CDKL3 p.Asn476=
c.1428T>C · rs17165391 · VCV787043
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.21%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.004 | GERP -5.4, phastCons 0.009 |
| Overall | ||
| CADD | 1.375 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.21%
African / African-American · 2,346/73,134 alleles
Filtering AF
3.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.06%
Overall
0.178%
2,832/1,594,250 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.21% | 31 |
| Admixed American | 0.297% | 336 |
| Remaining individualsnot grpmax-eligible | 0.277% | 361 |
| Middle Eastern | 0.267% | 374 |
| European (non-Finnish) | 0.0108% | 9,237 |
| South Asian | 0.00912% | 10,967 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- CDKL3
- Protein
- p.Asn476=
- Coding
- c.1428T>C
- MANE Select
- NM_001113575
- dbSNP
- rs17165391
- Type
- single nucleotide variant
- Location
- chr5:134306639 (GRCh38)
- Gene constraint
- LOEUF 1.523 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 64.87 · 1 PDB
- Residue 476
- the 'disordered' region
Similar variants
- CDKL3 p.Ala195Thr Uncertain significance ★ ⚠ same type
- CDKL3 p.Ala235Ser Uncertain significance ★ ⚠ same type
- CDKL3 p.Arg101Gln Uncertain significance ★ ⚠ same type
- CDKL3 p.Arg111Pro Uncertain significance ★ ⚠ same type
- CDKL3 p.Arg148Gln Uncertain significance ★ ⚠ same type
- CDKL3 p.Arg164His Uncertain significance ★ ⚠ same type
- CDKL3 p.Arg367Thr Uncertain significance ★ ⚠ same type
- CDKL3 p.Arg463Ser Uncertain significance ★ ⚠ 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/cdkl3-p-asn476 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown