CDKL5 p.Lys43del
c.126_128del · rs2147132248 · VCV1311402
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
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 2.7 | GERP 0.81, phastCons 1 |
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
- Protein
- p.Lys43del
- Coding
- c.126_128del
- MANE Select
- NM_001323289
- dbSNP
- rs2147132248
- Type
- Deletion
- Location
- chrX:18564501 (GRCh38)
- Structure
- AlphaFold pLDDT 53.76 · 3 PDB
- Residue 43
- the protein kinase domain; a β-strand
Similar variants
- CDKL5 p.His124fs Pathogenic ★★★ same type
- CDKL5 p.Tyr941fs Pathogenic ★★★ same type
- RS1 p.Arg174fs Pathogenic ★★★ same type
- CDKL5 p.Lys432_Tyr433delinsAsn Uncertain significance ★★★ same type
- RS1 p.Asn85del Uncertain significance ★★★ same type
- CDKL5 p.Ala486_Lys487del Benign ★★★ same type
- CDKL5 p.Ala372fs Pathogenic ★★ same type
- CDKL5 p.Ala811fs 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/cdkl5-p-lys43del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown