DCX p.Ser361=
c.1083G>A · rs757705937 · VCV2661204
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0229%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.066 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.4 | GERP -3.7, phastCons 0.23 |
| Overall | ||
| CADD | 0.553 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0229%
Middle Eastern · 1/4,370 alleles
Filtering AF
0.000908%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00071%
Overall
0.00141%
17/1,209,345 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0229% | 4,370 |
| Admixed American | 0.00219% | 45,766 |
| African / African-American | 0.00175% | 57,057 |
| European (non-Finnish) | 0.00156% | 63,911 |
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.Ser361=
- Coding
- c.1083G>A
- MANE Select
- NM_001195553
- dbSNP
- rs757705937
- Type
- single nucleotide variant
- Location
- chrX:111301705 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 361
- the 'disordered' region
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-p-ser361 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown