Is CDKL5 p.Ser446= (c.1338A>T) pathogenic?

CDKL5 p.Ser446= (c.1338A>T) is classified Benign/Likely benign in CDKL5 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2025-12-21). Ultra-rare (popmax 0.0994%, afr); Associated with Inborn genetic diseases.

What condition is associated with CDKL5 p.Ser446= (c.1338A>T)?

CDKL5 p.Ser446= (c.1338A>T) is associated with Inborn genetic diseases, developmental and epileptic encephalopathy, 2 (ClinVar).

How common is CDKL5 p.Ser446= (c.1338A>T) in the general population?

CDKL5 p.Ser446= (c.1338A>T) is ultra-rare (popmax 0.0994%, afr) (gnomAD).

CDKL5 p.Ser446=

c.1338A>T · rs139329419 · VCV288260

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0994%, afr)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.2	GERP -4.8
Overall
CADD	0.201	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0994% African / African-American · 57/57,317 alleles

Filtering AF 0.0787% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0714%

Overall 0.00512% 62/1,210,444 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0994%	1,006
Remaining individualsnot grpmax-eligible	0.0084%	11,907
Admixed American	0.00218%	45,834

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.Ser446=
Coding: c.1338A>T
MANE Select: NM_001323289
dbSNP: rs139329419
Type: single nucleotide variant
Location: chrX:18604262 (GRCh38)
Structure: AlphaFold pLDDT 53.76 · 3 PDB
Residue 446: the 'disordered' region

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: developmental and epileptic encephalopathy, 2

Similar variants

CDKL5 p.Ser446Ter Pathogenic ★ same residue
CDKL5 p.Ser446Leu 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

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-ser446 (accessed [today's date]).

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