Is CDKL5 p.Arg956Cys (c.2866C>T) pathogenic?

CDKL5 p.Arg956Cys (c.2866C>T) is classified Uncertain significance in CDKL5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-03-04). Very rare (popmax 0.00886%, eas); Associated with Angelman syndrome-like.

What condition is associated with CDKL5 p.Arg956Cys (c.2866C>T)?

CDKL5 p.Arg956Cys (c.2866C>T) is associated with Angelman syndrome-like, developmental and epileptic encephalopathy, 2 (ClinVar).

How common is CDKL5 p.Arg956Cys (c.2866C>T) in the general population?

CDKL5 p.Arg956Cys (c.2866C>T) is very rare (popmax 0.00886%, eas) (gnomAD).

CDKL5 p.Arg956Cys

c.2866C>T · rs1398393336 · VCV585659

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00886%, eas)

Conditions

Angelman syndrome-like

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.114	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.7	GERP -2.6
Overall
CADD	13.88	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00886% East Asian · 3/33,854 alleles

Filtering AF 0.00235% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00125%

Overall 0.000638% 7/1,097,915 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00886%	11,285
Admixed American	0.00217%	46,091
Finnishnot grpmax-eligible	0.00213%	46,947
Remaining individualsnot grpmax-eligible	0.0021%	47,651
European (non-Finnish)	0.000112%	895,327

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: CDKL5
Protein: p.Arg956Cys
Coding: c.2866C>T
MANE Select: NM_001323289 · reported on NM_003159
dbSNP: rs1398393336
Type: single nucleotide variant
Location: chrX:18650478 (GRCh38)
Structure: AlphaFold pLDDT 53.76 · 3 PDB
Residue 956: the 'disordered' region; a UniProt-annotated variant site (in dee2); a UniProt-annotated variant site (found in a patient with infatile spasms; likely pathogenic)

Full CDKL5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Angelman syndrome-like — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: developmental and epileptic encephalopathy, 2

Similar variants

CDKL5 p.Arg956His Benign/Likely benign ★★ same residue
CDKL5 c.146-1G>A Pathogenic ★★★ same condition
CDKL5 p.Ala157Pro Likely pathogenic ★★★ same condition
CDKL5 p.Ala157Val Likely pathogenic ★★★ same condition
CDKL5 p.Ala40Val Pathogenic ★★★ same condition
CDKL5 p.Arg178Gln Pathogenic ★★★ same condition
CDKL5 p.Arg717= Likely pathogenic ★★★ same condition
CDKL5 p.Arg948Ter 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-arg956cys (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown