish)	0.00573%	17,458
Remaining individualsnot grpmax-eligible	0.005%	20,019

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.Ala114Val
Coding: c.341C>T
MANE Select: NM_024345
dbSNP: rs745311749
Type: single nucleotide variant
Location: chr9:37801207 (GRCh38)
Gene constraint: LOEUF 0.664 · pLI 0.06 (gnomAD)
Structure: AlphaFold pLDDT 70.93
Residue 114: the 'disordered' region

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

Similar variants

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
DCAF10 p.Arg56Ser 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-ala114val (accessed [today's date]).

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