Is DCX p.Asp12fs (c.34_35dup) pathogenic?

DCX p.Asp12fs (c.3435dup) is classified Pathogenic in DCX (ClinVar, No assertion criteria, 1 submitter; last evaluated 1998-01-09). Absent from gnomAD; Associated with Subcortical laminar heterotopia, X-linked.

What condition is associated with DCX p.Asp12fs (c.34_35dup)?

DCX p.Asp12fs (c.34_35dup) is associated with Subcortical laminar heterotopia, X-linked (ClinVar).

How common is DCX p.Asp12fs (c.34_35dup) in the general population?

DCX p.Asp12fs (c.34_35dup) is absent from gnomAD (gnomAD).

DCX p.Asp12fs

c.34_35dup · rs1569498597 · VCV11604

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

Subcortical laminar heterotopia, X-linked

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 2 of 7
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.9	GERP -4.2, 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.Asp12fs
Coding: c.34_35dup
MANE Select: NM_001195553
dbSNP: rs1569498597
Type: Microsatellite
Location: chrX:111410363 (GRCh38)
Structure: AlphaFold pLDDT 67.19 · 14 PDB
Residue 12: the 'disordered' region

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

Disease context

Subcortical laminar heterotopia, X-linked — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DCX p.Asp12Gly Uncertain significance ★ ⚠ same residue
DCX p.Leu231fs Pathogenic same condition
DCX c.705+1del Pathogenic ★ same condition
DCX p.Leu119fs Pathogenic ★ same condition
DCX c.808+1G>A Pathogenic same condition
DCX p.Ala71Ser Pathogenic same condition
DCX p.Arg59Leu Pathogenic same condition
DCX p.Arg89Gly 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-asp12fs (accessed [today's date]).

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