DCX p.Ser279=
c.837A>G · rs1275724985 · VCV1763136
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00217%, amr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.071 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.11 | GERP 0.33, phastCons 0.62 |
| Overall | ||
| CADD | 7.227 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00217%
Admixed American · 1/46,038 alleles
Overall
9.11e-05%
1/1,097,963 alleles · very 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
- Protein
- p.Ser279=
- Coding
- c.837A>G
- MANE Select
- NM_001195553
- dbSNP
- rs1275724985
- Type
- single nucleotide variant
- Location
- chrX:111331013 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 279
- 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.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-ser279 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown