CDKL5 p.Ile72del
c.214_216del · rs786204960 · VCV189545
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Not reported
no gnomAD frequency available for this variant
Conditions
1
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 0.38 | GERP -0.083, phastCons 0.99 |
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.Ile72del
- Coding
- c.214_216del
- MANE Select
- NM_001323289
- dbSNP
- rs786204960
- Type
- Deletion
- Location
- chrX:18575422 (GRCh38)
- Structure
- AlphaFold pLDDT 53.76 · 3 PDB
- Residue 72
- the protein kinase domain; a UniProt-annotated variant site (in dee2)
Similar variants
- CDKL5 p.Ile72Thr Pathogenic ★★★ same residue
- CDKL5 p.Ile72Asn Likely pathogenic ★ same residue
- CDKL5 p.Ile72= Likely benign ★ same residue
- CDKL5 p.His124fs Pathogenic ★★★ same condition
- CDKL5 p.Tyr941fs Pathogenic ★★★ same condition
- RS1 p.Glu72Lys Pathogenic ★★★ same residue
- CDKL5 p.Lys432_Tyr433delinsAsn Uncertain significance ★★★ same condition
- CDKL5 p.Ala486_Lys487del Benign ★★★ 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-ile72del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown