Is DDX20 p.Phe403Val (c.1207T>G) pathogenic?

DDX20 p.Phe403Val (c.1207T>G) is classified Uncertain significance in DDX20 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-01-23). AlphaMissense: likely pathogenic (0.9686); Absent from gnomAD v4.1.

How common is DDX20 p.Phe403Val (c.1207T>G) in the general population?

DDX20 p.Phe403Val (c.1207T>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DDX20 p.Phe403Val (c.1207T>G)?

AlphaMissense predicts likely pathogenic (score 0.9686) — an in-silico prediction, not a clinical call.

DDX20 p.Phe403Val

c.1207T>G · rs2524942860 · VCV2466979

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9686 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,607,982)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9686	likely pathogenic · top 9% in DDX20
REVEL	0.883	moderately pathogenic-leaning
SaProt	LLR -9.98	tolerated
⇒ AlphaMissense and REVEL call this damaging; SaProt does not.
Splicing
SpliceAI	Δ0.33	donor gain · deltas
Constraint at this position
Conservation	phyloP 7.9	GERP 1.6, phastCons 1
Regional constraint	o/e 0.91	unconstrained · MANE · 6,154 bp · p 0.016 · 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

No allele count reported in gnomAD v4.1 (AN 1,607,982). 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: DDX20
Protein: p.Phe403Val
Coding: c.1207T>G
MANE Select: NM_007204
dbSNP: rs2524942860
Type: single nucleotide variant
Location: chr1:111762779 (GRCh38)
Gene constraint: LOEUF 0.965 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 61.40 · 2 PDB
Residue 403: the helicase c-terminal domain

Full DDX20 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DDX20 p.Ala592Asp Benign ★★ same type
DDX20 p.Ala10Thr Uncertain significance ★ ⚠ same type
DDX20 p.Ala12Val Uncertain significance ★ ⚠ same type
DDX20 p.Ala2Gly Uncertain significance ★ ⚠ same type
DDX20 p.Ala326Val Uncertain significance ★ ⚠ same type
DDX20 p.Ala336Asp Uncertain significance ★ ⚠ same type
DDX20 p.Ala375Thr Uncertain significance ★ ⚠ same type
DDX20 p.Ala791Thr 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/ddx20-p-phe403val (accessed [today's date]).

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