CDKL5 p.Val9=
c.27G>A · VCV3345106
Uncertain significance
No assertion criteria
Classification
Uncertain significance
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
CDKL5-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.30 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.28 | gain · loss 0.14 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 14.29 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CDKL5
- Protein
- p.Val9=
- Coding
- c.27G>A
- MANE Select
- NM_001323289
- Type
- single nucleotide variant
- Location
- chrX:18507123 (GRCh38)
- Structure
- AlphaFold pLDDT 53.76 · 3 PDB
Disease context
CDKL5-related disorder
Similar variants
- CDKL5 p.Val9Ala Uncertain significance ★ ⚠ same residue
- CDKL5 c.2152+5G>A Likely pathogenic ★★ same condition
- CDKL5 p.Arg178Gly Pathogenic/Likely pathogenic ★★ same condition
- CDKL5 p.Gln643Ter Pathogenic ★★ same condition
- RS1 c.326+2T>G Pathogenic/Likely pathogenic ★★ same condition
- RS1 c.522+1G>A Pathogenic ★★ same condition
- RS1 p.Ala98Glu Pathogenic ★★ ⚠ same condition
- RS1 p.Arg197His 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-p-val9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown