Is CDKL5 p.His690Arg (c.2069A>G) pathogenic?

CDKL5 p.His690Arg (c.2069A>G) is classified Uncertain significance in CDKL5 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-08). AlphaMissense: likely benign (0.1257); Very rare (popmax 0.00526%, afr); Associated with developmental and epileptic encephalopathy, 2.

What condition is associated with CDKL5 p.His690Arg (c.2069A>G)?

CDKL5 p.His690Arg (c.2069A>G) is associated with developmental and epileptic encephalopathy, 2 (ClinVar).

How common is CDKL5 p.His690Arg (c.2069A>G) in the general population?

CDKL5 p.His690Arg (c.2069A>G) is very rare (popmax 0.00526%, afr) (gnomAD).

How is CDKL5-deficiency disorder inherited?

Typically X-linked dominant (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about CDKL5 p.His690Arg (c.2069A>G)?

AlphaMissense predicts likely benign (score 0.1257) — an in-silico prediction, not a clinical call.

CDKL5 p.His690Arg

c.2069A>G · rs945311782 · VCV418116

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1257 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00526%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

developmental and epileptic encephalopathy, 2

Computational evidence

Protein change
AlphaMissense	0.1257	likely benign
REVEL	0.345	indeterminate
SaProt	LLR -5.25	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.5, phastCons 1
Regional constraint	o/e 0.70	unconstrained · MANE · 30 kb · p 1.5e-11 · regional, not allelic
Overall
CADD	22.2	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00526% African / African-American · 3/56,995 alleles

Filtering AF 0.0014% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000687%

Overall 0.000248% 3/1,209,613 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.His690Arg
Coding: c.2069A>G
MANE Select: NM_001323289
dbSNP: rs945311782
Type: single nucleotide variant
Location: chrX:18609487 (GRCh38)
Structure: AlphaFold pLDDT 53.76 · 3 PDB
Residue 690: the 'disordered' region

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

Disease context

developmental and epileptic encephalopathy, 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For CDKL5-deficiency disorder (Orphanet):

Inheritance: X-linked dominant
Onset: Infancy, Neonatal

Similar variants

CDKL5 p.His690Gln Uncertain significance ★ ⚠ same residue
CDKL5 p.His690_Ser691insTer Pathogenic ★★ 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

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-his690arg (accessed [today's date]).

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