Is CDKL5 p.Asp135His (c.403G>C) pathogenic?

CDKL5 p.Asp135His (c.403G>C) is classified Likely pathogenic in CDKL5 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-08-05). AlphaMissense: likely pathogenic (1); Absent from gnomAD v4.1.

How common is CDKL5 p.Asp135His (c.403G>C) in the general population?

CDKL5 p.Asp135His (c.403G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CDKL5 p.Asp135His (c.403G>C)?

AlphaMissense predicts likely pathogenic (score 1) — an in-silico prediction, not a clinical call.

CDKL5 p.Asp135His

c.403G>C · rs1064794919 · VCV421114

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

1 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	1	likely pathogenic ✓ concordant with ClinVar · top 4% in CDKL5
REVEL	0.916	moderately pathogenic-leaning
SaProt	LLR -16.89	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2.4, phastCons 1
Regional constraint	o/e 0.35	constrained · MANE · 91 kb · p 1.2e-21 · regional, not allelic
Overall
CADD	34.0	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

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.Asp135His
Coding: c.403G>C
MANE Select: NM_001323289
dbSNP: rs1064794919
Type: single nucleotide variant
Location: chrX:18579968 (GRCh38)
Structure: AlphaFold pLDDT 53.76 · 3 PDB
Residue 135: the protein kinase domain; an active site

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

Similar variants

CDKL5 p.Asp135Val Uncertain significance ★★ ⚠ same residue
RS1 p.Gly135Glu Pathogenic ★ same residue
CDKL5 p.Asp135Glu Uncertain significance ★ same residue
CDKL5 p.Asp135Gly Uncertain significance ★ ⚠ same residue
RS1 p.Gly135Ala Conflicting classifications of pathogenicity ★ ⚠ same residue
RS1 p.Gly135Arg Uncertain significance ★ ⚠ same residue
CDKL5 p.Asp135= Likely benign ★ same residue
CDKL5 c.146-1G>A 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-asp135his (accessed [today's date]).

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