CDKL5 p.Ser580fs
c.1734_1738dup · VCV3602049
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Conditions
1
CDKL5 disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 12 of 18 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 12 | GERP 2.5, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- CDKL5
- Protein
- p.Ser580fs
- Coding
- c.1734_1738dup
- MANE Select
- NM_001323289
- Type
- Duplication
- Location
- chrX:18604656 (GRCh38)
- Structure
- AlphaFold pLDDT 53.76 · 3 PDB
Similar variants
- CDKL5 p.Ser438fs Pathogenic ★★★ same condition
- CDKL5 c.65dupG Pathogenic/Likely pathogenic ★★ same condition
- CDKL5 p.Ala166fs Pathogenic ★★ same condition
- CDKL5 p.Arg558fs Pathogenic/Likely pathogenic ★★ same condition
- CDKL5 p.Leu184fs Pathogenic ★★ same condition
- CDKL5 p.Thr792fs Pathogenic/Likely pathogenic ★★ same condition
- CDKL5 p.Ala122fs Pathogenic ★ same condition
- CDKL5 p.Ala362fs 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-ser580fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown