DCX c.705+19T>A
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0263%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.3 | GERP 0.61, phastCons 0.37 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 5.797 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0263%
African / African-American · 15/57,113 alleles
Filtering AF
0.0161%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.013%
Overall
0.00126%
15/1,193,337 alleles · ultra-rare
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
- Coding
- c.705+19T>A
- MANE Select
- NM_001195553
- Type
- single nucleotide variant
- Location
- chrX:111400971 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
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-c-705-plus-19t-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown