Is DCX p.Gln261fs (c.781del) pathogenic?

DCX p.Gln261fs (c.781del) is classified Pathogenic in DCX (ClinVar, No assertion criteria, 1 submitter). Absent from gnomAD; Associated with Abnormal cerebral morphology.

What condition is associated with DCX p.Gln261fs (c.781del)?

DCX p.Gln261fs (c.781del) is associated with Abnormal cerebral morphology (ClinVar).

How common is DCX p.Gln261fs (c.781del) in the general population?

DCX p.Gln261fs (c.781del) is absent from gnomAD (gnomAD).

DCX p.Gln261fs

c.781del · rs2147635268 · VCV1701040

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

Abnormal cerebral morphology

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 4 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.2	GERP 2.1, 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.Gln261fs
Coding: c.781del
MANE Select: NM_001195553
dbSNP: rs2147635268
Type: Deletion
Location: chrX:111333078 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 261: the doublecortin 2 domain

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

Disease context

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

Similar variants

DCX p.Gln261Ter Pathogenic ★★ same residue
DCX p.Lys227fs Pathogenic/Likely pathogenic ★★ same type
DCX c.364+1del Pathogenic ★ same type
DCX c.367del Pathogenic ★ same type
DCX c.705_705+12del Likely pathogenic ★ same type
DCX c.705+1del Pathogenic ★ same type
DCX c.-22-345_326del Pathogenic ★ same type
DCX p.Arg11_Asp12insTer Pathogenic ★ 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/dcx-p-gln261fs (accessed [today's date]).

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