DCX p.Thr336=
c.1008G>A · VCV3677007
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0119%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.15 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>G here scores Δ0.30 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP -0.45 | GERP -4, phastCons 0.06 |
| Overall | ||
| CADD | 6.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0119%
East Asian · 4/33,740 alleles
Filtering AF
0.00396%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00236%
Overall
0.00223%
27/1,209,594 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0119% | 8,435 |
| South Asian | 0.00529% | 18,910 |
| European (non-Finnish) | 0.00212% | 47,115 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,605 |
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.Thr336=
- Coding
- c.1008G>A
- MANE Select
- NM_001195553
- Type
- single nucleotide variant
- Location
- chrX:111312675 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 336
- a modified residue (phosphothreonine; by mapk); 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-thr336 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown