CDKL5 c.65dupG
Pathogenic/Likely pathogenic
Multiple submitters
Classification
Pathogenic/Likely pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
2
CDKL5 disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 1.7, phastCons 1 |
| Non-coding constraint | — | not assessed · autosomes only, so chrX has no window · absence ≠ unconstrained |
Population frequency
dbSNP / gnomAD
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CDKL5
- Coding
- c.65dupG
- MANE Select
- NM_001323289 · reported on NM_003159
- dbSNP
- rs267608420
- Type
- Duplication
- Location
- chrX:18510818 (GRCh38)
- Structure
- AlphaFold pLDDT 53.76 · 3 PDB
Similar variants
- CDKL5 p.Ser438fs Pathogenic ★★★ same condition
- CDKL5 c.825+1dup Likely pathogenic ★★ same condition
- CDKL5 p.Ala166fs Pathogenic ★★ same condition
- CDKL5 p.Arg558fs Pathogenic/Likely pathogenic ★★ same condition
- CDKL5 p.Asn293fs Pathogenic ★★ same condition
- CDKL5 p.Glu170fs Likely pathogenic ★★ same condition
- CDKL5 p.Leu184fs Pathogenic ★★ same condition
- CDKL5 p.Thr792fs Pathogenic/Likely pathogenic ★★ 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/cdkl5-c-65dupg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown