DCX p.Ala316=
c.948A>C · rs770799939 · VCV590104
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0175%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.033 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP -4.2, phastCons 1 |
| Overall | ||
| CADD | 12.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0175%
Admixed American · 8/45,702 alleles
Filtering AF
0.0087%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00781%
Overall
0.00852%
103/1,209,215 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0175% | 5,713 |
| European (non-Finnish) | 0.0102% | 9,832 |
| Remaining individualsnot grpmax-eligible | 0.00631% | 15,855 |
| African / African-American | 0.00175% | 57,005 |
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.Ala316=
- Coding
- c.948A>C
- MANE Select
- NM_001195553
- dbSNP
- rs770799939
- Type
- single nucleotide variant
- Location
- chrX:111312735 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 316
- the 'disordered' region
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.Arg196= 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-ala316 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown