DCX p.Lys202=
c.606G>A · rs974830548 · VCV2661205
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0457%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.369 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -0.68, phastCons 1 |
| Overall | ||
| CADD | 7.931 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0457%
Middle Eastern · 2/4,374 alleles
Filtering AF
0.00809%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00339%
Overall
0.00157%
19/1,209,848 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0457% | 2,187 |
| African / African-American | 0.00701% | 14,265 |
| Remaining individualsnot grpmax-eligible | 0.0063% | 15,870 |
| South Asian | 0.00176% | 56,785 |
| European (non-Finnish) | 0.00101% | 99,473 |
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.Lys202=
- Coding
- c.606G>A
- MANE Select
- NM_001195553
- dbSNP
- rs974830548
- Type
- single nucleotide variant
- Location
- chrX:111401089 (GRCh38)
- Structure
- AlphaFold pLDDT 67.19 · 14 PDB
- Residue 202
- the doublecortin 2 domain; a turn
Similar variants
- DCX p.Lys202Glu Uncertain significance ★ ⚠ same residue
- DCX p.Lys202del Uncertain significance ★ same residue
- 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
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-lys202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown