CDKL5 p.Asn95fs
c.284dup · VCV3602050
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
Rett syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function; NMD-escape possible for C-terminal truncations |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.6, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDKL5
- Protein
- p.Asn95fs
- Coding
- c.284dup
- MANE Select
- NM_001323289
- Type
- Duplication
- Location
- chrX:18579847 (GRCh38)
- Structure
- AlphaFold pLDDT 53.76 · 3 PDB
- Residue 95
- the protein kinase domain; a β-strand
Disease context
Rett syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Rett syndrome (Orphanet):
- Inheritance
- X-linked dominant
- Onset
- Infancy
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- RS1 p.Ser95= Benign/Likely benign ★★ same residue
- CDKL5 p.Leu653fs Likely pathogenic ★ same condition
- CDKL5 p.Ser745Ter Likely pathogenic ★ same condition
- CDKL5 p.Thr531fs Likely pathogenic ★ same condition
- CDKL5 p.Tyr86fs Likely pathogenic ★ same condition
- RS1 p.Ser95Ter Pathogenic ★ same residue
- RS1 p.Ser95del Conflicting classifications of pathogenicity ★ same residue
- CDKL5 p.Ile72Thr 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-p-asn95fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown