Is DDX52 p.Val593Ile (c.1777G>A) pathogenic?

DDX52 p.Val593Ile (c.1777G>A) is classified Uncertain significance in DDX52 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-07). AlphaMissense: likely benign (0.0682); Absent from gnomAD v4.1.

How common is DDX52 p.Val593Ile (c.1777G>A) in the general population?

DDX52 p.Val593Ile (c.1777G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DDX52 p.Val593Ile (c.1777G>A)?

AlphaMissense predicts likely benign (score 0.0682) — an in-silico prediction, not a clinical call.

DDX52 p.Val593Ile

c.1777G>A · VCV3500625

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0682 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,612,862)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0682	likely benign
REVEL	0.044	moderately benign-leaning
SaProt	LLR -6.70	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 1.9	GERP 1.5, phastCons 0.97
Overall
CADD	17.31	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

No allele count reported in gnomAD v4.1 (AN 1,612,862). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DDX52
Protein: p.Val593Ile
Coding: c.1777G>A
MANE Select: NM_007010
Type: single nucleotide variant
Location: chr17:37614319 (GRCh38)
Gene constraint: LOEUF 0.889 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 76.69 · 1 PDB
Residue 593: the 'disordered' region

Full DDX52 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DDX52 p.Ala247Thr Uncertain significance ★ ⚠ same type
DDX52 p.Ala26Ser Uncertain significance ★ ⚠ same type
DDX52 p.Ala336Pro Uncertain significance ★ ⚠ same type
DDX52 p.Ala354Val Uncertain significance ★ ⚠ same type
DDX52 p.Ala534Ser Uncertain significance ★ ⚠ same type
DDX52 p.Arg136Thr Uncertain significance ★ ⚠ same type
DDX52 p.Arg144Gln Uncertain significance ★ ⚠ same type
DDX52 p.Arg144Trp 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/ddx52-p-val593ile (accessed [today's date]).

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