Is CDKL5 p.Arg534Ser (c.1602A>C) pathogenic?

CDKL5 p.Arg534Ser (c.1602A>C) is classified Uncertain significance in CDKL5 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-02). AlphaMissense: ambiguous (0.5548); Very rare (popmax 0.000112%, nfe); Associated with Angelman syndrome-like.

What condition is associated with CDKL5 p.Arg534Ser (c.1602A>C)?

CDKL5 p.Arg534Ser (c.1602A>C) is associated with Angelman syndrome-like, developmental and epileptic encephalopathy, 2 (ClinVar).

How common is CDKL5 p.Arg534Ser (c.1602A>C) in the general population?

CDKL5 p.Arg534Ser (c.1602A>C) is very rare (popmax 0.000112%, nfe) (gnomAD).

What do computational predictors say about CDKL5 p.Arg534Ser (c.1602A>C)?

AlphaMissense predicts ambiguous (score 0.5548) — an in-silico prediction, not a clinical call.

CDKL5 p.Arg534Ser

c.1602A>C · rs1385183228 · VCV1022264

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5548 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

Conditions

Angelman syndrome-like

Computational evidence

Protein change
AlphaMissense	0.5548	ambiguous
REVEL	0.366	indeterminate
SaProt	LLR -5.99	tolerated
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.54	GERP -4.9, phastCons 0.99
Regional constraint	o/e 0.70	unconstrained · MANE · 30 kb · p 1.5e-11 · regional, not allelic
Overall
CADD	18.69	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000112% European (non-Finnish) · 1/895,450 alleles

Overall 9.11e-05% 1/1,098,187 alleles · very rare

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.Arg534Ser
Coding: c.1602A>C
MANE Select: NM_001323289
dbSNP: rs1385183228
Type: single nucleotide variant
Location: chrX:18604526 (GRCh38)
Structure: AlphaFold pLDDT 53.76 · 3 PDB
Residue 534: the 'disordered' region

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.Arg534Gly Uncertain significance ★ ⚠ 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-arg534ser (accessed [today's date]).

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