Is DCAF13 p.Val235Phe (c.703G>T) pathogenic?

DCAF13 p.Val235Phe (c.703G>T) is classified Uncertain significance in DCAF13 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-09). AlphaMissense: ambiguous (0.5636); Very rare (popmax 0.000348%, nfe).

How common is DCAF13 p.Val235Phe (c.703G>T) in the general population?

DCAF13 p.Val235Phe (c.703G>T) is very rare (popmax 0.000348%, nfe) (gnomAD).

What do computational predictors say about DCAF13 p.Val235Phe (c.703G>T)?

AlphaMissense predicts ambiguous (score 0.5636) — an in-silico prediction, not a clinical call.

DCAF13 p.Val235Phe

c.703G>T · VCV3499867

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5636 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000348%, nfe)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5636	ambiguous
REVEL	0.273	benign-leaning
SaProt	LLR -11.14	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	Δ0.21	acceptor gain · deltas
Pangolin	Δ0.26	loss · gain 0.06 · SpliceAI calls gain · independent
Constraint at this position
Conservation	phyloP 12	GERP 1.9, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 25 kb · p 0.027 · regional, not allelic
Overall
CADD	34.0	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 0.000348% European (non-Finnish) · 4/1,149,696 alleles

Filtering AF 8.1e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.5e-05%

Overall 0.000254% 4/1,576,316 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: DCAF13
Protein: p.Val235Phe
Coding: c.703G>T
MANE Select: NM_015420
Type: single nucleotide variant
Location: chr8:103432659 (GRCh38)
Gene constraint: LOEUF 0.848 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.84 · 3 PDB
Residue 235: a β-strand

Full DCAF13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DCAF13 p.His327Arg Uncertain significance ★★ ⚠ same type
DCAF13 p.Phe381Cys Uncertain significance ★★ ⚠ same type
DCAF13 p.Ala109Gly Benign ★★ same type
DCAF13 p.Ala70= Benign ★★ same type
DCAF13 c.-20C>T Uncertain significance ★ same type
DCAF13 c.-30T>C Uncertain significance ★ same type
DCAF13 c.-33A>G Uncertain significance ★ same type
DCAF13 c.-38C>A 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/dcaf13-p-val235phe (accessed [today's date]).

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