Is DDX3X p.Arg276fs (c.828_831del) pathogenic?

DDX3X p.Arg276fs (c.828831del) is classified Pathogenic in DDX3X (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-05-07). Absent from gnomAD; Associated with intellectual disability, X-linked 102.

What condition is associated with DDX3X p.Arg276fs (c.828_831del)?

DDX3X p.Arg276fs (c.828_831del) is associated with intellectual disability, X-linked 102 (ClinVar).

How common is DDX3X p.Arg276fs (c.828_831del) in the general population?

DDX3X p.Arg276fs (c.828_831del) is absent from gnomAD (gnomAD).

DDX3X p.Arg276fs

c.828_831del · rs1602131859 · VCV989448

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

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.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 9 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6	GERP 2.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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.Arg276fs
Coding: c.828_831del
MANE Select: NM_001356
dbSNP: rs1602131859
Type: Microsatellite
Location: chrX:41344089 (GRCh38)
Structure: AlphaFold pLDDT 73.24 · 17 PDB
Residue 276: an α-helix; 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-arg276fs (accessed [today's date]).

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