Is DCX p.Thr293fs (c.875dup) pathogenic?

DCX p.Thr293fs (c.875dup) is classified Pathogenic in DCX (ClinVar, Single submitter, 1 submitter; last evaluated 2013-02-08). Absent from gnomAD; Associated with Abnormal cortical gyration.

What condition is associated with DCX p.Thr293fs (c.875dup)?

DCX p.Thr293fs (c.875dup) is associated with Abnormal cortical gyration (ClinVar).

How common is DCX p.Thr293fs (c.875dup) in the general population?

DCX p.Thr293fs (c.875dup) is absent from gnomAD (gnomAD).

DCX p.Thr293fs

c.875dup · rs797045520 · VCV210837

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Abnormal cortical gyration

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 5 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.1	GERP -2.5, 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: DCX
Protein: p.Thr293fs
Coding: c.875dup
MANE Select: NM_001195553
dbSNP: rs797045520
Type: Duplication
Location: chrX:111330974 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 293: the 'disordered' region

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

Disease context

Abnormal cortical gyration — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DCX p.Leu228fs Pathogenic ★★ same condition
DCX p.Gly114fs Pathogenic ★ same condition
DCX p.Pro29fs Pathogenic ★ same condition
DCX p.Tyr105dup Likely pathogenic ★ same condition
DCX p.Tyr229_Gly233dup Pathogenic ★ same condition
DCX c.226_234delCGTTTTCGCins2 Pathogenic ★ same condition
DCX p.Asn94Asp Pathogenic ★ same condition
DCX p.His7_Phe8insTer Pathogenic ★ 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/dcx-p-thr293fs (accessed [today's date]).

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