Is DDX3X p.Val321del (c.959TAG[1]) pathogenic?

DDX3X p.Val321del (c.959TAG[1]) is classified Conflicting classifications of pathogenicity in DDX3X (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2024-01-04). Absent from gnomAD; Associated with intellectual disability, X-linked 102.

What condition is associated with DDX3X p.Val321del (c.959TAG[1])?

DDX3X p.Val321del (c.959TAG[1]) is associated with intellectual disability, X-linked 102 (ClinVar).

How common is DDX3X p.Val321del (c.959TAG[1]) in the general population?

DDX3X p.Val321del (c.959TAG[1]) is absent from gnomAD (gnomAD).

DDX3X p.Val321del

c.959TAG[1] · rs1555953527 · VCV451203

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual disability, X-linked 102

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.23	GERP -4.5, phastCons 0.48

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: DDX3X
Protein: p.Val321del
Coding: c.959TAG[1]
MANE Select: NM_001356
dbSNP: rs1555953527
Type: Microsatellite
Location: chrX:41344333 (GRCh38)
Structure: AlphaFold pLDDT 73.24 · 17 PDB
Residue 321: a β-strand; the helicase atp-binding domain; the 'interaction with gsk3b' region

Full DDX3X gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability, X-linked 102 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DDX3X p.Leu560del Pathogenic/Likely pathogenic ★★ same condition
DDX3X p.Phe402del Pathogenic/Likely pathogenic ★★ same condition
DDX3X p.Pro41del Pathogenic/Likely pathogenic ★★ same condition
DDX3X p.Phe85del Uncertain significance ★★ same condition
DDX3X p.Asn174fs Likely pathogenic ★ same condition
DDX3X p.Lys35fs Pathogenic ★ same condition
DDX3X c.103+4_103+7del Uncertain significance ★ same condition
DDX3X p.Pro142del Uncertain significance ★ same condition

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/ddx3x-p-val321del (accessed [today's date]).

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