DCX c.705+29G>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 5.34%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +29 | near-intronic (+29 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1 | GERP -2.5, phastCons 0.81 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
| Overall | ||
| CADD | 1.689 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.34%
African / African-American · 3,024/56,579 alleles
Filtering AF
5.19%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.12%
Overall
0.58%
6,813/1,175,072 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.34% | 19 |
| South Asian | 0.978% | 102 |
| Middle Eastern | 0.728% | 137 |
| Remaining individualsnot grpmax-eligible | 0.624% | 160 |
| Admixed American | 0.53% | 189 |
| European (non-Finnish) | 0.305% | 328 |
| Finnishnot grpmax-eligible | 0.0648% | 1,542 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0275% | 3,632 |
| East Asian | 0.0239% | 4,192 |
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+29G>A
- MANE Select
- NM_001195553
- dbSNP
- rs61036541
- Type
- single nucleotide variant
- Location
- chrX:111400961 (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-29g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown