DCX p.Val225=
c.675C>G · rs749873088 · VCV1755276
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00469%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.6 | GERP -3.1, phastCons 1 |
| Overall | ||
| CADD | 4.879 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00469%
European (non-Finnish) · 42/894,742 alleles
Filtering AF
0.00351%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00311%
Overall
0.00356%
43/1,209,220 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00469% | 21,303 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,579 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- DCX
- Protein
- p.Val225=
- Coding
- c.675C>G
- MANE Select
- NM_001195553
- dbSNP
- rs749873088
- Type
- single nucleotide variant
- Location
- chrX:111401020 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 225
- the doublecortin 2 domain; an α-helix
Similar variants
- DCX p.Arg196His Pathogenic/Likely pathogenic ★★ same condition
- DCX p.Arg39Ter Pathogenic ★★ same condition
- DCX p.Ala295Thr Uncertain significance ★★ ⚠ same condition
- DCX p.Cys35Arg Uncertain significance ★★ ⚠ same condition
- DCX p.Ile107Thr Uncertain significance ★★ ⚠ same condition
- DCX c.706-4A>G Benign/Likely benign ★★ same condition
- DCX p.Ala286Ser Benign/Likely benign ★★ same condition
- DCX p.Ala316= Benign/Likely benign ★★ 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-val225 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown