DCX p.Asp315=
c.945C>T · rs927836147 · VCV2161183
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0229%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.047 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.25 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 13.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0229%
Middle Eastern · 1/4,370 alleles
Filtering AF
0.00263%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00231%
Overall
0.00339%
41/1,210,120 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0229% | 4,370 |
| South Asian | 0.00528% | 18,952 |
| Admixed American | 0.00437% | 22,908 |
| European (non-Finnish) | 0.00369% | 27,124 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,579 |
| African / African-American | 0.00174% | 57,344 |
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.Asp315=
- Coding
- c.945C>T
- MANE Select
- NM_001195553
- dbSNP
- rs927836147
- Type
- single nucleotide variant
- Location
- chrX:111330905 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 315
- the 'disordered' region
Similar variants
- DCX c.364+1G>A Likely pathogenic ★★ same type
- DCX c.705+1G>A Pathogenic ★★ same type
- DCX c.706-2A>G Pathogenic ★★ same type
- DCX c.809-1G>A Pathogenic/Likely pathogenic ★★ same type
- DCX p.Ala204Asp Pathogenic ★★ same type
- DCX p.Ala251Ser Pathogenic ★★ same type
- DCX p.Arg178Cys Pathogenic/Likely pathogenic ★★ same type
- DCX p.Arg186Cys 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-asp315 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown