Is CDKL5 p.Phe13fs (c.39del) pathogenic?

CDKL5 p.Phe13fs (c.39del) is classified Likely pathogenic in CDKL5 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-09-20). Absent from gnomAD; Associated with CDKL5 disorder.

What condition is associated with CDKL5 p.Phe13fs (c.39del)?

CDKL5 p.Phe13fs (c.39del) is associated with CDKL5 disorder, developmental and epileptic encephalopathy, 2 (ClinVar).

How common is CDKL5 p.Phe13fs (c.39del) in the general population?

CDKL5 p.Phe13fs (c.39del) is absent from gnomAD (gnomAD).

CDKL5 p.Phe13fs

c.39del · rs267608415 · VCV143819

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

CDKL5 disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 2 of 18
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 1.9, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CDKL5
Protein: p.Phe13fs
Coding: c.39del
MANE Select: NM_001323289
dbSNP: rs267608415
Type: Deletion
Location: chrX:18507133 (GRCh38)
Structure: AlphaFold pLDDT 53.76 · 3 PDB
Residue 13: the protein kinase domain; a β-strand

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

Disease context

CDKL5 disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: developmental and epileptic encephalopathy, 2

Similar variants

CDKL5 p.Phe13Ser Likely pathogenic ★★★ same residue
CDKL5 p.Phe13Ile Uncertain significance ★ ⚠ same residue
CDKL5 p.His124fs Pathogenic ★★★ same condition
CDKL5 p.Tyr941fs Pathogenic ★★★ same condition
CDKL5 p.Lys432_Tyr433delinsAsn Uncertain significance ★★★ same condition
CDKL5 p.Ala486_Lys487del Benign ★★★ same condition
CDKL5 p.Ala372fs Pathogenic ★★ same condition
CDKL5 p.Ala811fs 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-phe13fs (accessed [today's date]).

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