DCX p.Ser32=
c.96C>T · rs148472336 · VCV384621
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.174%, afr)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.274 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.47 | GERP -4.2, phastCons 0.001 |
| Overall | ||
| CADD | 5.134 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.174%
African / African-American · 99/56,989 alleles
Filtering AF
0.146%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.136%
Overall
0.0113%
137/1,209,384 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.174% | 576 |
| South Asian | 0.0264% | 3,782 |
| Remaining individualsnot grpmax-eligible | 0.0252% | 3,968 |
| Middle Eastern | 0.023% | 4,347 |
| Admixed American | 0.0153% | 6,520 |
| European (non-Finnish) | 0.000335% | 298,380 |
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.Ser32=
- Coding
- c.96C>T
- MANE Select
- NM_001195553
- dbSNP
- rs148472336
- Type
- single nucleotide variant
- Location
- chrX:111410303 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
Similar variants
- DCX p.Ser32Asn Pathogenic ★ ⚠ same residue
- DCX p.Ser32Arg Uncertain significance ★ ⚠ same residue
- 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
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-ser32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown