CDKL5 p.His945Arg
c.2834A>G · rs1057523930 · VCV390956
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.187 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.047 | GERP -1.2 |
| Overall | ||
| CADD | 2.637 | 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.His945Arg
- Coding
- c.2834A>G
- MANE Select
- NM_001323289 · reported on NM_003159
- dbSNP
- rs1057523930
- Type
- single nucleotide variant
- Location
- chrX:18650446 (GRCh38)
- Structure
- AlphaFold pLDDT 53.76 · 3 PDB
- Residue 945
- the 'disordered' region; a UniProt-annotated variant site (in dee2); a UniProt-annotated variant site (found in a patient with infatile spasms; likely pathogenic)
Similar variants
- CDKL5 p.His945Tyr Uncertain significance ★ same residue
- CDKL5 c.146-1G>A Pathogenic ★★★ same type
- CDKL5 p.Ala157Pro Likely pathogenic ★★★ same type
- CDKL5 p.Ala157Val Likely pathogenic ★★★ same type
- CDKL5 p.Ala40Val Pathogenic ★★★ same type
- CDKL5 p.Arg178Gln Pathogenic ★★★ same type
- CDKL5 p.Arg717= Likely pathogenic ★★★ same type
- CDKL5 p.Arg948Ter 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-his945arg (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown