DCX p.Asp262Glu
c.786T>A · VCV4952418
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
AlphaMissense
likely pathogenic
0.9542 · ACMG-weighted
gnomAD v4.1
Absent
absent from gnomAD v4.1
Missense predictors
2/3 damaging
AlphaMissense, REVEL, SaProt
Conditions
1
DCX-related disorder
Computational evidence
| Protein change | ||
| AlphaMissense | 0.9542 | likely pathogenic ✓ concordant with ClinVar |
|---|---|---|
| REVEL | 0.802 | moderately pathogenic-leaning |
| SaProt | LLR -8.18 | tolerated |
| ⇒ AlphaMissense and REVEL call this damaging; SaProt does not. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP 0.89, phastCons 1 |
| Regional constraint | o/e 0.31 | constrained · MANE · 77 kb · p 4.4e-24 · regional, not allelic |
| Overall | ||
| CADD | 22.0 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- DCX
- Protein
- p.Asp262Glu
- Coding
- c.786T>A
- MANE Select
- NM_001195553
- Type
- single nucleotide variant
- Location
- chrX:111333073 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 262
- the doublecortin 2 domain; a UniProt-annotated variant site (in lisx1 and sbhx; decreased tubulin binding)
Similar variants
- DCX p.Asp262Gly Uncertain significance ★ ⚠ same residue
- DCX c.364+1G>A Likely pathogenic ★★ same condition
- DCX p.Arg19Ter Pathogenic ★★ same condition
- DCX p.Arg303Ter Pathogenic ★★ same condition
- DCX p.Arg76Cys Pathogenic/Likely pathogenic ★★ same condition
- DCX p.Gly67Glu Pathogenic/Likely pathogenic ★★ same condition
- DCX p.Lys50Asn Pathogenic/Likely pathogenic ★★ same condition
- DCX p.Arg302Cys 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/dcx-p-asp262glu (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown